[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/15074660/ACC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/15081748/transformed.cor.cli.txt"

nPatients in clinical file=92, in cluster file=90, common to both=90
[1] 46 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(4Q35.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                           29                            61 
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                           29                            61 
[1] "AMP PEAK  4(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            65                             25 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            65                             25 
[1] "AMP PEAK  5(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                           63                            27 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                           63                            27 
[1] "AMP PEAK  6(6P21.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE 
                            19                             71 
  AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE 
                            19                             71 
[1] "AMP PEAK  7(6Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE 
                           19                            71 
  AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE 
                           19                            71 
[1] "AMP PEAK  8(7P22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                           54                            36 
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                           54                            36 
[1] "AMP PEAK  9(9Q31.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE 
                           34                            56 
  AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE 
                           34                            56 
[1] "AMP PEAK 10(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                            70                             20 
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                            70                             20 
[1] "AMP PEAK 11(14Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                            27                             63 
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                            27                             63 
[1] "AMP PEAK 12(16P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                            50                             40 
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                            50                             40 
[1] "AMP PEAK 13(16Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                            56                             34 
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                            56                             34 
[1] "AMP PEAK 14(16Q24.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                            49                             41 
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                            49                             41 
[1] "AMP PEAK 15(17Q25.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE 
                            18                             72 
  AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE 
                            18                             72 
[1] "AMP PEAK 16(19P13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                             58                              32 
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                             58                              32 
[1] "AMP PEAK 17(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                          56                           34 
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                          56                           34 
[1] "AMP PEAK 18(XP11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE 
                            49                             41 
  AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE 
                            49                             41 
[1] "AMP PEAK 19(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE 
                         46                          44 
  AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(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(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                         18                          72 
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                         18                          72 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           18                            72 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           18                            72 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           21                            69 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           21                            69 
[1] "DEL PEAK  5(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            25                             65 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) 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 
                           25                            65 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           25                            65 
[1] "DEL PEAK  7(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                           28                            62 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                           28                            62 
[1] "DEL PEAK  8(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q35.1) MUTATED DEL PEAK  8(4Q35.1) WILD-TYPE 
                           30                            60 
  DEL PEAK  8(4Q35.1) MUTATED DEL PEAK  8(4Q35.1) WILD-TYPE 
                           30                            60 
[1] "DEL PEAK  9(6P24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(6P24.3) MUTATED DEL PEAK  9(6P24.3) WILD-TYPE 
                           20                            70 
  DEL PEAK  9(6P24.3) MUTATED DEL PEAK  9(6P24.3) WILD-TYPE 
                           20                            70 
[1] "DEL PEAK 10(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE 
                         21                          69 
  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE 
                         21                          69 
[1] "DEL PEAK 11(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE 
                           11                            79 
  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE 
                           11                            79 
[1] "DEL PEAK 12(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE 
                         24                          66 
  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE 
                         24                          66 
[1] "DEL PEAK 13(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                           27                            63 
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                           27                            63 
[1] "DEL PEAK 14(10Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(10Q23.1) MUTATED DEL PEAK 14(10Q23.1) WILD-TYPE 
                            11                             79 
  DEL PEAK 14(10Q23.1) MUTATED DEL PEAK 14(10Q23.1) WILD-TYPE 
                            11                             79 
[1] "DEL PEAK 15(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(11P15.5) MUTATED DEL PEAK 15(11P15.5) WILD-TYPE 
                            27                             63 
  DEL PEAK 15(11P15.5) MUTATED DEL PEAK 15(11P15.5) WILD-TYPE 
                            27                             63 
[1] "DEL PEAK 16(11Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(11Q14.1) MUTATED DEL PEAK 16(11Q14.1) WILD-TYPE 
                            25                             65 
  DEL PEAK 16(11Q14.1) MUTATED DEL PEAK 16(11Q14.1) WILD-TYPE 
                            25                             65 
[1] "DEL PEAK 17(12Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(12Q14.2) MUTATED DEL PEAK 17(12Q14.2) WILD-TYPE 
                             5                             85 
  DEL PEAK 17(12Q14.2) MUTATED DEL PEAK 17(12Q14.2) WILD-TYPE 
                             5                             85 
[1] "DEL PEAK 18(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                            42                             48 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                            42                             48 
[1] "DEL PEAK 19(14Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(14Q21.2) MUTATED DEL PEAK 19(14Q21.2) WILD-TYPE 
                            20                             70 
  DEL PEAK 19(14Q21.2) MUTATED DEL PEAK 19(14Q21.2) WILD-TYPE 
                            20                             70 
[1] "DEL PEAK 20(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE 
                             7                             83 
  DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE 
                             7                             83 
[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(17Q21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(17Q21.31) MUTATED DEL PEAK 23(17Q21.31) WILD-TYPE 
                             26                              64 
  DEL PEAK 23(17Q21.31) MUTATED DEL PEAK 23(17Q21.31) 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(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE 
                            36                             54 
  DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE 
                            36                             54 
[1] "DEL PEAK 26(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(20P12.1) MUTATED DEL PEAK 26(20P12.1) WILD-TYPE 
                            12                             78 
  DEL PEAK 26(20P12.1) MUTATED DEL PEAK 26(20P12.1) WILD-TYPE 
                            12                             78 
[1] "DEL PEAK 27(22Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(22Q12.1) MUTATED DEL PEAK 27(22Q12.1) WILD-TYPE 
                            50                             40 
  DEL PEAK 27(22Q12.1) MUTATED DEL PEAK 27(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] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATION_THERAPY"                     
[12] "RADIATIONS_RADIATION_REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 90 columns.

[1] "Batch" "15"   
[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=31,	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=60,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH_NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 90 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"        "NEOPLASM_DISEASESTAGE" "PATHOLOGY_T_STAGE"    
[4] "PATHOLOGY_N_STAGE"     "GENDER"                "RACE"                 
[7] "ETHNICITY"            
YEARS_TO_BIRTH, nv=50, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 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
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 52 21
  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                          21 
$`AMP PEAK  1(1Q22) MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JK 
       44.55        55.13        16.11        18.12        69.21        49.22 
TCGA-OR-A5JV TCGA-OR-A5K0 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KX 
       66.51        33.83        16.37        11.31        24.36        44.84 
TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LL TCGA-P6-A5OG TCGA-PK-A5HC 
        5.23        21.76        53.03        12.59        22.32 

$`AMP PEAK  1(1Q22) WILD-TYPE`
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-A5JD TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH 
       30.31        57.53        91.46        66.25        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       46.82        16.11        22.03        18.48        29.23        15.25 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW 
       36.26       121.25        12.59        29.82         9.50        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23        18.15        27.02        96.59        32.68       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ 
       22.98        49.08        24.62        46.49        91.30        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY 
       83.80        95.18       153.63       127.50        50.37        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD 
       28.31        29.10        28.64        23.64        39.58        39.35 
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        73.05 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        62.99        69.11        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-A5HB 
       42.51 

  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                       38.50 
[1] "5.2 - 69.2 (24.4)"  "0.0 - 153.6 (38.5)"
[1] "hr=" "2.9"
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
                             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
D1V7, 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"
D1V8, 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 29 20
  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                            20 
$`AMP PEAK  2(4P16.3) MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA 
       44.55        13.91        12.00        16.11        44.45        30.31 
TCGA-OR-A5JC TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       57.53        66.25        69.37        46.82        16.11        49.22 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       22.03        15.25        36.26       121.25        29.82        66.51 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO 
      100.18        22.98        16.37        24.62        24.36        46.49 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5L1 TCGA-OR-A5LA 
       83.80        95.18       153.63        50.37        58.55        23.64 
TCGA-OR-A5LB TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       39.58        14.63        78.41        73.05        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PK-A5HC 
       62.99        36.03        18.05        38.50        22.32 

$`AMP PEAK  2(4P16.3) WILD-TYPE`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD 
       55.13        68.75        88.87        19.04        18.12        91.46 
TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JU 
       69.21        17.79        18.48        29.23        12.59         9.50 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       72.39        31.23        18.15        27.02        33.83        96.59 
TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KV 
       32.68        49.08        11.31        91.30        88.01       127.50 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84        12.85         4.11        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LC TCGA-OR-A5LD 
       43.30        28.31        29.10        28.64         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LO TCGA-OR-A5LP 
       21.76        52.24        14.33        36.33        69.11        61.05 
TCGA-OR-A5LR TCGA-P6-A5OG TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       28.04        12.59         0.00        24.85        20.25        39.48 
TCGA-PK-A5HB 
       42.51 

  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 
                        44.45                         31.79 
[1] "12.0 - 153.6 (44.5)" "0.0 - 152.2 (31.8)" 
[1] "hr=" "1.6"
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
                               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
D2V7, 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"
D2V8, 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(4Q35.1) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  3(4Q35.1) MUTATED   23  6
  AMP PEAK  3(4Q35.1) WILD-TYPE 35 26
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                           29                            61 
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                            6                            26 
$`AMP PEAK  3(4Q35.1) MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       12.00        44.45        57.53        69.37        46.82        49.22 
TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JZ 
       22.03        36.26       121.25        29.82        66.51        27.02 
TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KZ 
       22.98        24.62        46.49        83.80       153.63         4.11 
TCGA-OR-A5L1 TCGA-OR-A5LA TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LK TCGA-OR-A5LL 
       58.55        23.64        14.63        78.41        73.05        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LT TCGA-OU-A5PI 
       61.08        62.99        69.11        18.05        38.50 

$`AMP PEAK  3(4Q35.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        68.75        13.91        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        30.31        18.12        91.46        69.21        66.25 
TCGA-OR-A5JG TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS 
       17.79        16.11        18.48        29.23        15.25        12.59 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K1 
        9.50        72.39        31.23        18.15        33.83        96.59 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB 
       32.68       100.18        16.37        49.08        11.31        24.36 
TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       91.30        88.01        95.18       127.50        50.37        44.84 
TCGA-OR-A5KY TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       12.85        60.89       152.15        31.79        43.30        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       29.10        28.64        39.58         5.23        39.35        21.76 
TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       52.24        14.33        36.33        61.05        28.04        36.03 
TCGA-P6-A5OG TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       12.59         0.00        24.85        20.25        39.48        42.51 
TCGA-PK-A5HC 
       22.32 

  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                         4.11                          0.00 
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                       153.63                        152.15 
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                        46.82                         31.79 
[1] "4.1 - 153.6 (46.8)" "0.0 - 152.2 (31.8)"
[1] "hr=" "2.5"
D3V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  3(4Q35.1) MUTATED         3       18         4        3
  AMP PEAK  3(4Q35.1) WILD-TYPE       6       25        14       15
D3V3, multiclass
           clus
vv          AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE
  STAGE I                             3                             6
  STAGE II                           18                            25
  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  3(4Q35.1) MUTATED    3 19  2  4
  AMP PEAK  3(4Q35.1) WILD-TYPE  6 29  9 16
D3V4, multiclass
    clus
vv   AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE
  T1                           3                             6
  T2                          19                            29
  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"
D3V5, binary
                               cls
clus                             0  1
  AMP PEAK  3(4Q35.1) MUTATED   27  1
  AMP PEAK  3(4Q35.1) WILD-TYPE 51  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(4Q35.1) MUTATED     27    1
  AMP PEAK  3(4Q35.1) WILD-TYPE   51    9
   clus
vv  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE
  0                          27                            51
  1                           1                             9
[1] 2 2
[1] FALSE
D3V6, binary
                               cls
clus                             0  1
  AMP PEAK  3(4Q35.1) MUTATED   16 13
  AMP PEAK  3(4Q35.1) WILD-TYPE 43 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(4Q35.1) MUTATED     16   13
  AMP PEAK  3(4Q35.1) WILD-TYPE   43   18
        clus
vv       AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE
  FEMALE                          16                            43
  MALE                            13                            18
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(4Q35.1) MUTATED       0                         0    23
  AMP PEAK  3(4Q35.1) WILD-TYPE     2                         1    53
D3V7, multiclass
                           clus
vv                          AMP PEAK  3(4Q35.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              23
                           clus
vv                          AMP PEAK  3(4Q35.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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"
D3V8, binary
                               cls
clus                             0  1
  AMP PEAK  3(4Q35.1) MUTATED    2 10
  AMP PEAK  3(4Q35.1) WILD-TYPE  6 28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(4Q35.1) MUTATED      2   10
  AMP PEAK  3(4Q35.1) WILD-TYPE    6   28
                        clus
vv                       AMP PEAK  3(4Q35.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          10
                        clus
vv                       AMP PEAK  3(4Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            28
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(5P15.33) MUTATION ANALYSIS
D4V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  4(5P15.33) MUTATED   42 23
  AMP PEAK  4(5P15.33) WILD-TYPE 16  9
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            65                             25 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            23                              9 
$`AMP PEAK  4(5P15.33) MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        68.75        13.91        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        44.45        30.31        57.53        69.21        66.25 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       17.79        69.37        46.82        16.11        49.22        22.03 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY 
       36.26       121.25        29.82        66.51        72.39        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       27.02        96.59        32.68       100.18        22.98        16.37 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU 
       24.62        11.31        24.36        46.49        83.80       153.63 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.37        44.84         4.11        58.55        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       28.31        29.10        28.64        23.64        39.58         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        73.05 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       53.03        61.08        62.99        69.11        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  4(5P15.33) WILD-TYPE`
TCGA-OR-A5J2 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       55.13        18.12        91.46        18.48        29.23        15.25 
TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JX TCGA-OR-A5K0 TCGA-OR-A5K6 TCGA-OR-A5KP 
       12.59         9.50        31.23        33.83        49.08        91.30 
TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KY TCGA-OR-A5L2 TCGA-OR-A5L3 
       88.01        95.18       127.50        12.85        60.89       152.15 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       39.35        21.76        12.59        20.25        39.48        42.51 
TCGA-PK-A5HC 
       22.32 

  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           0.0                            9.5 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                        153.63                         152.15 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                         36.33                          33.83 
[1] "0.0 - 153.6 (36.3)" "9.5 - 152.2 (33.8)"
[1] "hr=" "1"  
D4V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  4(5P15.33) MUTATED         5       33        13       13
  AMP PEAK  4(5P15.33) WILD-TYPE       4       10         5        5
D4V3, multiclass
           clus
vv          AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(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  4(5P15.33) MUTATED    5 37  8 14
  AMP PEAK  4(5P15.33) WILD-TYPE  4 11  3  6
D4V4, multiclass
    clus
vv   AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(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"
D4V5, binary
                                cls
clus                              0  1
  AMP PEAK  4(5P15.33) MUTATED   56  8
  AMP PEAK  4(5P15.33) WILD-TYPE 22  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     56    8
  AMP PEAK  4(5P15.33) WILD-TYPE   22    2
   clus
vv  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  0                           56                             22
  1                            8                              2
[1] 2 2
[1] FALSE
D4V6, binary
                                cls
clus                              0  1
  AMP PEAK  4(5P15.33) MUTATED   41 24
  AMP PEAK  4(5P15.33) WILD-TYPE 18  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     41   24
  AMP PEAK  4(5P15.33) WILD-TYPE   18    7
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  FEMALE                           41                             18
  MALE                             24                              7
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(5P15.33) MUTATED       0                         1    55
  AMP PEAK  4(5P15.33) WILD-TYPE     2                         0    21
D4V7, multiclass
                           clus
vv                          AMP PEAK  4(5P15.33) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               55
                           clus
vv                          AMP PEAK  4(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"
D4V8, binary
                                cls
clus                              0  1
  AMP PEAK  4(5P15.33) MUTATED    7 25
  AMP PEAK  4(5P15.33) WILD-TYPE  1 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED      7   25
  AMP PEAK  4(5P15.33) WILD-TYPE    1   13
                        clus
vv                       AMP PEAK  4(5P15.33) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           25
                        clus
vv                       AMP PEAK  4(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             13
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(5Q35.3) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  5(5Q35.3) MUTATED   44 19
  AMP PEAK  5(5Q35.3) WILD-TYPE 14 13
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                           63                            27 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                           19                            13 
$`AMP PEAK  5(5Q35.3) MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        68.75        13.91        12.00        88.87        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-A5JL TCGA-OR-A5JQ 
       69.37        46.82        16.11        49.22        22.03        36.26 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
      121.25        12.59        29.82        66.51        72.39        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       27.02        96.59       100.18        22.98        16.37        24.62 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY 
       24.36        46.49        83.80       153.63        50.37        12.85 
TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
       58.55        31.79        43.30        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ 
       23.64        39.58         5.23        14.63        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       73.05        53.03        61.08        62.99        69.11        61.05 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-P6-A5OH 
       28.04        36.03        18.05        38.50        12.59         0.00 
TCGA-PA-A5YG TCGA-PK-A5HA TCGA-PK-A5HC 
       24.85        39.48        22.32 

$`AMP PEAK  5(5Q35.3) WILD-TYPE`
TCGA-OR-A5J2 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JM TCGA-OR-A5JO 
       55.13        19.04        18.12        91.46        18.48        29.23 
TCGA-OR-A5JP TCGA-OR-A5JU TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K6 
       15.25         9.50        18.15        33.83        32.68        49.08 
TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX 
       11.31        91.30        88.01        95.18       127.50        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG 
        4.11        60.89       152.15        39.35        21.76        52.24 
TCGA-OR-A5LI TCGA-PK-A5H9 TCGA-PK-A5HB 
       14.33        20.25        42.51 

  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                         0.00                          4.11 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                       153.63                        152.15 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                        36.33                         33.83 
[1] "0.0 - 153.6 (36.3)" "4.1 - 152.2 (33.8)"
[1] "hr=" "1.6"
D5V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  5(5Q35.3) MUTATED         6       32        11       13
  AMP PEAK  5(5Q35.3) WILD-TYPE       3       11         7        5
D5V3, multiclass
           clus
vv          AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(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  5(5Q35.3) MUTATED    6 35  7 14
  AMP PEAK  5(5Q35.3) WILD-TYPE  3 13  4  6
D5V4, multiclass
    clus
vv   AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(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"
D5V5, binary
                               cls
clus                             0  1
  AMP PEAK  5(5Q35.3) MUTATED   55  7
  AMP PEAK  5(5Q35.3) WILD-TYPE 23  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.3) MUTATED     55    7
  AMP PEAK  5(5Q35.3) WILD-TYPE   23    3
   clus
vv  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  0                          55                            23
  1                           7                             3
[1] 2 2
[1] FALSE
D5V6, binary
                               cls
clus                             0  1
  AMP PEAK  5(5Q35.3) MUTATED   40 23
  AMP PEAK  5(5Q35.3) WILD-TYPE 19  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.3) MUTATED     40   23
  AMP PEAK  5(5Q35.3) WILD-TYPE   19    8
        clus
vv       AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  FEMALE                          40                            19
  MALE                            23                             8
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(5Q35.3) MUTATED       1                         1    51
  AMP PEAK  5(5Q35.3) WILD-TYPE     1                         0    25
D5V7, multiclass
                           clus
vv                          AMP PEAK  5(5Q35.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              51
                           clus
vv                          AMP PEAK  5(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"
D5V8, binary
                               cls
clus                             0  1
  AMP PEAK  5(5Q35.3) MUTATED    6 24
  AMP PEAK  5(5Q35.3) WILD-TYPE  2 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.3) MUTATED      6   24
  AMP PEAK  5(5Q35.3) WILD-TYPE    2   14
                        clus
vv                       AMP PEAK  5(5Q35.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          24
                        clus
vv                       AMP PEAK  5(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            14
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(6P21.31) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  6(6P21.31) MUTATED   11  8
  AMP PEAK  6(6P21.31) WILD-TYPE 47 24
  AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE 
                            19                             71 
  AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE 
                             8                             24 
$`AMP PEAK  6(6P21.31) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE 
       13.91        88.87        16.11        30.31        57.53        69.21 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KZ 
       22.03        18.48        24.36        46.49        91.30         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        73.05        61.08        62.99 
TCGA-PK-A5HC 
       22.32 

$`AMP PEAK  6(6P21.31) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5J9 
       44.55        55.13        68.75        12.00        19.04        44.45 
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        91.46        66.25        17.79        69.37        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       16.11        49.22        29.23        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-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       18.15        27.02        33.83        96.59        32.68       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KQ 
       22.98        16.37        49.08        24.62        11.31        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        50.37        44.84 
TCGA-OR-A5KY TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       12.85        60.89       152.15        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       28.64        23.64        39.58         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO 
       14.63        52.24        78.41        36.33        53.03        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       61.05        28.04        36.03        18.05        38.50        12.59 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
        0.00        24.85        20.25        39.48        42.51 

  AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE 
                          4.11                           0.00 
  AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE 
                         91.30                         153.63 
  AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE 
                         31.79                          36.33 
[1] "4.1 - 91.3 (31.8)"  "0.0 - 153.6 (36.3)"
[1] "hr=" "1.2"
D6V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  6(6P21.31) MUTATED         2        8         3        5
  AMP PEAK  6(6P21.31) WILD-TYPE       7       35        15       13
D6V3, multiclass
           clus
vv          AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(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  6(6P21.31) MUTATED    2  8  2  6
  AMP PEAK  6(6P21.31) WILD-TYPE  7 40  9 14
D6V4, multiclass
    clus
vv   AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(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"
D6V5, binary
                                cls
clus                              0  1
  AMP PEAK  6(6P21.31) MUTATED   17  1
  AMP PEAK  6(6P21.31) WILD-TYPE 61  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(6P21.31) MUTATED     17    1
  AMP PEAK  6(6P21.31) WILD-TYPE   61    9
   clus
vv  AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE
  0                           17                             61
  1                            1                              9
[1] 2 2
[1] FALSE
D6V6, binary
                                cls
clus                              0  1
  AMP PEAK  6(6P21.31) MUTATED   15  4
  AMP PEAK  6(6P21.31) WILD-TYPE 44 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(6P21.31) MUTATED     15    4
  AMP PEAK  6(6P21.31) WILD-TYPE   44   27
        clus
vv       AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE
  FEMALE                           15                             44
  MALE                              4                             27
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(6P21.31) MUTATED       1                         1    14
  AMP PEAK  6(6P21.31) WILD-TYPE     1                         0    62
D6V7, multiclass
                           clus
vv                          AMP PEAK  6(6P21.31) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               14
                           clus
vv                          AMP PEAK  6(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"
D6V8, binary
                                cls
clus                              0  1
  AMP PEAK  6(6P21.31) MUTATED    3  8
  AMP PEAK  6(6P21.31) WILD-TYPE  5 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(6P21.31) MUTATED      3    8
  AMP PEAK  6(6P21.31) WILD-TYPE    5   30
                        clus
vv                       AMP PEAK  6(6P21.31) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                            8
                        clus
vv                       AMP PEAK  6(6P21.31) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             30
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(6Q24.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  7(6Q24.3) MUTATED   12  7
  AMP PEAK  7(6Q24.3) WILD-TYPE 46 25
  AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE 
                           19                            71 
  AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE 
                            7                            25 
$`AMP PEAK  7(6Q24.3) MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JL 
       88.87        19.04        30.31        57.53        69.21        22.03 
TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KZ 
       33.83        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        73.05        61.08        62.99        39.48 
TCGA-PK-A5HC 
       22.32 

$`AMP PEAK  7(6Q24.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 
       44.55        55.13        68.75        13.91        12.00        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH 
       44.45        18.12        91.46        66.25        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       46.82        16.11        49.22        18.48        29.23        15.25 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
       36.26       121.25        12.59        29.82         9.50        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
       72.39        31.23        18.15        27.02        96.59       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KQ 
       22.98        16.37        49.08        11.31        91.30        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        50.37        44.84 
TCGA-OR-A5KY TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 
       12.85        58.55        60.89       152.15        43.30        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       29.10        28.64        23.64        39.58         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LL 
       21.76        14.63        52.24        78.41        36.33        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       69.11        61.05        28.04        36.03        18.05        38.50 
TCGA-P6-A5OG TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HB 
       12.59         0.00        24.85        20.25        42.51 

  AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE 
                         4.11                          0.00 
  AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE 
                        88.87                        153.63 
  AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE 
                        32.68                         38.50 
[1] "4.1 - 88.9 (32.7)"  "0.0 - 153.6 (38.5)"
[1] "hr=" "1.1"
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  7(6Q24.3) MUTATED         3        8         4        3
  AMP PEAK  7(6Q24.3) WILD-TYPE       6       35        14       15
D7V3, multiclass
           clus
vv          AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(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  7(6Q24.3) MUTATED    3  8  1  6
  AMP PEAK  7(6Q24.3) WILD-TYPE  6 40 10 14
D7V4, multiclass
    clus
vv   AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(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"
D7V5, binary
                               cls
clus                             0  1
  AMP PEAK  7(6Q24.3) MUTATED   18  0
  AMP PEAK  7(6Q24.3) WILD-TYPE 60 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6Q24.3) MUTATED     18    0
  AMP PEAK  7(6Q24.3) WILD-TYPE   60   10
   clus
vv  AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE
  0                          18                            60
  1                           0                            10
[1] 2 2
[1] FALSE
D7V6, binary
                               cls
clus                             0  1
  AMP PEAK  7(6Q24.3) MUTATED   12  7
  AMP PEAK  7(6Q24.3) WILD-TYPE 47 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6Q24.3) MUTATED     12    7
  AMP PEAK  7(6Q24.3) WILD-TYPE   47   24
        clus
vv       AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE
  FEMALE                          12                            47
  MALE                             7                            24
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(6Q24.3) MUTATED       1                         1    13
  AMP PEAK  7(6Q24.3) WILD-TYPE     1                         0    63
D7V7, multiclass
                           clus
vv                          AMP PEAK  7(6Q24.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              13
                           clus
vv                          AMP PEAK  7(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"
D7V8, binary
                               cls
clus                             0  1
  AMP PEAK  7(6Q24.3) MUTATED    2  7
  AMP PEAK  7(6Q24.3) WILD-TYPE  6 31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6Q24.3) MUTATED      2    7
  AMP PEAK  7(6Q24.3) WILD-TYPE    6   31
                        clus
vv                       AMP PEAK  7(6Q24.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           7
                        clus
vv                       AMP PEAK  7(6Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            31
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(7P22.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  8(7P22.1) MUTATED   33 21
  AMP PEAK  8(7P22.1) WILD-TYPE 25 11
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                           54                            36 
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                           21                            11 
$`AMP PEAK  8(7P22.1) MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       55.13        68.75        12.00        88.87        16.11        19.04 
TCGA-OR-A5JA TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JJ TCGA-OR-A5JK 
       30.31        66.25        17.79        69.37        16.11        49.22 
TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX 
       22.03        36.26       121.25        29.82        66.51        31.23 
TCGA-OR-A5JY TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
       18.15        96.59       100.18        16.37        49.08        24.62 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       46.49        83.80       153.63        50.37        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LA 
        4.11        58.55        60.89        31.79        29.10        23.64 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH 
       39.58         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        73.05        53.03        61.08        62.99        69.11 
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  8(7P22.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       44.55        13.91        44.45        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JI TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS 
       69.21        46.82        18.48        29.23        15.25        12.59 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K4 
        9.50        72.39        27.02        33.83        32.68        22.98 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV 
       11.31        24.36        91.30        88.01        95.18       127.50 
TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LG TCGA-OR-A5LI 
      152.15        43.30        28.31        28.64        52.24        14.33 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       28.04        18.05        12.59        20.25        39.48        42.51 

  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                          0.0                           9.5 
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                       153.63                        152.15 
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                       38.925                        30.955 
[1] "0.0 - 153.6 (38.9)" "9.5 - 152.2 (31.0)"
[1] "hr=" "1.2"
D8V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  8(7P22.1) MUTATED         2       27        12       13
  AMP PEAK  8(7P22.1) WILD-TYPE       7       16         6        5
D8V3, multiclass
           clus
vv          AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(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  8(7P22.1) MUTATED    2 31  7 14
  AMP PEAK  8(7P22.1) WILD-TYPE  7 17  4  6
D8V4, multiclass
    clus
vv   AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(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"
D8V5, binary
                               cls
clus                             0  1
  AMP PEAK  8(7P22.1) MUTATED   46  8
  AMP PEAK  8(7P22.1) WILD-TYPE 32  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P22.1) MUTATED     46    8
  AMP PEAK  8(7P22.1) WILD-TYPE   32    2
   clus
vv  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE
  0                          46                            32
  1                           8                             2
[1] 2 2
[1] FALSE
D8V6, binary
                               cls
clus                             0  1
  AMP PEAK  8(7P22.1) MUTATED   35 19
  AMP PEAK  8(7P22.1) WILD-TYPE 24 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P22.1) MUTATED     35   19
  AMP PEAK  8(7P22.1) WILD-TYPE   24   12
        clus
vv       AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE
  FEMALE                          35                            24
  MALE                            19                            12
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(7P22.1) MUTATED       1                         1    45
  AMP PEAK  8(7P22.1) WILD-TYPE     1                         0    31
D8V7, multiclass
                           clus
vv                          AMP PEAK  8(7P22.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              45
                           clus
vv                          AMP PEAK  8(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"
D8V8, binary
                               cls
clus                             0  1
  AMP PEAK  8(7P22.1) MUTATED    6 25
  AMP PEAK  8(7P22.1) WILD-TYPE  2 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P22.1) MUTATED      6   25
  AMP PEAK  8(7P22.1) WILD-TYPE    2   13
                        clus
vv                       AMP PEAK  8(7P22.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          25
                        clus
vv                       AMP PEAK  8(7P22.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            13
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(9Q31.3) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  9(9Q31.3) MUTATED   17 17
  AMP PEAK  9(9Q31.3) WILD-TYPE 41 15
  AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE 
                           34                            56 
  AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE 
                           17                            15 
$`AMP PEAK  9(9Q31.3) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA 
       13.91        12.00        16.11        19.04        44.45        30.31 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JJ TCGA-OR-A5JQ 
       69.21        66.25        17.79        69.37        16.11        36.26 
TCGA-OR-A5JV TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO 
       66.51        33.83        32.68        24.62        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
       91.30        83.80        44.84        12.85         4.11        58.55 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LS 
       39.58         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  9(9Q31.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5JB TCGA-OR-A5JC 
       44.55        55.13        68.75        88.87        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       91.46        46.82        49.22        22.03        18.48        29.23 
TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW 
       15.25       121.25        12.59        29.82         9.50        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        96.59       100.18        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KU 
       16.37        49.08        11.31        88.01        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
      127.50        50.37        60.89       152.15        31.79        43.30 
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-A5LG TCGA-OR-A5LH TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN 
       14.63        52.24        78.41        73.05        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 
       69.11        61.05        28.04        12.59        24.85        20.25 
TCGA-PK-A5HA TCGA-PK-A5HB 
       39.48        42.51 

  AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE 
                          0.0                           9.5 
  AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE 
                        91.30                        153.63 
  AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE 
                       33.255                        42.905 
[1] "0.0 - 91.3 (33.3)"  "9.5 - 153.6 (42.9)"
[1] "hr=" "2.4"
D9V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  9(9Q31.3) MUTATED         1       14         7       12
  AMP PEAK  9(9Q31.3) WILD-TYPE       8       29        11        6
D9V3, multiclass
           clus
vv          AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(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  9(9Q31.3) MUTATED    1 17  4 12
  AMP PEAK  9(9Q31.3) WILD-TYPE  8 31  7  8
D9V4, multiclass
    clus
vv   AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(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"
D9V5, binary
                               cls
clus                             0  1
  AMP PEAK  9(9Q31.3) MUTATED   27  7
  AMP PEAK  9(9Q31.3) WILD-TYPE 51  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(9Q31.3) MUTATED     27    7
  AMP PEAK  9(9Q31.3) WILD-TYPE   51    3
   clus
vv  AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE
  0                          27                            51
  1                           7                             3
[1] 2 2
[1] FALSE
D9V6, binary
                               cls
clus                             0  1
  AMP PEAK  9(9Q31.3) MUTATED   24 10
  AMP PEAK  9(9Q31.3) WILD-TYPE 35 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(9Q31.3) MUTATED     24   10
  AMP PEAK  9(9Q31.3) WILD-TYPE   35   21
        clus
vv       AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE
  FEMALE                          24                            35
  MALE                            10                            21
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(9Q31.3) MUTATED       1                         0    30
  AMP PEAK  9(9Q31.3) WILD-TYPE     1                         1    46
D9V7, multiclass
                           clus
vv                          AMP PEAK  9(9Q31.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              30
                           clus
vv                          AMP PEAK  9(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"
D9V8, binary
                               cls
clus                             0  1
  AMP PEAK  9(9Q31.3) MUTATED    5 16
  AMP PEAK  9(9Q31.3) WILD-TYPE  3 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(9Q31.3) MUTATED      5   16
  AMP PEAK  9(9Q31.3) WILD-TYPE    3   22
                        clus
vv                       AMP PEAK  9(9Q31.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          16
                        clus
vv                       AMP PEAK  9(9Q31.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            22
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(12Q14.1) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 10(12Q14.1) MUTATED   44 26
  AMP PEAK 10(12Q14.1) WILD-TYPE 14  6
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                            70                             20 
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                            26                              6 
$`AMP PEAK 10(12Q14.1) MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        13.91        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        44.45        30.31        57.53        69.21        66.25 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       17.79        69.37        46.82        16.11        49.22        22.03 
TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       18.48        15.25        36.26       121.25        29.82        66.51 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23        18.15        27.02        96.59        32.68       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KS 
       22.98        16.37        24.62        11.31        91.30        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
       95.18       153.63        50.37        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       58.55        60.89        31.79        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LF 
       28.64        23.64        39.58         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        73.05        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       69.11        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 10(12Q14.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JU 
       44.55        18.12        91.46        29.23        12.59         9.50 
TCGA-OR-A5JW TCGA-OR-A5K0 TCGA-OR-A5K6 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       72.39        33.83        49.08        24.36        46.49        88.01 
TCGA-OR-A5KV TCGA-OR-A5L3 TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LL TCGA-P6-A5OG 
      127.50       152.15        21.76        52.24        53.03        12.59 
TCGA-PK-A5H9 TCGA-PK-A5HB 
       20.25        42.51 

  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                           0.0                            9.5 
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                        153.63                         152.15 
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                        36.145                         43.530 
[1] "0.0 - 153.6 (36.1)" "9.5 - 152.2 (43.5)"
[1] "hr=" "1.3"
D10V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 10(12Q14.1) MUTATED         7       32        15       15
  AMP PEAK 10(12Q14.1) WILD-TYPE       2       11         3        3
D10V3, multiclass
           clus
vv          AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(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 10(12Q14.1) MUTATED    7 36  9 17
  AMP PEAK 10(12Q14.1) WILD-TYPE  2 12  2  3
D10V4, multiclass
    clus
vv   AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(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"
D10V5, binary
                                cls
clus                              0  1
  AMP PEAK 10(12Q14.1) MUTATED   60  9
  AMP PEAK 10(12Q14.1) WILD-TYPE 18  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(12Q14.1) MUTATED     60    9
  AMP PEAK 10(12Q14.1) WILD-TYPE   18    1
   clus
vv  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE
  0                           60                             18
  1                            9                              1
[1] 2 2
[1] FALSE
D10V6, binary
                                cls
clus                              0  1
  AMP PEAK 10(12Q14.1) MUTATED   45 25
  AMP PEAK 10(12Q14.1) WILD-TYPE 14  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(12Q14.1) MUTATED     45   25
  AMP PEAK 10(12Q14.1) WILD-TYPE   14    6
        clus
vv       AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE
  FEMALE                           45                             14
  MALE                             25                              6
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(12Q14.1) MUTATED       1                         1    59
  AMP PEAK 10(12Q14.1) WILD-TYPE     1                         0    17
D10V7, multiclass
                           clus
vv                          AMP PEAK 10(12Q14.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               59
                           clus
vv                          AMP PEAK 10(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"
D10V8, binary
                                cls
clus                              0  1
  AMP PEAK 10(12Q14.1) MUTATED    8 28
  AMP PEAK 10(12Q14.1) WILD-TYPE  0 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(12Q14.1) MUTATED      8   28
  AMP PEAK 10(12Q14.1) WILD-TYPE    0   10
                        clus
vv                       AMP PEAK 10(12Q14.1) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           28
                        clus
vv                       AMP PEAK 10(12Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                             10
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(14Q11.2) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 11(14Q11.2) MUTATED   16 11
  AMP PEAK 11(14Q11.2) WILD-TYPE 42 21
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                            27                             63 
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                            11                             21 
$`AMP PEAK 11(14Q11.2) MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC 
       68.75        13.91        12.00        44.45        30.31        57.53 
TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JP 
       69.21        17.79        16.11        22.03        18.48        15.25 
TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L2 
       24.62        46.49        91.30        50.37        44.84        60.89 
TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO 
       31.79        29.10        39.58        53.03        61.08        69.11 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HC 
       36.03        38.50        22.32 

$`AMP PEAK 11(14Q11.2) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB 
       44.55        55.13        88.87        16.11        19.04        18.12 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JO 
       91.46        66.25        69.37        46.82        49.22        29.23 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
       36.26       121.25        12.59        29.82         9.50        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       72.39        31.23        18.15        27.02        33.83        96.59 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       32.68       100.18        22.98        16.37        49.08        11.31 
TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       24.36        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 
       12.85         4.11        58.55       152.15        43.30        28.31 
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-A5LN 
       52.24        78.41        14.33        36.33        73.05        62.99 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG TCGA-P6-A5OH TCGA-PA-A5YG 
       61.05        28.04        18.05        12.59         0.00        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       20.25        39.48        42.51 

  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                            12                              0 
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                         91.30                         153.63 
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                         38.50                          36.26 
[1] "12.0 - 91.3 (38.5)" "0.0 - 153.6 (36.3)"
[1] "hr=" "1.3"
D11V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 11(14Q11.2) MUTATED         2       10         6        8
  AMP PEAK 11(14Q11.2) WILD-TYPE       7       33        12       10
D11V3, multiclass
           clus
vv          AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(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 11(14Q11.2) MUTATED    2 13  2  9
  AMP PEAK 11(14Q11.2) WILD-TYPE  7 35  9 11
D11V4, multiclass
    clus
vv   AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(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"
D11V5, binary
                                cls
clus                              0  1
  AMP PEAK 11(14Q11.2) MUTATED   20  6
  AMP PEAK 11(14Q11.2) WILD-TYPE 58  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(14Q11.2) MUTATED     20    6
  AMP PEAK 11(14Q11.2) WILD-TYPE   58    4
   clus
vv  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE
  0                           20                             58
  1                            6                              4
[1] 2 2
[1] FALSE
D11V6, binary
                                cls
clus                              0  1
  AMP PEAK 11(14Q11.2) MUTATED   19  8
  AMP PEAK 11(14Q11.2) WILD-TYPE 40 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(14Q11.2) MUTATED     19    8
  AMP PEAK 11(14Q11.2) WILD-TYPE   40   23
        clus
vv       AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE
  FEMALE                           19                             40
  MALE                              8                             23
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(14Q11.2) MUTATED       1                         0    22
  AMP PEAK 11(14Q11.2) WILD-TYPE     1                         1    54
D11V7, multiclass
                           clus
vv                          AMP PEAK 11(14Q11.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               22
                           clus
vv                          AMP PEAK 11(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"
D11V8, binary
                                cls
clus                              0  1
  AMP PEAK 11(14Q11.2) MUTATED    4 11
  AMP PEAK 11(14Q11.2) WILD-TYPE  4 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(14Q11.2) MUTATED      4   11
  AMP PEAK 11(14Q11.2) WILD-TYPE    4   27
                        clus
vv                       AMP PEAK 11(14Q11.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           11
                        clus
vv                       AMP PEAK 11(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             27
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(16P13.3) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 12(16P13.3) MUTATED   36 14
  AMP PEAK 12(16P13.3) WILD-TYPE 22 18
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                            50                             40 
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                            14                             18 
$`AMP PEAK 12(16P13.3) MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA 
       44.55        68.75        13.91        12.00        44.45        30.31 
TCGA-OR-A5JC TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       57.53        66.25        17.79        69.37        46.82        16.11 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22        22.03        36.26       121.25        29.82        66.51 
TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       31.23        27.02        96.59       100.18        22.98        16.37 
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        50.37        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
        4.11        58.55        31.79        43.30        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 12(16P13.3) WILD-TYPE`
TCGA-OR-A5J2 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD 
       55.13        88.87        16.11        19.04        18.12        91.46 
TCGA-OR-A5JE TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU 
       69.21        18.48        29.23        15.25        12.59         9.50 
TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K9 
       72.39        18.15        33.83        32.68        49.08        11.31 
TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX 
       24.36        91.30        88.01        95.18       127.50        44.84 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5LB TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH 
       60.89       152.15        39.58        21.76        52.24        78.41 
TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LN TCGA-OR-A5LO TCGA-P6-A5OG 
       14.33        36.33        73.05        62.99        69.11        12.59 
TCGA-P6-A5OH TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
        0.00        20.25        39.48        42.51 

  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                          4.11                           0.00 
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                        153.63                         152.15 
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                         33.91                          39.53 
[1] "4.1 - 153.6 (33.9)" "0.0 - 152.2 (39.5)"
[1] "hr=" "1.5"
D12V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 12(16P13.3) MUTATED         4       25        11        9
  AMP PEAK 12(16P13.3) WILD-TYPE       5       18         7        9
D12V3, multiclass
           clus
vv          AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(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 12(16P13.3) MUTATED    4 27  6 12
  AMP PEAK 12(16P13.3) WILD-TYPE  5 21  5  8
D12V4, multiclass
    clus
vv   AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(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"
D12V5, binary
                                cls
clus                              0  1
  AMP PEAK 12(16P13.3) MUTATED   43  6
  AMP PEAK 12(16P13.3) WILD-TYPE 35  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(16P13.3) MUTATED     43    6
  AMP PEAK 12(16P13.3) WILD-TYPE   35    4
   clus
vv  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE
  0                           43                             35
  1                            6                              4
[1] 2 2
[1] FALSE
D12V6, binary
                                cls
clus                              0  1
  AMP PEAK 12(16P13.3) MUTATED   29 21
  AMP PEAK 12(16P13.3) WILD-TYPE 30 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(16P13.3) MUTATED     29   21
  AMP PEAK 12(16P13.3) WILD-TYPE   30   10
        clus
vv       AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE
  FEMALE                           29                             30
  MALE                             21                             10
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(16P13.3) MUTATED       1                         0    43
  AMP PEAK 12(16P13.3) WILD-TYPE     1                         1    33
D12V7, multiclass
                           clus
vv                          AMP PEAK 12(16P13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               43
                           clus
vv                          AMP PEAK 12(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"
D12V8, binary
                                cls
clus                              0  1
  AMP PEAK 12(16P13.3) MUTATED    4 20
  AMP PEAK 12(16P13.3) WILD-TYPE  4 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(16P13.3) MUTATED      4   20
  AMP PEAK 12(16P13.3) WILD-TYPE    4   18
                        clus
vv                       AMP PEAK 12(16P13.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           20
                        clus
vv                       AMP PEAK 12(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             18
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(16Q22.1) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 13(16Q22.1) MUTATED   38 18
  AMP PEAK 13(16Q22.1) WILD-TYPE 20 14
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                            56                             34 
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                            18                             14 
$`AMP PEAK 13(16Q22.1) MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA 
       68.75        13.91        12.00        16.11        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        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       16.11        49.22        15.25        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        96.59       100.18        22.98 
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        50.37        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L5 
       12.85         4.11        58.55        60.89        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       28.31        29.10        28.64        23.64         5.23        39.35 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO 
       14.63        52.24        14.33        53.03        61.08        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       61.05        28.04        36.03        18.05        38.50        12.59 
TCGA-P6-A5OH TCGA-PA-A5YG 
        0.00        24.85 

$`AMP PEAK 13(16Q22.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD 
       44.55        55.13        88.87        19.04        18.12        91.46 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW 
       22.03        18.48        29.23        12.59         9.50        72.39 
TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.15        33.83        32.68        16.37        49.08        11.31 
TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5L3 
       24.36        91.30        88.01        95.18       127.50       152.15 
TCGA-OR-A5LB TCGA-OR-A5LE TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LN 
       39.58        21.76        78.41        36.33        73.05        62.99 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       20.25        39.48        42.51        22.32 

  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                           0.0                            9.5 
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                        153.63                         152.15 
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                        36.145                         37.905 
[1] "0.0 - 153.6 (36.1)" "9.5 - 152.2 (37.9)"
[1] "hr=" "1.1"
D13V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 13(16Q22.1) MUTATED         4       27        12       12
  AMP PEAK 13(16Q22.1) WILD-TYPE       5       16         6        6
D13V3, multiclass
           clus
vv          AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(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 13(16Q22.1) MUTATED    4 30  7 14
  AMP PEAK 13(16Q22.1) WILD-TYPE  5 18  4  6
D13V4, multiclass
    clus
vv   AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(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"
D13V5, binary
                                cls
clus                              0  1
  AMP PEAK 13(16Q22.1) MUTATED   48  7
  AMP PEAK 13(16Q22.1) WILD-TYPE 30  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(16Q22.1) MUTATED     48    7
  AMP PEAK 13(16Q22.1) WILD-TYPE   30    3
   clus
vv  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE
  0                           48                             30
  1                            7                              3
[1] 2 2
[1] FALSE
D13V6, binary
                                cls
clus                              0  1
  AMP PEAK 13(16Q22.1) MUTATED   34 22
  AMP PEAK 13(16Q22.1) WILD-TYPE 25  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(16Q22.1) MUTATED     34   22
  AMP PEAK 13(16Q22.1) WILD-TYPE   25    9
        clus
vv       AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE
  FEMALE                           34                             25
  MALE                             22                              9
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(16Q22.1) MUTATED       0                         0    49
  AMP PEAK 13(16Q22.1) WILD-TYPE     2                         1    27
D13V7, multiclass
                           clus
vv                          AMP PEAK 13(16Q22.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               49
                           clus
vv                          AMP PEAK 13(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"
D13V8, binary
                                cls
clus                              0  1
  AMP PEAK 13(16Q22.1) MUTATED    5 25
  AMP PEAK 13(16Q22.1) WILD-TYPE  3 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(16Q22.1) MUTATED      5   25
  AMP PEAK 13(16Q22.1) WILD-TYPE    3   13
                        clus
vv                       AMP PEAK 13(16Q22.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           25
                        clus
vv                       AMP PEAK 13(16Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             13
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(16Q24.2) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 14(16Q24.2) MUTATED   36 13
  AMP PEAK 14(16Q24.2) WILD-TYPE 22 19
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                            49                             41 
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                            13                             19 
$`AMP PEAK 14(16Q24.2) MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC 
       44.55        68.75        12.00        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        46.82        16.11 
TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX 
       49.22        36.26       121.25        29.82        66.51        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KO 
       27.02        96.59       100.18        22.98        24.62        46.49 
TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
       83.80       153.63        50.37        12.85         4.11        58.55 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       31.79        43.30        28.31        29.10        28.64        23.64 
TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP 
        5.23        14.63        53.03        61.08        69.11        61.05 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG 
       28.04        36.03        18.05        38.50        12.59        24.85 
TCGA-PK-A5HC 
       22.32 

$`AMP PEAK 14(16Q24.2) WILD-TYPE`
TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB 
       55.13        13.91        88.87        16.11        19.04        18.12 
TCGA-OR-A5JD TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS 
       91.46        22.03        18.48        29.23        15.25        12.59 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 
        9.50        72.39        18.15        33.83        32.68        16.37 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT 
       49.08        11.31        24.36        91.30        88.01        95.18 
TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5LB TCGA-OR-A5LD 
      127.50        44.84        60.89       152.15        39.58        39.35 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       21.76        52.24        78.41        14.33        36.33        73.05 
TCGA-OR-A5LN TCGA-P6-A5OH TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       62.99         0.00        20.25        39.48        42.51 

  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                          4.11                           0.00 
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                        153.63                         152.15 
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                         36.26                          36.33 
[1] "4.1 - 153.6 (36.3)" "0.0 - 152.2 (36.3)"
[1] "hr=" "1.7"
D14V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 14(16Q24.2) MUTATED         4       26         9        9
  AMP PEAK 14(16Q24.2) WILD-TYPE       5       17         9        9
D14V3, multiclass
           clus
vv          AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(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 14(16Q24.2) MUTATED    4 28  4 12
  AMP PEAK 14(16Q24.2) WILD-TYPE  5 20  7  8
D14V4, multiclass
    clus
vv   AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(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"
D14V5, binary
                                cls
clus                              0  1
  AMP PEAK 14(16Q24.2) MUTATED   43  5
  AMP PEAK 14(16Q24.2) WILD-TYPE 35  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16Q24.2) MUTATED     43    5
  AMP PEAK 14(16Q24.2) WILD-TYPE   35    5
   clus
vv  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE
  0                           43                             35
  1                            5                              5
[1] 2 2
[1] FALSE
D14V6, binary
                                cls
clus                              0  1
  AMP PEAK 14(16Q24.2) MUTATED   29 20
  AMP PEAK 14(16Q24.2) WILD-TYPE 30 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16Q24.2) MUTATED     29   20
  AMP PEAK 14(16Q24.2) WILD-TYPE   30   11
        clus
vv       AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE
  FEMALE                           29                             30
  MALE                             20                             11
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(16Q24.2) MUTATED       1                         0    41
  AMP PEAK 14(16Q24.2) WILD-TYPE     1                         1    35
D14V7, multiclass
                           clus
vv                          AMP PEAK 14(16Q24.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               41
                           clus
vv                          AMP PEAK 14(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"
D14V8, binary
                                cls
clus                              0  1
  AMP PEAK 14(16Q24.2) MUTATED    3 20
  AMP PEAK 14(16Q24.2) WILD-TYPE  5 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16Q24.2) MUTATED      3   20
  AMP PEAK 14(16Q24.2) WILD-TYPE    5   18
                        clus
vv                       AMP PEAK 14(16Q24.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           20
                        clus
vv                       AMP PEAK 14(16Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             18
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(17Q25.3) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 15(17Q25.3) MUTATED   10  8
  AMP PEAK 15(17Q25.3) WILD-TYPE 48 24
  AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE 
                            18                             72 
  AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE 
                             8                             24 
$`AMP PEAK 15(17Q25.3) MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JH TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JY 
       19.04        69.37        18.48        15.25        36.26        18.15 
TCGA-OR-A5K6 TCGA-OR-A5KP TCGA-OR-A5KU TCGA-OR-A5L2 TCGA-OR-A5LD TCGA-OR-A5LF 
       49.08        91.30       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        69.11        18.05         0.00        39.48        22.32 

$`AMP PEAK 15(17Q25.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        44.45        30.31        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       69.21        66.25        17.79        46.82        16.11        49.22 
TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
       22.03        29.23       121.25        12.59        29.82         9.50 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       66.51        72.39        31.23        27.02        33.83        96.59 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       32.68       100.18        22.98        16.37        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV 
       24.36        46.49        88.01        83.80        95.18       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 
       50.37        44.84        12.85         4.11        58.55       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       31.79        43.30        28.31        29.10        28.64        23.64 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       39.58         5.23        21.76        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR 
       73.05        53.03        61.08        62.99        61.05        28.04 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HB 
       36.03        38.50        12.59        24.85        20.25        42.51 

  AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE 
                          0.00                           4.11 
  AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE 
                        153.63                         152.15 
  AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE 
                        29.290                         37.415 
[1] "0.0 - 153.6 (29.3)" "4.1 - 152.2 (37.4)"
[1] "hr=" "1.5"
D15V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 15(17Q25.3) MUTATED         1        8         5        4
  AMP PEAK 15(17Q25.3) WILD-TYPE       8       35        13       14
D15V3, multiclass
           clus
vv          AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(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 15(17Q25.3) MUTATED    1  8  3  6
  AMP PEAK 15(17Q25.3) WILD-TYPE  8 40  8 14
D15V4, multiclass
    clus
vv   AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(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"
D15V5, binary
                                cls
clus                              0  1
  AMP PEAK 15(17Q25.3) MUTATED   17  1
  AMP PEAK 15(17Q25.3) WILD-TYPE 61  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(17Q25.3) MUTATED     17    1
  AMP PEAK 15(17Q25.3) WILD-TYPE   61    9
   clus
vv  AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE
  0                           17                             61
  1                            1                              9
[1] 2 2
[1] FALSE
D15V6, binary
                                cls
clus                              0  1
  AMP PEAK 15(17Q25.3) MUTATED   13  5
  AMP PEAK 15(17Q25.3) WILD-TYPE 46 26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(17Q25.3) MUTATED     13    5
  AMP PEAK 15(17Q25.3) WILD-TYPE   46   26
        clus
vv       AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE
  FEMALE                           13                             46
  MALE                              5                             26
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(17Q25.3) MUTATED       1                         0    14
  AMP PEAK 15(17Q25.3) WILD-TYPE     1                         1    62
D15V7, multiclass
                           clus
vv                          AMP PEAK 15(17Q25.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               14
                           clus
vv                          AMP PEAK 15(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"
D15V8, binary
                                cls
clus                              0  1
  AMP PEAK 15(17Q25.3) MUTATED    1  9
  AMP PEAK 15(17Q25.3) WILD-TYPE  7 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(17Q25.3) MUTATED      1    9
  AMP PEAK 15(17Q25.3) WILD-TYPE    7   29
                        clus
vv                       AMP PEAK 15(17Q25.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            9
                        clus
vv                       AMP PEAK 15(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             29
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(19P13.12) MUTATION ANALYSIS
D16V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 16(19P13.12) MUTATED   34 24
  AMP PEAK 16(19P13.12) WILD-TYPE 24  8
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                             58                              32 
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                             24                               8 
$`AMP PEAK 16(19P13.12) MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        13.91        12.00        88.87        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-A5JM TCGA-OR-A5JP 
       69.37        46.82        16.11        49.22        18.48        15.25 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5K0 TCGA-OR-A5K2 
       36.26       121.25        66.51        31.23        33.83        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP 
      100.18        16.37        24.62        11.31        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
       83.80       153.63        50.37        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LC 
       58.55        60.89        31.79        29.10        39.58         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        73.05        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OR-A5LT 
       61.08        62.99        69.11        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 16(19P13.12) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JL TCGA-OR-A5JO 
       44.55        19.04        18.12        91.46        22.03        29.23 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ 
       12.59        29.82         9.50        72.39        18.15        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KT 
       96.59        22.98        49.08        24.36        88.01        95.18 
TCGA-OR-A5KV TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA 
      127.50       152.15        43.30        28.31        28.64        23.64 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PK-A5H9 
       21.76        52.24        14.33        28.04        12.59        20.25 
TCGA-PK-A5HA TCGA-PK-A5HB 
       39.48        42.51 

  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                            0.0                             9.5 
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                         153.63                          152.15 
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                         39.465                          28.475 
[1] "0.0 - 153.6 (39.5)" "9.5 - 152.2 (28.5)"
[1] "hr=" "1.6"
D16V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 16(19P13.12) MUTATED         3       27        13       14
  AMP PEAK 16(19P13.12) WILD-TYPE       6       16         5        4
D16V3, multiclass
           clus
vv          AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(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 16(19P13.12) MUTATED    3 31  8 15
  AMP PEAK 16(19P13.12) WILD-TYPE  6 17  3  5
D16V4, multiclass
    clus
vv   AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(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"
D16V5, binary
                                 cls
clus                               0  1
  AMP PEAK 16(19P13.12) MUTATED   49  8
  AMP PEAK 16(19P13.12) WILD-TYPE 29  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(19P13.12) MUTATED     49    8
  AMP PEAK 16(19P13.12) WILD-TYPE   29    2
   clus
vv  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE
  0                            49                              29
  1                             8                               2
[1] 2 2
[1] FALSE
D16V6, binary
                                 cls
clus                               0  1
  AMP PEAK 16(19P13.12) MUTATED   38 20
  AMP PEAK 16(19P13.12) WILD-TYPE 21 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(19P13.12) MUTATED     38   20
  AMP PEAK 16(19P13.12) WILD-TYPE   21   11
        clus
vv       AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE
  FEMALE                            38                              21
  MALE                              20                              11
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(19P13.12) MUTATED       1                         1    48
  AMP PEAK 16(19P13.12) WILD-TYPE     1                         0    28
D16V7, multiclass
                           clus
vv                          AMP PEAK 16(19P13.12) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                48
                           clus
vv                          AMP PEAK 16(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"
D16V8, binary
                                 cls
clus                               0  1
  AMP PEAK 16(19P13.12) MUTATED    7 23
  AMP PEAK 16(19P13.12) WILD-TYPE  1 15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(19P13.12) MUTATED      7   23
  AMP PEAK 16(19P13.12) WILD-TYPE    1   15
                        clus
vv                       AMP PEAK 16(19P13.12) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            23
                        clus
vv                       AMP PEAK 16(19P13.12) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                              15
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(19Q12) MUTATION ANALYSIS
D17V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 17(19Q12) MUTATED   31 25
  AMP PEAK 17(19Q12) WILD-TYPE 27  7
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                          56                           34 
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                          25                            7 
$`AMP PEAK 17(19Q12) MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF 
       16.11        44.45        30.31        57.53        69.21        66.25 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM 
       17.79        69.37        46.82        16.11        49.22        18.48 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5K2 
       15.25        36.26       121.25        66.51        31.23        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP 
      100.18        16.37        24.62        11.31        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
       83.80       153.63        44.84        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       60.89        31.79        29.10        39.58         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        73.05        53.03        61.08 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       69.11        61.05        36.03        18.05        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5HC 
       24.85        22.32 

$`AMP PEAK 17(19Q12) WILD-TYPE`
TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JS 
       19.04        18.12        91.46        22.03        29.23        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 
       29.82         9.50        72.39        18.15        27.02        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KT 
       96.59        22.98        49.08        24.36        88.01        95.18 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
      127.50        50.37       152.15        43.30        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LN TCGA-OR-A5LR 
       23.64        21.76        14.63        52.24        62.99        28.04 
TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       12.59        20.25        39.48        42.51 

  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                         0.0                          9.5 
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                      153.63                       152.15 
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                      39.465                       28.935 
[1] "0.0 - 153.6 (39.5)" "9.5 - 152.2 (28.9)"
[1] "hr=" "2.1"
D17V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 17(19Q12) MUTATED         3       26        11       15
  AMP PEAK 17(19Q12) WILD-TYPE       6       17         7        3
D17V3, multiclass
           clus
vv          AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(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 17(19Q12) MUTATED    3 29  7 16
  AMP PEAK 17(19Q12) WILD-TYPE  6 19  4  4
D17V4, multiclass
    clus
vv   AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(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"
D17V5, binary
                              cls
clus                            0  1
  AMP PEAK 17(19Q12) MUTATED   48  7
  AMP PEAK 17(19Q12) WILD-TYPE 30  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(19Q12) MUTATED     48    7
  AMP PEAK 17(19Q12) WILD-TYPE   30    3
   clus
vv  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE
  0                         48                           30
  1                          7                            3
[1] 2 2
[1] FALSE
D17V6, binary
                              cls
clus                            0  1
  AMP PEAK 17(19Q12) MUTATED   35 21
  AMP PEAK 17(19Q12) WILD-TYPE 24 10
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(19Q12) MUTATED     35   21
  AMP PEAK 17(19Q12) WILD-TYPE   24   10
        clus
vv       AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE
  FEMALE                         35                           24
  MALE                           21                           10
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(19Q12) MUTATED       1                         1    47
  AMP PEAK 17(19Q12) WILD-TYPE     1                         0    29
D17V7, multiclass
                           clus
vv                          AMP PEAK 17(19Q12) MUTATED
  ASIAN                                              1
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             47
                           clus
vv                          AMP PEAK 17(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"
D17V8, binary
                              cls
clus                            0  1
  AMP PEAK 17(19Q12) MUTATED    7 22
  AMP PEAK 17(19Q12) WILD-TYPE  1 16
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(19Q12) MUTATED      7   22
  AMP PEAK 17(19Q12) WILD-TYPE    1   16
                        clus
vv                       AMP PEAK 17(19Q12) MUTATED
  HISPANIC OR LATINO                              7
  NOT HISPANIC OR LATINO                         22
                        clus
vv                       AMP PEAK 17(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           16
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(XP11.22) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 18(XP11.22) MUTATED   32 17
  AMP PEAK 18(XP11.22) WILD-TYPE 26 15
  AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE 
                            49                             41 
  AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE 
                            17                             15 
$`AMP PEAK 18(XP11.22) MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        13.91        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ 
       19.04        44.45        30.31        69.21        66.25        16.11 
TCGA-OR-A5JL TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 
       22.03       121.25        29.82        18.15        27.02        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO 
       96.59       100.18        22.98        24.62        24.36        46.49 
TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ 
       83.80       153.63       127.50        50.37        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 
       58.55        60.89        31.79        43.30        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ 
       23.64        39.58        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        69.11        61.05        28.04        18.05        24.85 
TCGA-PK-A5HC 
       22.32 

$`AMP PEAK 18(XP11.22) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH 
       44.55        18.12        57.53        91.46        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       46.82        49.22        18.48        29.23        15.25        36.26 
TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 
       12.59         9.50        66.51        72.39        31.23        32.68 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT 
       16.37        49.08        11.31        91.30        88.01        95.18 
TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG 
       44.84       152.15        28.31         5.23        21.76        52.24 
TCGA-OR-A5LI TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI 
       14.33        73.05        53.03        62.99        36.03        38.50 
TCGA-P6-A5OG TCGA-P6-A5OH TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       12.59         0.00        20.25        39.48        42.51 

  AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE 
                          4.11                           0.00 
  AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE 
                        153.63                         152.15 
  AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE 
                         33.83                          38.50 
[1] "4.1 - 153.6 (33.8)" "0.0 - 152.2 (38.5)"
[1] "hr=" "1.1"
D18V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 18(XP11.22) MUTATED         4       24        12        9
  AMP PEAK 18(XP11.22) WILD-TYPE       5       19         6        9
D18V3, multiclass
           clus
vv          AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(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 18(XP11.22) MUTATED    4 27  7 11
  AMP PEAK 18(XP11.22) WILD-TYPE  5 21  4  9
D18V4, multiclass
    clus
vv   AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(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"
D18V5, binary
                                cls
clus                              0  1
  AMP PEAK 18(XP11.22) MUTATED   42  7
  AMP PEAK 18(XP11.22) WILD-TYPE 36  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(XP11.22) MUTATED     42    7
  AMP PEAK 18(XP11.22) WILD-TYPE   36    3
   clus
vv  AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE
  0                           42                             36
  1                            7                              3
[1] 2 2
[1] FALSE
D18V6, binary
                                cls
clus                              0  1
  AMP PEAK 18(XP11.22) MUTATED   34 15
  AMP PEAK 18(XP11.22) WILD-TYPE 25 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(XP11.22) MUTATED     34   15
  AMP PEAK 18(XP11.22) WILD-TYPE   25   16
        clus
vv       AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE
  FEMALE                           34                             25
  MALE                             15                             16
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(XP11.22) MUTATED       1                         1    42
  AMP PEAK 18(XP11.22) WILD-TYPE     1                         0    34
D18V7, multiclass
                           clus
vv                          AMP PEAK 18(XP11.22) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               42
                           clus
vv                          AMP PEAK 18(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"
D18V8, binary
                                cls
clus                              0  1
  AMP PEAK 18(XP11.22) MUTATED    8 23
  AMP PEAK 18(XP11.22) WILD-TYPE  0 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(XP11.22) MUTATED      8   23
  AMP PEAK 18(XP11.22) WILD-TYPE    0   15
                        clus
vv                       AMP PEAK 18(XP11.22) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           23
                        clus
vv                       AMP PEAK 18(XP11.22) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                             15
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(XQ28) MUTATION ANALYSIS
D19V1, survival
                             sevent
clus2                          0  1
  AMP PEAK 19(XQ28) MUTATED   32 14
  AMP PEAK 19(XQ28) WILD-TYPE 26 18
  AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE 
                         46                          44 
  AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE 
                         14                          18 
$`AMP PEAK 19(XQ28) MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J9 TCGA-OR-A5JE 
       55.13        68.75        12.00        88.87        44.45        69.21 
TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JY 
       66.25        16.11        22.03       121.25        29.82        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       27.02        96.59       100.18        22.98        16.37        24.62 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5KY 
       24.36        46.49        83.80       153.63        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 
        4.11        58.55        31.79        43.30        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ 
       23.64        39.58        39.35        14.63        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       73.05        61.08        69.11        61.05        28.04        18.05 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5HB TCGA-PK-A5HC 
        0.00        24.85        42.51        22.32 

$`AMP PEAK 19(XQ28) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       44.55        13.91        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        91.46        17.79        69.37        46.82        49.22 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JU 
       18.48        29.23        15.25        36.26        12.59         9.50 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K6 
       66.51        72.39        31.23        33.83        32.68        49.08 
TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        91.30        88.01        95.18       127.50        50.37 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG 
       60.89       152.15        28.31         5.23        21.76        52.24 
TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG 
       14.33        53.03        62.99        36.03        38.50        12.59 
TCGA-PK-A5H9 TCGA-PK-A5HA 
       20.25        39.48 

  AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE 
                       0.00                        5.23 
  AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE 
                     153.63                      152.15 
  AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE 
                     37.840                      36.145 
[1] "0.0 - 153.6 (37.8)" "5.2 - 152.2 (36.1)"
[1] "hr=" "1.4"
D19V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 19(XQ28) MUTATED         4       23        10        8
  AMP PEAK 19(XQ28) WILD-TYPE       5       20         8       10
D19V3, multiclass
           clus
vv          AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(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 19(XQ28) MUTATED    4 25  5 11
  AMP PEAK 19(XQ28) WILD-TYPE  5 23  6  9
D19V4, multiclass
    clus
vv   AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(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"
D19V5, binary
                             cls
clus                           0  1
  AMP PEAK 19(XQ28) MUTATED   40  5
  AMP PEAK 19(XQ28) WILD-TYPE 38  5
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 19(XQ28) MUTATED     40    5
  AMP PEAK 19(XQ28) WILD-TYPE   38    5
   clus
vv  AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE
  0                        40                          38
  1                         5                           5
[1] 2 2
[1] FALSE
D19V6, binary
                             cls
clus                           0  1
  AMP PEAK 19(XQ28) MUTATED   30 16
  AMP PEAK 19(XQ28) WILD-TYPE 29 15
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 19(XQ28) MUTATED     30   16
  AMP PEAK 19(XQ28) WILD-TYPE   29   15
        clus
vv       AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE
  FEMALE                        30                          29
  MALE                          16                          15
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(XQ28) MUTATED       1                         1    37
  AMP PEAK 19(XQ28) WILD-TYPE     1                         0    39
D19V7, multiclass
                           clus
vv                          AMP PEAK 19(XQ28) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            37
                           clus
vv                          AMP PEAK 19(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"
D19V8, binary
                             cls
clus                           0  1
  AMP PEAK 19(XQ28) MUTATED    5 22
  AMP PEAK 19(XQ28) WILD-TYPE  3 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 19(XQ28) MUTATED      5   22
  AMP PEAK 19(XQ28) WILD-TYPE    3   16
                        clus
vv                       AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             5                           3
  NOT HISPANIC OR LATINO                        22                          16
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK  1(1P36.23) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.23) MUTATED   22 16
  DEL PEAK  1(1P36.23) WILD-TYPE 36 16
  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                             16 
$`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        91.46 
TCGA-OR-A5JE TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM 
       69.21        69.37        46.82        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        62.99        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-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        22.03        29.23       121.25 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 
       29.82         9.50        27.02        33.83        96.59       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ 
       22.98        24.62        24.36        46.49        91.30        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY 
       83.80        95.18       153.63       127.50        50.37        12.85 
TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       58.55        31.79        43.30        29.10        28.64        23.64 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ 
       39.58        39.35        21.76        14.63        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OG 
       73.05        53.03        69.11        61.05        28.04        12.59 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HB TCGA-PK-A5HC 
       24.85        20.25        42.51        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                          35.08 
[1] "0.0 - 152.2 (37.4)" "9.5 - 153.6 (35.1)"
[1] "hr=" "1.6"
D20V2, 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
D20V3, 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
D20V4, 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"
D20V5, 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
D20V6, 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
                                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
D20V7, 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"
D20V8, 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(21) Variable = DEL PEAK  2(1Q43) MUTATION ANALYSIS
D21V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  2(1Q43) MUTATED   11  7
  DEL PEAK  2(1Q43) WILD-TYPE 47 25
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                         18                          72 
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                          7                          25 
$`DEL PEAK  2(1Q43) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH 
       13.91        19.04        30.31        57.53        91.46        69.37 
TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       46.82        22.03        36.26        72.39        31.23        18.15 
TCGA-OR-A5KT TCGA-OR-A5L2 TCGA-OR-A5L6 TCGA-OR-A5LF TCGA-OR-A5LM TCGA-OU-A5PI 
       95.18        60.89        28.31        14.63        61.08        38.50 

$`DEL PEAK  2(1Q43) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        68.75        12.00        88.87        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JJ 
       44.45        18.12        69.21        66.25        17.79        16.11 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS 
       49.22        18.48        29.23        15.25       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       29.82         9.50        66.51        27.02        33.83        96.59 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
       32.68       100.18        22.98        16.37        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS 
       11.31        24.36        46.49        91.30        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        50.37        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 
       58.55       152.15        31.79        43.30        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG 
       23.64        39.58         5.23        39.35        21.76        52.24 
TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN 
       78.41        14.33        36.33        73.05        53.03        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-P6-A5OG 
       69.11        61.05        28.04        36.03        18.05        12.59 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
        0.00        24.85        20.25        39.48        42.51        22.32 

  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                      13.91                        0.00 
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                      95.18                      153.63 
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                      37.38                       36.18 
[1] "13.9 - 95.2 (37.4)" "0.0 - 153.6 (36.2)"
[1] "hr=" "1"  
D21V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  2(1Q43) MUTATED         3        7         3        4
  DEL PEAK  2(1Q43) WILD-TYPE       6       36        15       14
D21V3, multiclass
           clus
vv          DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE
  STAGE I                           3                           6
  STAGE II                          7                          36
  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  2(1Q43) MUTATED    3  8  4  2
  DEL PEAK  2(1Q43) WILD-TYPE  6 40  7 18
D21V4, multiclass
    clus
vv   DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE
  T1                         3                           6
  T2                         8                          40
  T3                         4                           7
  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"
D21V5, binary
                             cls
clus                           0  1
  DEL PEAK  2(1Q43) MUTATED   14  3
  DEL PEAK  2(1Q43) WILD-TYPE 64  7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q43) MUTATED     14    3
  DEL PEAK  2(1Q43) WILD-TYPE   64    7
   clus
vv  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE
  0                        14                          64
  1                         3                           7
[1] 2 2
[1] FALSE
D21V6, binary
                             cls
clus                           0  1
  DEL PEAK  2(1Q43) MUTATED   11  7
  DEL PEAK  2(1Q43) WILD-TYPE 48 24
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q43) MUTATED     11    7
  DEL PEAK  2(1Q43) WILD-TYPE   48   24
        clus
vv       DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE
  FEMALE                        11                          48
  MALE                           7                          24
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1Q43) MUTATED       0                         0    17
  DEL PEAK  2(1Q43) WILD-TYPE     2                         1    59
D21V7, multiclass
                           clus
vv                          DEL PEAK  2(1Q43) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            17
                           clus
vv                          DEL PEAK  2(1Q43) 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"
D21V8, binary
                             cls
clus                           0  1
  DEL PEAK  2(1Q43) MUTATED    2  5
  DEL PEAK  2(1Q43) WILD-TYPE  6 33
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q43) MUTATED      2    5
  DEL PEAK  2(1Q43) WILD-TYPE    6   33
                        clus
vv                       DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE
  HISPANIC OR LATINO                             2                           6
  NOT HISPANIC OR LATINO                         5                          33
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D22V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(2Q22.1) MUTATED   15  3
  DEL PEAK  3(2Q22.1) WILD-TYPE 43 29
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           18                            72 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            3                            29 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JL 
       30.31        57.53        91.46        69.37        49.22        22.03 
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        62.99        36.03        38.50        39.48 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        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        46.82        16.11        18.48        29.23        15.25 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
      121.25        29.82         9.50        27.02        33.83        96.59 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
       32.68       100.18        22.98        16.37        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       11.31        46.49        91.30        88.01        83.80        95.18 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      127.50        50.37        44.84        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       60.89       152.15        31.79        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       28.64        23.64        39.58         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        73.05 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       53.03        61.08        69.11        61.05        28.04        18.05 
TCGA-P6-A5OG TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HB TCGA-PK-A5HC 
       12.59         0.00        24.85        20.25        42.51        22.32 

  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                        12.59                          0.00 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       153.63                        152.15 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       38.990                        33.255 
[1] "12.6 - 153.6 (39.0)" "0.0 - 152.2 (33.3)" 
[1] "hr=" "2.8"
D22V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  3(2Q22.1) MUTATED         2       10         1        4
  DEL PEAK  3(2Q22.1) WILD-TYPE       7       33        17       14
D22V3, multiclass
           clus
vv          DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(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  3(2Q22.1) MUTATED    2 11  1  3
  DEL PEAK  3(2Q22.1) WILD-TYPE  7 37 10 17
D22V4, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(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"
D22V5, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   15  2
  DEL PEAK  3(2Q22.1) WILD-TYPE 63  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     15    2
  DEL PEAK  3(2Q22.1) WILD-TYPE   63    8
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          15                            63
  1                           2                             8
[1] 2 2
[1] FALSE
D22V6, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   12  6
  DEL PEAK  3(2Q22.1) WILD-TYPE 47 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     12    6
  DEL PEAK  3(2Q22.1) WILD-TYPE   47   25
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                          12                            47
  MALE                             6                            25
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q22.1) MUTATED       0                         0    15
  DEL PEAK  3(2Q22.1) WILD-TYPE     2                         1    61
D22V7, multiclass
                           clus
vv                          DEL PEAK  3(2Q22.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              15
                           clus
vv                          DEL PEAK  3(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"
D22V8, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED    0  3
  DEL PEAK  3(2Q22.1) WILD-TYPE  8 35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      0    3
  DEL PEAK  3(2Q22.1) WILD-TYPE    8   35
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                            35
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D23V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(2Q37.3) MUTATED   15  6
  DEL PEAK  4(2Q37.3) WILD-TYPE 43 26
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           21                            69 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            6                            26 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH 
       13.91        44.45        30.31        57.53        91.46        69.37 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW 
       49.22        22.03        36.26        12.59        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5K0 TCGA-OR-A5L2 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LN 
       31.23        33.83        60.89        39.58         5.23        62.99 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
       36.03        38.50        39.48 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        68.75        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JI 
       19.04        18.12        69.21        66.25        17.79        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT 
       16.11        18.48        29.23        15.25       121.25        29.82 
TCGA-OR-A5JU TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
        9.50        18.15        27.02        96.59        32.68       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       22.98        16.37        49.08        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       46.49        91.30        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        50.37        44.84        12.85         4.11        58.55 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      152.15        31.79        43.30        28.31        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-A5LM TCGA-OR-A5LO 
       14.33        36.33        73.05        53.03        61.08        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG TCGA-P6-A5OH TCGA-PA-A5YG 
       61.05        28.04        18.05        12.59         0.00        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HB TCGA-PK-A5HC 
       20.25        42.51        22.32 

  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         5.23                          0.00 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                        91.46                        153.63 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                        39.48                         31.79 
[1] "5.2 - 91.5 (39.5)"  "0.0 - 153.6 (31.8)"
[1] "hr=" "1.4"
D23V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  4(2Q37.3) MUTATED         2       11         1        6
  DEL PEAK  4(2Q37.3) WILD-TYPE       7       32        17       12
D23V3, multiclass
           clus
vv          DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(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  4(2Q37.3) MUTATED    2 12  2  4
  DEL PEAK  4(2Q37.3) WILD-TYPE  7 36  9 16
D23V4, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(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"
D23V5, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.3) MUTATED   18  2
  DEL PEAK  4(2Q37.3) WILD-TYPE 60  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     18    2
  DEL PEAK  4(2Q37.3) WILD-TYPE   60    8
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                          18                            60
  1                           2                             8
[1] 2 2
[1] FALSE
D23V6, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.3) MUTATED   14  7
  DEL PEAK  4(2Q37.3) WILD-TYPE 45 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     14    7
  DEL PEAK  4(2Q37.3) WILD-TYPE   45   24
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                          14                            45
  MALE                             7                            24
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED       0                         0    18
  DEL PEAK  4(2Q37.3) WILD-TYPE     2                         1    58
D23V7, multiclass
                           clus
vv                          DEL PEAK  4(2Q37.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              18
                           clus
vv                          DEL PEAK  4(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"
D23V8, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.3) MUTATED    2  4
  DEL PEAK  4(2Q37.3) WILD-TYPE  6 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      2    4
  DEL PEAK  4(2Q37.3) WILD-TYPE    6   34
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            34
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK  5(3Q13.31) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  5(3Q13.31) MUTATED   13 12
  DEL PEAK  5(3Q13.31) WILD-TYPE 45 20
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            25                             65 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            12                             20 
$`DEL PEAK  5(3Q13.31) MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JG 
       88.87        16.11        19.04        30.31        57.53        17.79 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       49.22        22.03        15.25        72.39        31.23        18.15 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5L6 TCGA-OR-A5LC 
       24.62        11.31        91.30        83.80        28.31         5.23 
TCGA-OR-A5LE TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LS TCGA-P6-A5OH 
       21.76        14.33        53.03        61.08        36.03         0.00 
TCGA-PK-A5HB 
       42.51 

$`DEL PEAK  5(3Q13.31) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J9 
       44.55        55.13        68.75        13.91        12.00        44.45 
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        91.46        69.21        66.25        69.37        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       16.11        18.48        29.23        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       29.82         9.50        66.51        27.02        33.83        96.59 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5KB 
       32.68       100.18        22.98        16.37        49.08        24.36 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        88.01        95.18       153.63       127.50        50.37 
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-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       31.79        43.30        29.10        28.64        23.64        39.58 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.35        14.63        52.24        78.41        36.33        73.05 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-OU-A5PI 
       62.99        69.11        61.05        28.04        18.05        38.50 
TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       12.59        24.85        20.25        39.48        22.32 

  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                          0.00                           4.11 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                         91.30                         153.63 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                         28.31                          39.48 
[1] "0.0 - 91.3 (28.3)"  "4.1 - 153.6 (39.5)"
[1] "hr=" "1.9"
D24V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  5(3Q13.31) MUTATED         1       12         3        7
  DEL PEAK  5(3Q13.31) WILD-TYPE       8       31        15       11
D24V3, multiclass
           clus
vv          DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(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  5(3Q13.31) MUTATED    1 12  3  7
  DEL PEAK  5(3Q13.31) WILD-TYPE  8 36  8 13
D24V4, multiclass
    clus
vv   DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(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"
D24V5, binary
                                cls
clus                              0  1
  DEL PEAK  5(3Q13.31) MUTATED   21  2
  DEL PEAK  5(3Q13.31) WILD-TYPE 57  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3Q13.31) MUTATED     21    2
  DEL PEAK  5(3Q13.31) WILD-TYPE   57    8
   clus
vv  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  0                           21                             57
  1                            2                              8
[1] 2 2
[1] FALSE
D24V6, binary
                                cls
clus                              0  1
  DEL PEAK  5(3Q13.31) MUTATED   12 13
  DEL PEAK  5(3Q13.31) WILD-TYPE 47 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3Q13.31) MUTATED     12   13
  DEL PEAK  5(3Q13.31) WILD-TYPE   47   18
        clus
vv       DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  FEMALE                           12                             47
  MALE                             13                             18
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3Q13.31) MUTATED       0                         1    20
  DEL PEAK  5(3Q13.31) WILD-TYPE     2                         0    56
D24V7, multiclass
                           clus
vv                          DEL PEAK  5(3Q13.31) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               20
                           clus
vv                          DEL PEAK  5(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"
D24V8, binary
                                cls
clus                              0  1
  DEL PEAK  5(3Q13.31) MUTATED    3  8
  DEL PEAK  5(3Q13.31) WILD-TYPE  5 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3Q13.31) MUTATED      3    8
  DEL PEAK  5(3Q13.31) WILD-TYPE    5   30
                        clus
vv                       DEL PEAK  5(3Q13.31) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                            8
                        clus
vv                       DEL PEAK  5(3Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             30
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK  6(4Q34.3) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(4Q34.3) MUTATED   12 13
  DEL PEAK  6(4Q34.3) WILD-TYPE 46 19
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           25                            65 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           13                            19 
$`DEL PEAK  6(4Q34.3) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP 
       13.91        16.11        18.12        49.22        18.48        15.25 
TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K8 
       12.59        66.51        18.15        32.68        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KS TCGA-OR-A5KY TCGA-OR-A5L2 TCGA-OR-A5LC 
       11.31        24.36        83.80        12.85        60.89         5.23 
TCGA-OR-A5LE TCGA-OR-A5LI TCGA-OR-A5LS TCGA-P6-A5OH TCGA-PK-A5HA TCGA-PK-A5HB 
       21.76        14.33        36.03         0.00        39.48        42.51 
TCGA-PK-A5HC 
       22.32 

$`DEL PEAK  6(4Q34.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       44.55        55.13        68.75        12.00        88.87        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       44.45        30.31        57.53        91.46        69.21        66.25 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO 
       17.79        69.37        46.82        16.11        22.03        29.23 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26       121.25        29.82         9.50        72.39        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       27.02        33.83        96.59       100.18        22.98        16.37 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        91.30        88.01        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 
       50.37        44.84         4.11        58.55       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       43.30        28.31        29.10        28.64        23.64        39.58 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.35        14.63        52.24        78.41        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       53.03        61.08        62.99        69.11        61.05        28.04 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 
       18.05        38.50        12.59        24.85        20.25 

  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                         0.00                          4.11 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                        83.80                        153.63 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                        21.76                         44.45 
[1] "0.0 - 83.8 (21.8)"  "4.1 - 153.6 (44.5)"
[1] "hr=" "2.9"
D25V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  6(4Q34.3) MUTATED         1       11         3        9
  DEL PEAK  6(4Q34.3) WILD-TYPE       8       32        15        9
D25V3, multiclass
           clus
vv          DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(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  6(4Q34.3) MUTATED    1 11  2 10
  DEL PEAK  6(4Q34.3) WILD-TYPE  8 37  9 10
D25V4, multiclass
    clus
vv   DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(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"
D25V5, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED   21  3
  DEL PEAK  6(4Q34.3) WILD-TYPE 57  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     21    3
  DEL PEAK  6(4Q34.3) WILD-TYPE   57    7
   clus
vv  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  0                          21                            57
  1                           3                             7
[1] 2 2
[1] FALSE
D25V6, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED   16  9
  DEL PEAK  6(4Q34.3) WILD-TYPE 43 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     16    9
  DEL PEAK  6(4Q34.3) WILD-TYPE   43   22
        clus
vv       DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  FEMALE                          16                            43
  MALE                             9                            22
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4Q34.3) MUTATED       1                         0    21
  DEL PEAK  6(4Q34.3) WILD-TYPE     1                         1    55
D25V7, multiclass
                           clus
vv                          DEL PEAK  6(4Q34.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              21
                           clus
vv                          DEL PEAK  6(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"
D25V8, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED    2 11
  DEL PEAK  6(4Q34.3) WILD-TYPE  6 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED      2   11
  DEL PEAK  6(4Q34.3) WILD-TYPE    6   27
                        clus
vv                       DEL PEAK  6(4Q34.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          11
                        clus
vv                       DEL PEAK  6(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            27
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK  7(4Q34.3) MUTATION ANALYSIS
D26V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(4Q34.3) MUTATED   15 13
  DEL PEAK  7(4Q34.3) WILD-TYPE 43 19
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                           28                            62 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                           13                            19 
$`DEL PEAK  7(4Q34.3) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JK 
       13.91        16.11        44.45        30.31        18.12        49.22 
TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY 
       18.48        15.25        36.26        12.59        66.51        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KX TCGA-OR-A5L2 
       32.68        16.37        24.62        24.36        44.84        60.89 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LI TCGA-OR-A5LN TCGA-OR-A5LO 
       39.58         5.23        21.76        14.33        62.99        69.11 
TCGA-OR-A5LS TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       36.03        39.48        42.51        22.32 

$`DEL PEAK  7(4Q34.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       44.55        55.13        68.75        12.00        88.87        19.04 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH 
       57.53        91.46        69.21        66.25        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5JT 
       46.82        16.11        22.03        29.23       121.25        29.82 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
        9.50        72.39        31.23        27.02        33.83        96.59 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP 
      100.18        22.98        49.08        11.31        46.49        91.30 
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        50.37 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       12.85         4.11        58.55       152.15        31.79        43.30 
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-A5LM 
       52.24        78.41        36.33        73.05        53.03        61.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-P6-A5OH 
       61.05        28.04        18.05        38.50        12.59         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 
       24.85        20.25 

  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                         5.23                          0.00 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                        69.11                        153.63 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                       27.465                        43.925 
[1] "5.2 - 69.1 (27.5)"  "0.0 - 153.6 (43.9)"
[1] "hr=" "2.1"
D26V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  7(4Q34.3) MUTATED         1       12         5        9
  DEL PEAK  7(4Q34.3) WILD-TYPE       8       31        13        9
D26V3, multiclass
           clus
vv          DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(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  7(4Q34.3) MUTATED    1 13  3 10
  DEL PEAK  7(4Q34.3) WILD-TYPE  8 35  8 10
D26V4, multiclass
    clus
vv   DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(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"
D26V5, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q34.3) MUTATED   24  3
  DEL PEAK  7(4Q34.3) WILD-TYPE 54  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED     24    3
  DEL PEAK  7(4Q34.3) WILD-TYPE   54    7
   clus
vv  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  0                          24                            54
  1                           3                             7
[1] 2 2
[1] FALSE
D26V6, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q34.3) MUTATED   19  9
  DEL PEAK  7(4Q34.3) WILD-TYPE 40 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED     19    9
  DEL PEAK  7(4Q34.3) WILD-TYPE   40   22
        clus
vv       DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  FEMALE                          19                            40
  MALE                             9                            22
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4Q34.3) MUTATED       1                         0    22
  DEL PEAK  7(4Q34.3) WILD-TYPE     1                         1    54
D26V7, multiclass
                           clus
vv                          DEL PEAK  7(4Q34.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              22
                           clus
vv                          DEL PEAK  7(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"
D26V8, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q34.3) MUTATED    3  9
  DEL PEAK  7(4Q34.3) WILD-TYPE  5 29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      3    9
  DEL PEAK  7(4Q34.3) WILD-TYPE    5   29
                        clus
vv                       DEL PEAK  7(4Q34.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       DEL PEAK  7(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            29
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  8(4Q35.1) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(4Q35.1) MUTATED   15 15
  DEL PEAK  8(4Q35.1) WILD-TYPE 43 17
  DEL PEAK  8(4Q35.1) MUTATED DEL PEAK  8(4Q35.1) WILD-TYPE 
                           30                            60 
  DEL PEAK  8(4Q35.1) MUTATED DEL PEAK  8(4Q35.1) WILD-TYPE 
                           15                            17 
$`DEL PEAK  8(4Q35.1) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE 
       13.91        16.11        44.45        18.12        57.53        69.21 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JX 
       49.22        18.48        15.25        12.59        66.51        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KW 
       18.15        32.68        16.37        24.62        24.36        50.37 
TCGA-OR-A5L2 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LI TCGA-OR-A5LM 
       60.89        39.58         5.23        21.76        14.33        61.08 
TCGA-OR-A5LN TCGA-OR-A5LS TCGA-P6-A5OH TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       62.99        36.03         0.00        39.48        42.51        22.32 

$`DEL PEAK  8(4Q35.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       44.55        55.13        68.75        12.00        88.87        19.04 
TCGA-OR-A5JA TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       30.31        91.46        66.25        17.79        69.37        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       16.11        22.03        29.23        36.26       121.25        29.82 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 
        9.50        72.39        27.02        33.83        96.59       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ 
       22.98        49.08        11.31        46.49        91.30        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KY 
       83.80        95.18       153.63       127.50        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
        4.11        58.55       152.15        31.79        43.30        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG 
       29.10        28.64        23.64        39.35        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       78.41        36.33        73.05        53.03        69.11        61.05 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 
       28.04        18.05        38.50        12.59        24.85        20.25 

  DEL PEAK  8(4Q35.1) MUTATED DEL PEAK  8(4Q35.1) WILD-TYPE 
                         0.00                          4.11 
  DEL PEAK  8(4Q35.1) MUTATED DEL PEAK  8(4Q35.1) WILD-TYPE 
                        69.21                        153.63 
  DEL PEAK  8(4Q35.1) MUTATED DEL PEAK  8(4Q35.1) WILD-TYPE 
                       27.925                        41.325 
[1] "0.0 - 69.2 (27.9)"  "4.1 - 153.6 (41.3)"
[1] "hr=" "2.4"
D27V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  8(4Q35.1) MUTATED         2       11         6        9
  DEL PEAK  8(4Q35.1) WILD-TYPE       7       32        12        9
D27V3, multiclass
           clus
vv          DEL PEAK  8(4Q35.1) MUTATED DEL PEAK  8(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  8(4Q35.1) MUTATED    2 12  4 10
  DEL PEAK  8(4Q35.1) WILD-TYPE  7 36  7 10
D27V4, multiclass
    clus
vv   DEL PEAK  8(4Q35.1) MUTATED DEL PEAK  8(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"
D27V5, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.1) MUTATED   25  3
  DEL PEAK  8(4Q35.1) WILD-TYPE 53  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.1) MUTATED     25    3
  DEL PEAK  8(4Q35.1) WILD-TYPE   53    7
   clus
vv  DEL PEAK  8(4Q35.1) MUTATED DEL PEAK  8(4Q35.1) WILD-TYPE
  0                          25                            53
  1                           3                             7
[1] 2 2
[1] FALSE
D27V6, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.1) MUTATED   18 12
  DEL PEAK  8(4Q35.1) WILD-TYPE 41 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.1) MUTATED     18   12
  DEL PEAK  8(4Q35.1) WILD-TYPE   41   19
        clus
vv       DEL PEAK  8(4Q35.1) MUTATED DEL PEAK  8(4Q35.1) WILD-TYPE
  FEMALE                          18                            41
  MALE                            12                            19
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(4Q35.1) MUTATED       1                         0    24
  DEL PEAK  8(4Q35.1) WILD-TYPE     1                         1    52
D27V7, multiclass
                           clus
vv                          DEL PEAK  8(4Q35.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              24
                           clus
vv                          DEL PEAK  8(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"
D27V8, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.1) MUTATED    3 10
  DEL PEAK  8(4Q35.1) WILD-TYPE  5 28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.1) MUTATED      3   10
  DEL PEAK  8(4Q35.1) WILD-TYPE    5   28
                        clus
vv                       DEL PEAK  8(4Q35.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          10
                        clus
vv                       DEL PEAK  8(4Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            28
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  9(6P24.3) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(6P24.3) MUTATED   11  9
  DEL PEAK  9(6P24.3) WILD-TYPE 47 23
  DEL PEAK  9(6P24.3) MUTATED DEL PEAK  9(6P24.3) WILD-TYPE 
                           20                            70 
  DEL PEAK  9(6P24.3) MUTATED DEL PEAK  9(6P24.3) WILD-TYPE 
                            9                            23 
$`DEL PEAK  9(6P24.3) MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JP 
       19.04        91.46        17.79        69.37        49.22        15.25 
TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5K0 TCGA-OR-A5KT TCGA-OR-A5L2 TCGA-OR-A5LC 
       36.26        66.51        33.83        95.18        60.89         5.23 
TCGA-OR-A5LE TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       21.76        14.33        53.03        36.03        18.05        38.50 
TCGA-P6-A5OG TCGA-P6-A5OH 
       12.59         0.00 

$`DEL PEAK  9(6P24.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE 
       16.11        44.45        30.31        18.12        57.53        69.21 
TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       66.25        46.82        16.11        22.03        18.48        29.23 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX 
      121.25        12.59        29.82         9.50        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        96.59        32.68       100.18        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       16.37        49.08        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       91.30        88.01        83.80       153.63       127.50        50.37 
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-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       43.30        28.31        29.10        28.64        23.64        39.58 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.35        14.63        52.24        78.41        36.33        73.05 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG 
       61.08        62.99        69.11        61.05        28.04        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       20.25        39.48        42.51        22.32 

  DEL PEAK  9(6P24.3) MUTATED DEL PEAK  9(6P24.3) WILD-TYPE 
                         0.00                          4.11 
  DEL PEAK  9(6P24.3) MUTATED DEL PEAK  9(6P24.3) WILD-TYPE 
                        95.18                        153.63 
  DEL PEAK  9(6P24.3) MUTATED DEL PEAK  9(6P24.3) WILD-TYPE 
                       34.930                        39.415 
[1] "0.0 - 95.2 (34.9)"  "4.1 - 153.6 (39.4)"
[1] "hr=" "1.6"
D28V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  9(6P24.3) MUTATED         1       10         2        7
  DEL PEAK  9(6P24.3) WILD-TYPE       8       33        16       11
D28V3, multiclass
           clus
vv          DEL PEAK  9(6P24.3) MUTATED DEL PEAK  9(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  9(6P24.3) MUTATED    1 11  2  6
  DEL PEAK  9(6P24.3) WILD-TYPE  8 37  9 14
D28V4, multiclass
    clus
vv   DEL PEAK  9(6P24.3) MUTATED DEL PEAK  9(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"
D28V5, binary
                               cls
clus                             0  1
  DEL PEAK  9(6P24.3) MUTATED   18  2
  DEL PEAK  9(6P24.3) WILD-TYPE 60  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6P24.3) MUTATED     18    2
  DEL PEAK  9(6P24.3) WILD-TYPE   60    8
   clus
vv  DEL PEAK  9(6P24.3) MUTATED DEL PEAK  9(6P24.3) WILD-TYPE
  0                          18                            60
  1                           2                             8
[1] 2 2
[1] FALSE
D28V6, binary
                               cls
clus                             0  1
  DEL PEAK  9(6P24.3) MUTATED   13  7
  DEL PEAK  9(6P24.3) WILD-TYPE 46 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6P24.3) MUTATED     13    7
  DEL PEAK  9(6P24.3) WILD-TYPE   46   24
        clus
vv       DEL PEAK  9(6P24.3) MUTATED DEL PEAK  9(6P24.3) WILD-TYPE
  FEMALE                          13                            46
  MALE                             7                            24
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(6P24.3) MUTATED       0                         0    17
  DEL PEAK  9(6P24.3) WILD-TYPE     2                         1    59
D28V7, multiclass
                           clus
vv                          DEL PEAK  9(6P24.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              17
                           clus
vv                          DEL PEAK  9(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"
D28V8, binary
                               cls
clus                             0  1
  DEL PEAK  9(6P24.3) MUTATED    1  8
  DEL PEAK  9(6P24.3) WILD-TYPE  7 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6P24.3) MUTATED      1    8
  DEL PEAK  9(6P24.3) WILD-TYPE    7   30
                        clus
vv                       DEL PEAK  9(6P24.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           8
                        clus
vv                       DEL PEAK  9(6P24.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            30
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK 10(6Q26) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 10(6Q26) MUTATED   11 10
  DEL PEAK 10(6Q26) WILD-TYPE 47 22
  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE 
                         21                          69 
  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE 
                         10                          22 
$`DEL PEAK 10(6Q26) MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JK 
       16.11        18.12        91.46        17.79        69.37        49.22 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 
       36.26        12.59        66.51        18.15        33.83        32.68 
TCGA-OR-A5KO TCGA-OR-A5L2 TCGA-OR-A5LC TCGA-OR-A5LG TCGA-OR-A5LL TCGA-OR-A5LS 
       46.49        60.89         5.23        52.24        53.03        36.03 
TCGA-OU-A5PI TCGA-P6-A5OG TCGA-P6-A5OH 
       38.50        12.59         0.00 

$`DEL PEAK 10(6Q26) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        44.45        30.31        57.53        69.21        66.25 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       46.82        16.11        22.03        18.48        29.23        15.25 
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-A5K6 TCGA-OR-A5K8 
       96.59       100.18        22.98        16.37        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       11.31        24.36        91.30        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        50.37        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       58.55       152.15        31.79        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       28.64        23.64        39.58        39.35        21.76        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        73.05        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PA-A5YG TCGA-PK-A5H9 
       69.11        61.05        28.04        18.05        24.85        20.25 
TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       39.48        42.51        22.32 

  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE 
                       0.00                        4.11 
  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE 
                      91.46                      153.63 
  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE 
                      36.03                       39.35 
[1] "0.0 - 91.5 (36.0)"  "4.1 - 153.6 (39.4)"
[1] "hr=" "1.8"
D29V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 10(6Q26) MUTATED         0        9         3        9
  DEL PEAK 10(6Q26) WILD-TYPE       9       34        15        9
D29V3, multiclass
           clus
vv          DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(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 10(6Q26) MUTATED    0 10  2  9
  DEL PEAK 10(6Q26) WILD-TYPE  9 38  9 11
D29V4, multiclass
    clus
vv   DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(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"
D29V5, binary
                             cls
clus                           0  1
  DEL PEAK 10(6Q26) MUTATED   18  3
  DEL PEAK 10(6Q26) WILD-TYPE 60  7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q26) MUTATED     18    3
  DEL PEAK 10(6Q26) WILD-TYPE   60    7
   clus
vv  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE
  0                        18                          60
  1                         3                           7
[1] 2 2
[1] FALSE
D29V6, binary
                             cls
clus                           0  1
  DEL PEAK 10(6Q26) MUTATED   16  5
  DEL PEAK 10(6Q26) WILD-TYPE 43 26
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q26) MUTATED     16    5
  DEL PEAK 10(6Q26) WILD-TYPE   43   26
        clus
vv       DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE
  FEMALE                        16                          43
  MALE                           5                          26
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6Q26) MUTATED       0                         0    19
  DEL PEAK 10(6Q26) WILD-TYPE     2                         1    57
D29V7, multiclass
                           clus
vv                          DEL PEAK 10(6Q26) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            19
                           clus
vv                          DEL PEAK 10(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"
D29V8, binary
                             cls
clus                           0  1
  DEL PEAK 10(6Q26) MUTATED    1  7
  DEL PEAK 10(6Q26) WILD-TYPE  7 31
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q26) MUTATED      1    7
  DEL PEAK 10(6Q26) WILD-TYPE    7   31
                        clus
vv                       DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             1                           7
  NOT HISPANIC OR LATINO                         7                          31
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK 11(7Q36.3) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(7Q36.3) MUTATED    3  8
  DEL PEAK 11(7Q36.3) WILD-TYPE 55 24
  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE 
                           11                            79 
  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE 
                            8                            24 
$`DEL PEAK 11(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 11(7Q36.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        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        91.46        66.25        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JO 
       69.37        46.82        16.11        49.22        22.03        29.23 
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-A5K0 
       66.51        72.39        31.23        18.15        27.02        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
       96.59        32.68       100.18        22.98        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS 
       11.31        24.36        46.49        91.30        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        50.37        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
        4.11        58.55       152.15        31.79        43.30        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE 
       29.10        28.64        23.64        39.58         5.23        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       14.63        52.24        78.41        36.33        73.05        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        62.99        69.11        61.05        28.04        36.03 
TCGA-OU-A5PI TCGA-P6-A5OG TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       38.50        12.59         0.00        24.85        20.25        39.48 
TCGA-PK-A5HB 
       42.51 

  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE 
                        13.91                          0.00 
  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE 
                        69.21                        153.63 
  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE 
                        22.32                         36.33 
[1] "13.9 - 69.2 (22.3)" "0.0 - 153.6 (36.3)"
[1] "hr=" "2.8"
D30V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 11(7Q36.3) MUTATED         1        2         3        4
  DEL PEAK 11(7Q36.3) WILD-TYPE       8       41        15       14
D30V3, multiclass
           clus
vv          DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(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 11(7Q36.3) MUTATED    1  2  2  5
  DEL PEAK 11(7Q36.3) WILD-TYPE  8 46  9 15
D30V4, multiclass
    clus
vv   DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(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"
D30V5, binary
                               cls
clus                             0  1
  DEL PEAK 11(7Q36.3) MUTATED    9  1
  DEL PEAK 11(7Q36.3) WILD-TYPE 69  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(7Q36.3) MUTATED      9    1
  DEL PEAK 11(7Q36.3) WILD-TYPE   69    9
   clus
vv  DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE
  0                           9                            69
  1                           1                             9
[1] 2 2
[1] FALSE
D30V6, binary
                               cls
clus                             0  1
  DEL PEAK 11(7Q36.3) MUTATED    7  4
  DEL PEAK 11(7Q36.3) WILD-TYPE 52 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(7Q36.3) MUTATED      7    4
  DEL PEAK 11(7Q36.3) WILD-TYPE   52   27
        clus
vv       DEL PEAK 11(7Q36.3) MUTATED DEL PEAK 11(7Q36.3) WILD-TYPE
  FEMALE                           7                            52
  MALE                             4                            27
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(7Q36.3) MUTATED       1                         0     9
  DEL PEAK 11(7Q36.3) WILD-TYPE     1                         1    67
D30V7, multiclass
                           clus
vv                          DEL PEAK 11(7Q36.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               9
                           clus
vv                          DEL PEAK 11(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"
D30V8, binary
                               cls
clus                             0  1
  DEL PEAK 11(7Q36.3) MUTATED    1  5
  DEL PEAK 11(7Q36.3) WILD-TYPE  7 33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(7Q36.3) MUTATED      1    5
  DEL PEAK 11(7Q36.3) WILD-TYPE    7   33
                        clus
vv                       DEL PEAK 11(7Q36.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       DEL PEAK 11(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            33
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK 12(9P23) MUTATION ANALYSIS
D31V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 12(9P23) MUTATED   12 12
  DEL PEAK 12(9P23) WILD-TYPE 46 20
  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE 
                         24                          66 
  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE 
                         12                          20 
$`DEL PEAK 12(9P23) MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JK TCGA-OR-A5JL 
       16.11        19.04        44.45        57.53        49.22        22.03 
TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K0 
       18.48        15.25        12.59        66.51        18.15        33.83 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KZ TCGA-OR-A5L2 
       32.68        16.37        24.36        91.30         4.11        60.89 
TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LM TCGA-P6-A5OG 
      152.15         5.23        21.76        52.24        61.08        12.59 

$`DEL PEAK 12(9P23) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       30.31        18.12        91.46        69.21        66.25        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR 
       69.37        46.82        16.11        29.23        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
       29.82         9.50        72.39        31.23        27.02        96.59 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO 
      100.18        22.98        49.08        24.62        11.31        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        50.37 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       44.84        12.85        58.55        31.79        43.30        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF 
       29.10        28.64        23.64        39.58        39.35        14.63 
TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN 
       78.41        14.33        36.33        73.05        53.03        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       69.11        61.05        28.04        36.03        18.05        38.50 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
        0.00        24.85        20.25        39.48        42.51        22.32 

  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE 
                       4.11                        0.00 
  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE 
                     152.15                      153.63 
  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE 
                     23.195                      39.415 
[1] "4.1 - 152.2 (23.2)" "0.0 - 153.6 (39.4)"
[1] "hr=" "2"  
D31V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 12(9P23) MUTATED         2       11         5        5
  DEL PEAK 12(9P23) WILD-TYPE       7       32        13       13
D31V3, multiclass
           clus
vv          DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE
  STAGE I                           2                           7
  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 12(9P23) MUTATED    2 11  4  6
  DEL PEAK 12(9P23) WILD-TYPE  7 37  7 14
D31V4, multiclass
    clus
vv   DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE
  T1                         2                           7
  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"
D31V5, binary
                             cls
clus                           0  1
  DEL PEAK 12(9P23) MUTATED   22  1
  DEL PEAK 12(9P23) WILD-TYPE 56  9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(9P23) MUTATED     22    1
  DEL PEAK 12(9P23) WILD-TYPE   56    9
   clus
vv  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE
  0                        22                          56
  1                         1                           9
[1] 2 2
[1] FALSE
D31V6, binary
                             cls
clus                           0  1
  DEL PEAK 12(9P23) MUTATED   15  9
  DEL PEAK 12(9P23) WILD-TYPE 44 22
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(9P23) MUTATED     15    9
  DEL PEAK 12(9P23) WILD-TYPE   44   22
        clus
vv       DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE
  FEMALE                        15                          44
  MALE                           9                          22
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(9P23) MUTATED       0                         0    23
  DEL PEAK 12(9P23) WILD-TYPE     2                         1    53
D31V7, multiclass
                           clus
vv                          DEL PEAK 12(9P23) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            23
                           clus
vv                          DEL PEAK 12(9P23) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              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"
D31V8, binary
                             cls
clus                           0  1
  DEL PEAK 12(9P23) MUTATED    3  9
  DEL PEAK 12(9P23) WILD-TYPE  5 29
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(9P23) MUTATED      3    9
  DEL PEAK 12(9P23) WILD-TYPE    5   29
                        clus
vv                       DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE
  HISPANIC OR LATINO                             3                           5
  NOT HISPANIC OR LATINO                         9                          29
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK 13(9P21.3) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 13(9P21.3) MUTATED   14 13
  DEL PEAK 13(9P21.3) WILD-TYPE 44 19
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                           27                            63 
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                           13                            19 
$`DEL PEAK 13(9P21.3) MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JK TCGA-OR-A5JL 
       16.11        19.04        44.45        57.53        49.22        22.03 
TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JY 
       18.48        15.25        12.59        29.82        66.51        18.15 
TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB 
       33.83        32.68        16.37        49.08        11.31        24.36 
TCGA-OR-A5KP TCGA-OR-A5KZ TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LE 
       91.30         4.11        60.89       152.15         5.23        21.76 
TCGA-OR-A5LG TCGA-OR-A5LM TCGA-P6-A5OG 
       52.24        61.08        12.59 

$`DEL PEAK 13(9P21.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       30.31        18.12        91.46        69.21        66.25        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR 
       69.37        46.82        16.11        29.23        36.26       121.25 
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        96.59       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       22.98        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-A5L1 
      153.63       127.50        50.37        44.84        12.85        58.55 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       31.79        43.30        28.31        29.10        28.64        23.64 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ 
       39.58        39.35        14.63        78.41        14.33        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       73.05        53.03        62.99        69.11        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 TCGA-PK-A5HB TCGA-PK-A5HC 
       39.48        42.51        22.32 

  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                         4.11                          0.00 
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                       152.15                        153.63 
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                        24.36                         39.48 
[1] "4.1 - 152.2 (24.4)" "0.0 - 153.6 (39.5)"
[1] "hr=" "2.1"
D32V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 13(9P21.3) MUTATED         2       14         5        5
  DEL PEAK 13(9P21.3) WILD-TYPE       7       29        13       13
D32V3, multiclass
           clus
vv          DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  STAGE I                             2                             7
  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 13(9P21.3) MUTATED    2 14  4  6
  DEL PEAK 13(9P21.3) WILD-TYPE  7 34  7 14
D32V4, multiclass
    clus
vv   DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  T1                           2                             7
  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"
D32V5, binary
                               cls
clus                             0  1
  DEL PEAK 13(9P21.3) MUTATED   25  1
  DEL PEAK 13(9P21.3) WILD-TYPE 53  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9P21.3) MUTATED     25    1
  DEL PEAK 13(9P21.3) WILD-TYPE   53    9
   clus
vv  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  0                          25                            53
  1                           1                             9
[1] 2 2
[1] FALSE
D32V6, binary
                               cls
clus                             0  1
  DEL PEAK 13(9P21.3) MUTATED   18  9
  DEL PEAK 13(9P21.3) WILD-TYPE 41 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9P21.3) MUTATED     18    9
  DEL PEAK 13(9P21.3) WILD-TYPE   41   22
        clus
vv       DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  FEMALE                          18                            41
  MALE                             9                            22
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(9P21.3) MUTATED       0                         0    26
  DEL PEAK 13(9P21.3) WILD-TYPE     2                         1    50
D32V7, multiclass
                           clus
vv                          DEL PEAK 13(9P21.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              26
                           clus
vv                          DEL PEAK 13(9P21.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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"
D32V8, binary
                               cls
clus                             0  1
  DEL PEAK 13(9P21.3) MUTATED    3 10
  DEL PEAK 13(9P21.3) WILD-TYPE  5 28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9P21.3) MUTATED      3   10
  DEL PEAK 13(9P21.3) WILD-TYPE    5   28
                        clus
vv                       DEL PEAK 13(9P21.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          10
                        clus
vv                       DEL PEAK 13(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            28
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK 14(10Q23.1) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 14(10Q23.1) MUTATED    7  4
  DEL PEAK 14(10Q23.1) WILD-TYPE 51 28
  DEL PEAK 14(10Q23.1) MUTATED DEL PEAK 14(10Q23.1) WILD-TYPE 
                            11                             79 
  DEL PEAK 14(10Q23.1) MUTATED DEL PEAK 14(10Q23.1) WILD-TYPE 
                             4                             28 
$`DEL PEAK 14(10Q23.1) MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JS 
       30.31        17.79        69.37        22.03        36.26        12.59 
TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5L2 TCGA-OR-A5L6 TCGA-PK-A5HC 
       66.51        18.15        60.89        28.31        22.32 

$`DEL PEAK 14(10Q23.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        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        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM 
       69.21        66.25        46.82        16.11        49.22        18.48 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW 
       29.23        15.25       121.25        29.82         9.50        72.39 
TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23        27.02        33.83        96.59        32.68       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       22.98        16.37        49.08        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       46.49        91.30        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        50.37        44.84        12.85         4.11        58.55 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        29.10        28.64        23.64 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       39.58         5.23        39.35        21.76        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       78.41        14.33        36.33        73.05        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       62.99        69.11        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OG TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       38.50        12.59         0.00        24.85        20.25        39.48 
TCGA-PK-A5HB 
       42.51 

  DEL PEAK 14(10Q23.1) MUTATED DEL PEAK 14(10Q23.1) WILD-TYPE 
                         12.59                           0.00 
  DEL PEAK 14(10Q23.1) MUTATED DEL PEAK 14(10Q23.1) WILD-TYPE 
                         69.37                         153.63 
  DEL PEAK 14(10Q23.1) MUTATED DEL PEAK 14(10Q23.1) WILD-TYPE 
                         28.31                          39.35 
[1] "12.6 - 69.4 (28.3)" "0.0 - 153.6 (39.4)"
[1] "hr=" "1.2"
D33V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 14(10Q23.1) MUTATED         1        6         1        3
  DEL PEAK 14(10Q23.1) WILD-TYPE       8       37        17       15
D33V3, multiclass
           clus
vv          DEL PEAK 14(10Q23.1) MUTATED DEL PEAK 14(10Q23.1) WILD-TYPE
  STAGE I                              1                              8
  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 14(10Q23.1) MUTATED    1  6  0  4
  DEL PEAK 14(10Q23.1) WILD-TYPE  8 42 11 16
D33V4, multiclass
    clus
vv   DEL PEAK 14(10Q23.1) MUTATED DEL PEAK 14(10Q23.1) WILD-TYPE
  T1                            1                              8
  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"
D33V5, binary
                                cls
clus                              0  1
  DEL PEAK 14(10Q23.1) MUTATED    9  2
  DEL PEAK 14(10Q23.1) WILD-TYPE 69  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(10Q23.1) MUTATED      9    2
  DEL PEAK 14(10Q23.1) WILD-TYPE   69    8
   clus
vv  DEL PEAK 14(10Q23.1) MUTATED DEL PEAK 14(10Q23.1) WILD-TYPE
  0                            9                             69
  1                            2                              8
[1] 2 2
[1] FALSE
D33V6, binary
                                cls
clus                              0  1
  DEL PEAK 14(10Q23.1) MUTATED    8  3
  DEL PEAK 14(10Q23.1) WILD-TYPE 51 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(10Q23.1) MUTATED      8    3
  DEL PEAK 14(10Q23.1) WILD-TYPE   51   28
        clus
vv       DEL PEAK 14(10Q23.1) MUTATED DEL PEAK 14(10Q23.1) WILD-TYPE
  FEMALE                            8                             51
  MALE                              3                             28
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(10Q23.1) MUTATED       1                         0    10
  DEL PEAK 14(10Q23.1) WILD-TYPE     1                         1    66
D33V7, multiclass
                           clus
vv                          DEL PEAK 14(10Q23.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               10
                           clus
vv                          DEL PEAK 14(10Q23.1) 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"
D33V8, binary
                                cls
clus                              0  1
  DEL PEAK 14(10Q23.1) MUTATED    0  3
  DEL PEAK 14(10Q23.1) WILD-TYPE  8 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(10Q23.1) MUTATED      0    3
  DEL PEAK 14(10Q23.1) WILD-TYPE    8   35
                        clus
vv                       DEL PEAK 14(10Q23.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       DEL PEAK 14(10Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                             35
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 15(11P15.5) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 15(11P15.5) MUTATED   20  7
  DEL PEAK 15(11P15.5) WILD-TYPE 38 25
  DEL PEAK 15(11P15.5) MUTATED DEL PEAK 15(11P15.5) WILD-TYPE 
                            27                             63 
  DEL PEAK 15(11P15.5) MUTATED DEL PEAK 15(11P15.5) WILD-TYPE 
                             7                             25 
$`DEL PEAK 15(11P15.5) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH 
       13.91        30.31        57.53        91.46        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5JW 
       46.82        49.22        22.03        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        50.37 
TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OR-A5LT 
       28.31         5.23        61.08        62.99        36.03        18.05 
TCGA-OU-A5PI TCGA-PK-A5HA TCGA-PK-A5HB 
       38.50        39.48        42.51 

$`DEL PEAK 15(11P15.5) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        68.75        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ 
       19.04        44.45        18.12        69.21        66.25        16.11 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT 
       18.48        29.23        15.25       121.25        12.59        29.82 
TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
        9.50        27.02        33.83        96.59        32.68       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ 
       22.98        16.37        24.62        46.49        91.30        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KY 
       83.80        95.18       153.63       127.50        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE 
       29.10        28.64        23.64        39.58        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        73.05 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OG TCGA-P6-A5OH 
       53.03        69.11        61.05        28.04        12.59         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       24.85        20.25        22.32 

  DEL PEAK 15(11P15.5) MUTATED DEL PEAK 15(11P15.5) WILD-TYPE 
                          5.23                           0.00 
  DEL PEAK 15(11P15.5) MUTATED DEL PEAK 15(11P15.5) WILD-TYPE 
                         91.46                         153.63 
  DEL PEAK 15(11P15.5) MUTATED DEL PEAK 15(11P15.5) WILD-TYPE 
                         38.50                          33.83 
[1] "5.2 - 91.5 (38.5)"  "0.0 - 153.6 (33.8)"
[1] "hr=" "1.5"
D34V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 15(11P15.5) MUTATED         3       12         3        7
  DEL PEAK 15(11P15.5) WILD-TYPE       6       31        15       11
D34V3, multiclass
           clus
vv          DEL PEAK 15(11P15.5) MUTATED DEL PEAK 15(11P15.5) WILD-TYPE
  STAGE I                              3                              6
  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 15(11P15.5) MUTATED    3 14  3  5
  DEL PEAK 15(11P15.5) WILD-TYPE  6 34  8 15
D34V4, multiclass
    clus
vv   DEL PEAK 15(11P15.5) MUTATED DEL PEAK 15(11P15.5) WILD-TYPE
  T1                            3                              6
  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"
D34V5, binary
                                cls
clus                              0  1
  DEL PEAK 15(11P15.5) MUTATED   20  5
  DEL PEAK 15(11P15.5) WILD-TYPE 58  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11P15.5) MUTATED     20    5
  DEL PEAK 15(11P15.5) WILD-TYPE   58    5
   clus
vv  DEL PEAK 15(11P15.5) MUTATED DEL PEAK 15(11P15.5) WILD-TYPE
  0                           20                             58
  1                            5                              5
[1] 2 2
[1] FALSE
D34V6, binary
                                cls
clus                              0  1
  DEL PEAK 15(11P15.5) MUTATED   15 12
  DEL PEAK 15(11P15.5) WILD-TYPE 44 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11P15.5) MUTATED     15   12
  DEL PEAK 15(11P15.5) WILD-TYPE   44   19
        clus
vv       DEL PEAK 15(11P15.5) MUTATED DEL PEAK 15(11P15.5) WILD-TYPE
  FEMALE                           15                             44
  MALE                             12                             19
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(11P15.5) MUTATED       0                         0    21
  DEL PEAK 15(11P15.5) WILD-TYPE     2                         1    55
D34V7, multiclass
                           clus
vv                          DEL PEAK 15(11P15.5) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               21
                           clus
vv                          DEL PEAK 15(11P15.5) 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"
D34V8, binary
                                cls
clus                              0  1
  DEL PEAK 15(11P15.5) MUTATED    1  6
  DEL PEAK 15(11P15.5) WILD-TYPE  7 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11P15.5) MUTATED      1    6
  DEL PEAK 15(11P15.5) WILD-TYPE    7   32
                        clus
vv                       DEL PEAK 15(11P15.5) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       DEL PEAK 15(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             32
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 16(11Q14.1) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 16(11Q14.1) MUTATED   18  7
  DEL PEAK 16(11Q14.1) WILD-TYPE 40 25
  DEL PEAK 16(11Q14.1) MUTATED DEL PEAK 16(11Q14.1) WILD-TYPE 
                            25                             65 
  DEL PEAK 16(11Q14.1) MUTATED DEL PEAK 16(11Q14.1) WILD-TYPE 
                             7                             25 
$`DEL PEAK 16(11Q14.1) MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH 
       19.04        30.31        57.53        91.46        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV 
       46.82        49.22        22.03        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        62.99        36.03        38.50        39.48 
TCGA-PK-A5HB 
       42.51 

$`DEL PEAK 16(11Q14.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ 
       16.11        44.45        18.12        69.21        66.25        16.11 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU 
       18.48        29.23        15.25       121.25        29.82         9.50 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 
       31.23        18.15        27.02        33.83        96.59        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KP 
      100.18        22.98        16.37        24.62        46.49        91.30 
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        50.37 
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-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD 
       43.30        29.10        28.64        23.64        39.58        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-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       73.05        53.03        69.11        61.05        28.04        18.05 
TCGA-P6-A5OG TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       12.59         0.00        24.85        20.25        22.32 

  DEL PEAK 16(11Q14.1) MUTATED DEL PEAK 16(11Q14.1) WILD-TYPE 
                          5.23                           0.00 
  DEL PEAK 16(11Q14.1) MUTATED DEL PEAK 16(11Q14.1) WILD-TYPE 
                         91.46                         153.63 
  DEL PEAK 16(11Q14.1) MUTATED DEL PEAK 16(11Q14.1) WILD-TYPE 
                         39.48                          32.68 
[1] "5.2 - 91.5 (39.5)"  "0.0 - 153.6 (32.7)"
[1] "hr=" "1.4"
D35V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 16(11Q14.1) MUTATED         3       14         1        5
  DEL PEAK 16(11Q14.1) WILD-TYPE       6       29        17       13
D35V3, multiclass
           clus
vv          DEL PEAK 16(11Q14.1) MUTATED DEL PEAK 16(11Q14.1) WILD-TYPE
  STAGE I                              3                              6
  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 16(11Q14.1) MUTATED    3 15  1  4
  DEL PEAK 16(11Q14.1) WILD-TYPE  6 33 10 16
D35V4, multiclass
    clus
vv   DEL PEAK 16(11Q14.1) MUTATED DEL PEAK 16(11Q14.1) WILD-TYPE
  T1                            3                              6
  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"
D35V5, binary
                                cls
clus                              0  1
  DEL PEAK 16(11Q14.1) MUTATED   21  2
  DEL PEAK 16(11Q14.1) WILD-TYPE 57  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(11Q14.1) MUTATED     21    2
  DEL PEAK 16(11Q14.1) WILD-TYPE   57    8
   clus
vv  DEL PEAK 16(11Q14.1) MUTATED DEL PEAK 16(11Q14.1) WILD-TYPE
  0                           21                             57
  1                            2                              8
[1] 2 2
[1] FALSE
D35V6, binary
                                cls
clus                              0  1
  DEL PEAK 16(11Q14.1) MUTATED   14 11
  DEL PEAK 16(11Q14.1) WILD-TYPE 45 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(11Q14.1) MUTATED     14   11
  DEL PEAK 16(11Q14.1) WILD-TYPE   45   20
        clus
vv       DEL PEAK 16(11Q14.1) MUTATED DEL PEAK 16(11Q14.1) WILD-TYPE
  FEMALE                           14                             45
  MALE                             11                             20
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(11Q14.1) MUTATED       0                         0    20
  DEL PEAK 16(11Q14.1) WILD-TYPE     2                         1    56
D35V7, multiclass
                           clus
vv                          DEL PEAK 16(11Q14.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               20
                           clus
vv                          DEL PEAK 16(11Q14.1) 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"
D35V8, binary
                                cls
clus                              0  1
  DEL PEAK 16(11Q14.1) MUTATED    1  6
  DEL PEAK 16(11Q14.1) WILD-TYPE  7 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(11Q14.1) MUTATED      1    6
  DEL PEAK 16(11Q14.1) WILD-TYPE    7   32
                        clus
vv                       DEL PEAK 16(11Q14.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       DEL PEAK 16(11Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             32
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 17(12Q14.2) MUTATION ANALYSIS
D36V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(12Q14.2) MUTATED    1  4
  DEL PEAK 17(12Q14.2) WILD-TYPE 57 28
  DEL PEAK 17(12Q14.2) MUTATED DEL PEAK 17(12Q14.2) WILD-TYPE 
                             5                             85 
  DEL PEAK 17(12Q14.2) MUTATED DEL PEAK 17(12Q14.2) WILD-TYPE 
                             4                             28 
$`DEL PEAK 17(12Q14.2) MUTATED`
TCGA-OR-A5JB TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5LL TCGA-P6-A5OG 
       18.12        11.31        95.18        53.03        12.59 

$`DEL PEAK 17(12Q14.2) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        44.45        30.31        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        46.82        16.11 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       49.22        22.03        18.48        29.23        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-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 
       31.23        18.15        27.02        33.83        96.59        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KB 
      100.18        22.98        16.37        49.08        24.62        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        91.30        88.01        83.80       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       50.37        44.84        12.85         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      152.15        31.79        43.30        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       23.64        39.58         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-A5LM 
       52.24        78.41        14.33        36.33        73.05        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       62.99        69.11        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       38.50         0.00        24.85        20.25        39.48        42.51 
TCGA-PK-A5HC 
       22.32 

  DEL PEAK 17(12Q14.2) MUTATED DEL PEAK 17(12Q14.2) WILD-TYPE 
                         11.31                           0.00 
  DEL PEAK 17(12Q14.2) MUTATED DEL PEAK 17(12Q14.2) WILD-TYPE 
                         95.18                         153.63 
  DEL PEAK 17(12Q14.2) MUTATED DEL PEAK 17(12Q14.2) WILD-TYPE 
                         18.12                          36.33 
[1] "11.3 - 95.2 (18.1)" "0.0 - 153.6 (36.3)"
[1] "hr=" "3.1"
D36V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 17(12Q14.2) MUTATED         1        2         0        2
  DEL PEAK 17(12Q14.2) WILD-TYPE       8       41        18       16
D36V3, multiclass
           clus
vv          DEL PEAK 17(12Q14.2) MUTATED DEL PEAK 17(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 17(12Q14.2) MUTATED    1  2  0  2
  DEL PEAK 17(12Q14.2) WILD-TYPE  8 46 11 18
D36V4, multiclass
    clus
vv   DEL PEAK 17(12Q14.2) MUTATED DEL PEAK 17(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"
D36V5, binary
                                cls
clus                              0  1
  DEL PEAK 17(12Q14.2) MUTATED    5  0
  DEL PEAK 17(12Q14.2) WILD-TYPE 73 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(12Q14.2) MUTATED      5    0
  DEL PEAK 17(12Q14.2) WILD-TYPE   73   10
   clus
vv  DEL PEAK 17(12Q14.2) MUTATED DEL PEAK 17(12Q14.2) WILD-TYPE
  0                            5                             73
  1                            0                             10
[1] 2 2
[1] FALSE
D36V6, binary
                                cls
clus                              0  1
  DEL PEAK 17(12Q14.2) MUTATED    4  1
  DEL PEAK 17(12Q14.2) WILD-TYPE 55 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(12Q14.2) MUTATED      4    1
  DEL PEAK 17(12Q14.2) WILD-TYPE   55   30
        clus
vv       DEL PEAK 17(12Q14.2) MUTATED DEL PEAK 17(12Q14.2) WILD-TYPE
  FEMALE                            4                             55
  MALE                              1                             30
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(12Q14.2) MUTATED       0                         0     4
  DEL PEAK 17(12Q14.2) WILD-TYPE     2                         1    72
D36V7, multiclass
                           clus
vv                          DEL PEAK 17(12Q14.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                4
                           clus
vv                          DEL PEAK 17(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"
D36V8, binary
                                cls
clus                              0  1
  DEL PEAK 17(12Q14.2) MUTATED    0  2
  DEL PEAK 17(12Q14.2) WILD-TYPE  8 36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(12Q14.2) MUTATED      0    2
  DEL PEAK 17(12Q14.2) WILD-TYPE    8   36
                        clus
vv                       DEL PEAK 17(12Q14.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            2
                        clus
vv                       DEL PEAK 17(12Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                             36
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 18(13Q14.2) MUTATION ANALYSIS
D37V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(13Q14.2) MUTATED   23 19
  DEL PEAK 18(13Q14.2) WILD-TYPE 35 13
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                            42                             48 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                            19                             13 
$`DEL PEAK 18(13Q14.2) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       13.91        16.11        30.31        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP 
       69.21        17.79        69.37        46.82        49.22        15.25 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY 
       36.26        12.59         9.50        66.51        72.39        18.15 
TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       33.83        32.68        16.37        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       91.30        83.80       153.63         4.11        58.55        60.89 
TCGA-OR-A5L6 TCGA-OR-A5LD TCGA-OR-A5LI TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN 
       28.31        39.35        14.33        73.05        53.03        62.99 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-P6-A5OH TCGA-PK-A5HA TCGA-PK-A5HB 
       36.03        38.50        12.59         0.00        39.48        42.51 

$`DEL PEAK 18(13Q14.2) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       44.55        55.13        68.75        12.00        88.87        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       44.45        66.25        16.11        22.03        18.48        29.23 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
      121.25        29.82        31.23        27.02        96.59       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV 
       22.98        49.08        24.62        88.01        95.18       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.37        44.84        12.85       152.15        31.79        43.30 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE 
       29.10        28.64        23.64        39.58         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        69.11 
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 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                          0.00                           5.23 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                        153.63                         152.15 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                         37.38                          34.06 
[1] "0.0 - 153.6 (37.4)" "5.2 - 152.2 (34.1)"
[1] "hr=" "1.8"
D37V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 18(13Q14.2) MUTATED         3       21         5       11
  DEL PEAK 18(13Q14.2) WILD-TYPE       6       22        13        7
D37V3, multiclass
           clus
vv          DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(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 18(13Q14.2) MUTATED    3 22  4 11
  DEL PEAK 18(13Q14.2) WILD-TYPE  6 26  7  9
D37V4, multiclass
    clus
vv   DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(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"
D37V5, binary
                                cls
clus                              0  1
  DEL PEAK 18(13Q14.2) MUTATED   36  4
  DEL PEAK 18(13Q14.2) WILD-TYPE 42  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(13Q14.2) MUTATED     36    4
  DEL PEAK 18(13Q14.2) WILD-TYPE   42    6
   clus
vv  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  0                           36                             42
  1                            4                              6
[1] 2 2
[1] FALSE
D37V6, binary
                                cls
clus                              0  1
  DEL PEAK 18(13Q14.2) MUTATED   27 15
  DEL PEAK 18(13Q14.2) WILD-TYPE 32 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(13Q14.2) MUTATED     27   15
  DEL PEAK 18(13Q14.2) WILD-TYPE   32   16
        clus
vv       DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  FEMALE                           27                             32
  MALE                             15                             16
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(13Q14.2) MUTATED       0                         0    36
  DEL PEAK 18(13Q14.2) WILD-TYPE     2                         1    40
D37V7, multiclass
                           clus
vv                          DEL PEAK 18(13Q14.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               36
                           clus
vv                          DEL PEAK 18(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"
D37V8, binary
                                cls
clus                              0  1
  DEL PEAK 18(13Q14.2) MUTATED    2 14
  DEL PEAK 18(13Q14.2) WILD-TYPE  6 24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(13Q14.2) MUTATED      2   14
  DEL PEAK 18(13Q14.2) WILD-TYPE    6   24
                        clus
vv                       DEL PEAK 18(13Q14.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           14
                        clus
vv                       DEL PEAK 18(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             24
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 19(14Q21.2) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(14Q21.2) MUTATED   14  6
  DEL PEAK 19(14Q21.2) WILD-TYPE 44 26
  DEL PEAK 19(14Q21.2) MUTATED DEL PEAK 19(14Q21.2) WILD-TYPE 
                            20                             70 
  DEL PEAK 19(14Q21.2) MUTATED DEL PEAK 19(14Q21.2) WILD-TYPE 
                             6                             26 
$`DEL PEAK 19(14Q21.2) MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH 
       88.87        16.11        19.04        57.53        91.46        69.37 
TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       49.22        36.26        66.51        24.36        46.49        88.01 
TCGA-OR-A5KZ TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OR-A5LT 
        4.11        28.31         5.23        62.99        36.03        18.05 
TCGA-P6-A5OG TCGA-PK-A5HA 
       12.59        39.48 

$`DEL PEAK 19(14Q21.2) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J9 
       44.55        55.13        68.75        13.91        12.00        44.45 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JI 
       30.31        18.12        69.21        66.25        17.79        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR 
       16.11        22.03        18.48        29.23        15.25       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-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       27.02        33.83        96.59        32.68       100.18        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KS 
       16.37        49.08        24.62        11.31        91.30        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        50.37        44.84        12.85 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 
       58.55        60.89       152.15        31.79        43.30        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       28.64        23.64        39.58        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        73.05        53.03 
TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OU-A5PI TCGA-P6-A5OH 
       61.08        69.11        61.05        28.04        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HB TCGA-PK-A5HC 
       24.85        20.25        42.51        22.32 

  DEL PEAK 19(14Q21.2) MUTATED DEL PEAK 19(14Q21.2) WILD-TYPE 
                          4.11                           0.00 
  DEL PEAK 19(14Q21.2) MUTATED DEL PEAK 19(14Q21.2) WILD-TYPE 
                         91.46                         153.63 
  DEL PEAK 19(14Q21.2) MUTATED DEL PEAK 19(14Q21.2) WILD-TYPE 
                         37.87                          35.08 
[1] "4.1 - 91.5 (37.9)"  "0.0 - 153.6 (35.1)"
[1] "hr=" "1.2"
D38V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 19(14Q21.2) MUTATED         1       11         3        4
  DEL PEAK 19(14Q21.2) WILD-TYPE       8       32        15       14
D38V3, multiclass
           clus
vv          DEL PEAK 19(14Q21.2) MUTATED DEL PEAK 19(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 19(14Q21.2) MUTATED    1 11  3  4
  DEL PEAK 19(14Q21.2) WILD-TYPE  8 37  8 16
D38V4, multiclass
    clus
vv   DEL PEAK 19(14Q21.2) MUTATED DEL PEAK 19(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"
D38V5, binary
                                cls
clus                              0  1
  DEL PEAK 19(14Q21.2) MUTATED   19  0
  DEL PEAK 19(14Q21.2) WILD-TYPE 59 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(14Q21.2) MUTATED     19    0
  DEL PEAK 19(14Q21.2) WILD-TYPE   59   10
   clus
vv  DEL PEAK 19(14Q21.2) MUTATED DEL PEAK 19(14Q21.2) WILD-TYPE
  0                           19                             59
  1                            0                             10
[1] 2 2
[1] FALSE
D38V6, binary
                                cls
clus                              0  1
  DEL PEAK 19(14Q21.2) MUTATED   12  8
  DEL PEAK 19(14Q21.2) WILD-TYPE 47 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(14Q21.2) MUTATED     12    8
  DEL PEAK 19(14Q21.2) WILD-TYPE   47   23
        clus
vv       DEL PEAK 19(14Q21.2) MUTATED DEL PEAK 19(14Q21.2) WILD-TYPE
  FEMALE                           12                             47
  MALE                              8                             23
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(14Q21.2) MUTATED       0                         1    15
  DEL PEAK 19(14Q21.2) WILD-TYPE     2                         0    61
D38V7, multiclass
                           clus
vv                          DEL PEAK 19(14Q21.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               15
                           clus
vv                          DEL PEAK 19(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"
D38V8, binary
                                cls
clus                              0  1
  DEL PEAK 19(14Q21.2) MUTATED    3  7
  DEL PEAK 19(14Q21.2) WILD-TYPE  5 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(14Q21.2) MUTATED      3    7
  DEL PEAK 19(14Q21.2) WILD-TYPE    5   31
                        clus
vv                       DEL PEAK 19(14Q21.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                            7
                        clus
vv                       DEL PEAK 19(14Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             31
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 20(16P13.3) MUTATION ANALYSIS
D39V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 20(16P13.3) MUTATED    3  4
  DEL PEAK 20(16P13.3) WILD-TYPE 55 28
  DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE 
                             7                             83 
  DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE 
                             4                             28 
$`DEL PEAK 20(16P13.3) MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JY TCGA-OR-A5K8 TCGA-OR-A5LS 
       88.87        16.11        18.12        18.15        24.62        36.03 
TCGA-P6-A5OG 
       12.59 

$`DEL PEAK 20(16P13.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J8 
       44.55        55.13        68.75        13.91        12.00        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       44.45        30.31        57.53        91.46        69.21        66.25 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       17.79        69.37        46.82        16.11        49.22        22.03 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       18.48        29.23        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-A5JZ 
       29.82         9.50        66.51        72.39        31.23        27.02 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       33.83        96.59        32.68       100.18        22.98        16.37 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ 
       49.08        11.31        24.36        46.49        91.30        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        50.37        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.85         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       43.30        28.31        29.10        28.64        23.64        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
        5.23        39.35        21.76        14.63        52.24        78.41 
TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       14.33        36.33        73.05        53.03        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       69.11        61.05        28.04        18.05        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       24.85        20.25        39.48        42.51        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 
                         18.15                          39.35 
[1] "12.6 - 88.9 (18.1)" "0.0 - 153.6 (39.4)"
[1] "hr=" "2.3"
D39V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 20(16P13.3) MUTATED         0        3         1        3
  DEL PEAK 20(16P13.3) WILD-TYPE       9       40        17       15
D39V3, multiclass
           clus
vv          DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE
  STAGE I                              0                              9
  STAGE II                             3                             40
  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 20(16P13.3) MUTATED    0  3  1  3
  DEL PEAK 20(16P13.3) WILD-TYPE  9 45 10 17
D39V4, multiclass
    clus
vv   DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE
  T1                            0                              9
  T2                            3                             45
  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"
D39V5, binary
                                cls
clus                              0  1
  DEL PEAK 20(16P13.3) MUTATED    6  1
  DEL PEAK 20(16P13.3) WILD-TYPE 72  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16P13.3) MUTATED      6    1
  DEL PEAK 20(16P13.3) WILD-TYPE   72    9
   clus
vv  DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE
  0                            6                             72
  1                            1                              9
[1] 2 2
[1] FALSE
D39V6, binary
                                cls
clus                              0  1
  DEL PEAK 20(16P13.3) MUTATED    5  2
  DEL PEAK 20(16P13.3) WILD-TYPE 54 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16P13.3) MUTATED      5    2
  DEL PEAK 20(16P13.3) WILD-TYPE   54   29
        clus
vv       DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE
  FEMALE                            5                             54
  MALE                              2                             29
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(16P13.3) MUTATED       0                         1     5
  DEL PEAK 20(16P13.3) WILD-TYPE     2                         0    71
D39V7, multiclass
                           clus
vv                          DEL PEAK 20(16P13.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                                5
                           clus
vv                          DEL PEAK 20(16P13.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 71
[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"
D39V8, binary
                                cls
clus                              0  1
  DEL PEAK 20(16P13.3) MUTATED    2  2
  DEL PEAK 20(16P13.3) WILD-TYPE  6 36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16P13.3) MUTATED      2    2
  DEL PEAK 20(16P13.3) WILD-TYPE    6   36
                        clus
vv                       DEL PEAK 20(16P13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            2
                        clus
vv                       DEL PEAK 20(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             36
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 21(16Q23.1) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(16Q23.1) MUTATED    3  8
  DEL PEAK 21(16Q23.1) WILD-TYPE 55 24
  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                             24 
$`DEL PEAK 21(16Q23.1) MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5K0 TCGA-OR-A5KB TCGA-OR-A5L2 TCGA-OR-A5LB 
       16.11        18.12        33.83        24.36        60.89        39.58 
TCGA-OR-A5LD TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LL TCGA-P6-A5OG 
       39.35        52.24        14.33        53.03        12.59 

$`DEL PEAK 21(16Q23.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
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        91.46        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        46.82        16.11        49.22 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       22.03        18.48        29.23        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        96.59        32.68       100.18        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP 
       16.37        49.08        24.62        11.31        46.49        91.30 
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        50.37 
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-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       43.30        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM 
       21.76        14.63        78.41        36.33        73.05        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       62.99        69.11        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       38.50         0.00        24.85        20.25        39.48        42.51 
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                          36.33 
[1] "12.6 - 60.9 (33.8)" "0.0 - 153.6 (36.3)"
[1] "hr=" "3.1"
D40V2, 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
D40V3, 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
D40V4, 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"
D40V5, 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
D40V6, 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
                                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
D40V7, 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"
D40V8, 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(41) Variable = DEL PEAK 22(17Q11.2) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 22(17Q11.2) MUTATED   12 12
  DEL PEAK 22(17Q11.2) WILD-TYPE 46 20
  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                             20 
$`DEL PEAK 22(17Q11.2) MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JK 
       16.11        30.31        18.12        57.53        17.79        49.22 
TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K9 
       15.25        12.59        66.51        72.39        32.68        11.31 
TCGA-OR-A5KP TCGA-OR-A5KY TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       91.30        12.85        28.31         5.23        39.35        21.76 
TCGA-OR-A5LM TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5HA TCGA-PK-A5HB 
       61.08        36.03        38.50        12.59        39.48        42.51 

$`DEL PEAK 22(17Q11.2) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JH 
       19.04        44.45        91.46        69.21        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ 
       46.82        16.11        22.03        18.48        29.23        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
      121.25        29.82         9.50        31.23        18.15        27.02 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
       33.83        96.59       100.18        22.98        16.37        49.08 
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-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63       127.50        50.37        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 
       60.89       152.15        31.79        43.30        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
       23.64        39.58        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        73.05        53.03        62.99        69.11        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                         41.440 
[1] "5.2 - 91.3 (31.5)"  "0.0 - 153.6 (41.4)"
[1] "hr=" "2.2"
D41V2, 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
D41V3, 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
D41V4, 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"
D41V5, 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
D41V6, 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
                                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
D41V7, 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"
D41V8, 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(42) Variable = DEL PEAK 23(17Q21.31) MUTATION ANALYSIS
D42V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 23(17Q21.31) MUTATED   14 12
  DEL PEAK 23(17Q21.31) WILD-TYPE 44 20
  DEL PEAK 23(17Q21.31) MUTATED DEL PEAK 23(17Q21.31) WILD-TYPE 
                             26                              64 
  DEL PEAK 23(17Q21.31) MUTATED DEL PEAK 23(17Q21.31) WILD-TYPE 
                             12                              20 
$`DEL PEAK 23(17Q21.31) MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JK TCGA-OR-A5JP 
       16.11        30.31        57.53        17.79        49.22        15.25 
TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K9 TCGA-OR-A5KT 
       12.59        66.51        72.39        32.68        11.31        95.18 
TCGA-OR-A5KY TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG 
       12.85        28.31         5.23        39.35        21.76        52.24 
TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-P6-A5OH 
       61.08        69.11        36.03        38.50        12.59         0.00 
TCGA-PK-A5HA TCGA-PK-A5HB 
       39.48        42.51 

$`DEL PEAK 23(17Q21.31) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        44.45        18.12        91.46        69.21        66.25 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       69.37        46.82        16.11        22.03        18.48        29.23 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JX TCGA-OR-A5JY 
       36.26       121.25        29.82         9.50        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       27.02        33.83        96.59       100.18        22.98        16.37 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ 
       49.08        24.62        24.36        46.49        91.30        88.01 
TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       83.80       153.63       127.50        50.37        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 
       58.55        60.89       152.15        31.79        43.30        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI 
       28.64        23.64        39.58        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        73.05        53.03        62.99        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(17Q21.31) MUTATED DEL PEAK 23(17Q21.31) WILD-TYPE 
                           0.00                            4.11 
  DEL PEAK 23(17Q21.31) MUTATED DEL PEAK 23(17Q21.31) WILD-TYPE 
                          95.18                          153.63 
  DEL PEAK 23(17Q21.31) MUTATED DEL PEAK 23(17Q21.31) WILD-TYPE 
                         34.355                          37.955 
[1] "0.0 - 95.2 (34.4)"  "4.1 - 153.6 (38.0)"
[1] "hr=" "1.9"
D42V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 23(17Q21.31) MUTATED         2       10         4        8
  DEL PEAK 23(17Q21.31) WILD-TYPE       7       33        14       10
D42V3, multiclass
           clus
vv          DEL PEAK 23(17Q21.31) MUTATED DEL PEAK 23(17Q21.31) WILD-TYPE
  STAGE I                               2                               7
  STAGE II                             10                              33
  STAGE III                             4                              14
  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 23(17Q21.31) MUTATED    2 11  2  9
  DEL PEAK 23(17Q21.31) WILD-TYPE  7 37  9 11
D42V4, multiclass
    clus
vv   DEL PEAK 23(17Q21.31) MUTATED DEL PEAK 23(17Q21.31) WILD-TYPE
  T1                             2                               7
  T2                            11                              37
  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"
D42V5, binary
                                 cls
clus                               0  1
  DEL PEAK 23(17Q21.31) MUTATED   21  3
  DEL PEAK 23(17Q21.31) WILD-TYPE 57  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(17Q21.31) MUTATED     21    3
  DEL PEAK 23(17Q21.31) WILD-TYPE   57    7
   clus
vv  DEL PEAK 23(17Q21.31) MUTATED DEL PEAK 23(17Q21.31) WILD-TYPE
  0                            21                              57
  1                             3                               7
[1] 2 2
[1] FALSE
D42V6, binary
                                 cls
clus                               0  1
  DEL PEAK 23(17Q21.31) MUTATED   13 13
  DEL PEAK 23(17Q21.31) WILD-TYPE 46 18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(17Q21.31) MUTATED     13   13
  DEL PEAK 23(17Q21.31) WILD-TYPE   46   18
        clus
vv       DEL PEAK 23(17Q21.31) MUTATED DEL PEAK 23(17Q21.31) WILD-TYPE
  FEMALE                            13                              46
  MALE                              13                              18
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(17Q21.31) MUTATED       0                         0    21
  DEL PEAK 23(17Q21.31) WILD-TYPE     2                         1    55
D42V7, multiclass
                           clus
vv                          DEL PEAK 23(17Q21.31) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                21
                           clus
vv                          DEL PEAK 23(17Q21.31) 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"
D42V8, binary
                                 cls
clus                               0  1
  DEL PEAK 23(17Q21.31) MUTATED    1 10
  DEL PEAK 23(17Q21.31) WILD-TYPE  7 28
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(17Q21.31) MUTATED      1   10
  DEL PEAK 23(17Q21.31) WILD-TYPE    7   28
                        clus
vv                       DEL PEAK 23(17Q21.31) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            10
                        clus
vv                       DEL PEAK 23(17Q21.31) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                              28
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 24(17Q24.2) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(17Q24.2) MUTATED   12 12
  DEL PEAK 24(17Q24.2) WILD-TYPE 46 20
  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                             20 
$`DEL PEAK 24(17Q24.2) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JK 
       13.91        16.11        30.31        57.53        17.79        49.22 
TCGA-OR-A5JM TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.48        12.59        66.51        72.39        49.08        11.31 
TCGA-OR-A5KY TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG 
       12.85        28.31        39.58         5.23        21.76        52.24 
TCGA-OR-A5LM TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5HA TCGA-PK-A5HB 
       61.08        36.03        38.50        12.59        39.48        42.51 

$`DEL PEAK 24(17Q24.2) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       44.55        55.13        68.75        12.00        88.87        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JH 
       44.45        18.12        91.46        69.21        66.25        69.37 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       46.82        16.11        22.03        29.23        15.25        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
      121.25        29.82         9.50        31.23        18.15        27.02 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       33.83        96.59        32.68       100.18        22.98        16.37 
TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS 
       24.62        24.36        46.49        91.30        88.01        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       95.18       153.63       127.50        50.37        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 
       58.55        60.89       152.15        31.79        43.30        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        73.05        53.03        62.99        69.11        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 
                         33.17                          37.84 
[1] "5.2 - 72.4 (33.2)"  "0.0 - 153.6 (37.8)"
[1] "hr=" "2.3"
D43V2, 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
D43V3, 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
D43V4, 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"
D43V5, 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
D43V6, 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
                                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
D43V7, 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"
D43V8, 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(44) Variable = DEL PEAK 25(18Q21.2) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 25(18Q21.2) MUTATED   23 13
  DEL PEAK 25(18Q21.2) WILD-TYPE 35 19
  DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE 
                            36                             54 
  DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE 
                            13                             19 
$`DEL PEAK 25(18Q21.2) MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG 
       88.87        16.11        18.12        57.53        91.46        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JP 
       69.37        46.82        49.22        22.03        18.48        15.25 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26        12.59        29.82        66.51        72.39        31.23 
TCGA-OR-A5K2 TCGA-OR-A5KP TCGA-OR-A5KY TCGA-OR-A5L2 TCGA-OR-A5L6 TCGA-OR-A5LC 
       32.68        91.30        12.85        60.89        28.31         5.23 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS 
       21.76        52.24        53.03        61.08        62.99        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-P6-A5OH TCGA-PK-A5HA TCGA-PK-A5HB 
       18.05        38.50        12.59         0.00        39.48        42.51 

$`DEL PEAK 25(18Q21.2) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J8 
       44.55        55.13        68.75        13.91        12.00        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JO 
       44.45        30.31        69.21        66.25        16.11        29.23 
TCGA-OR-A5JR TCGA-OR-A5JU TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
      121.25         9.50        18.15        27.02        33.83        96.59 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 
      100.18        22.98        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-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 
      127.50        50.37        44.84         4.11        58.55       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       31.79        43.30        29.10        28.64        23.64        39.58 
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        73.05 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       69.11        61.05        28.04        24.85        20.25        22.32 

  DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE 
                          0.00                           4.11 
  DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE 
                         91.46                         153.63 
  DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE 
                        36.145                         37.840 
[1] "0.0 - 91.5 (36.1)"  "4.1 - 153.6 (37.8)"
[1] "hr=" "1.1"
D44V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 25(18Q21.2) MUTATED         3       17         5        9
  DEL PEAK 25(18Q21.2) WILD-TYPE       6       26        13        9
D44V3, multiclass
           clus
vv          DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE
  STAGE I                              3                              6
  STAGE II                            17                             26
  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 25(18Q21.2) MUTATED    3 18  4  9
  DEL PEAK 25(18Q21.2) WILD-TYPE  6 30  7 11
D44V4, multiclass
    clus
vv   DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE
  T1                            3                              6
  T2                           18                             30
  T3                            4                              7
  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"
D44V5, binary
                                cls
clus                              0  1
  DEL PEAK 25(18Q21.2) MUTATED   31  3
  DEL PEAK 25(18Q21.2) WILD-TYPE 47  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(18Q21.2) MUTATED     31    3
  DEL PEAK 25(18Q21.2) WILD-TYPE   47    7
   clus
vv  DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE
  0                           31                             47
  1                            3                              7
[1] 2 2
[1] FALSE
D44V6, binary
                                cls
clus                              0  1
  DEL PEAK 25(18Q21.2) MUTATED   20 16
  DEL PEAK 25(18Q21.2) WILD-TYPE 39 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(18Q21.2) MUTATED     20   16
  DEL PEAK 25(18Q21.2) WILD-TYPE   39   15
        clus
vv       DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE
  FEMALE                           20                             39
  MALE                             16                             15
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(18Q21.2) MUTATED       0                         1    28
  DEL PEAK 25(18Q21.2) WILD-TYPE     2                         0    48
D44V7, multiclass
                           clus
vv                          DEL PEAK 25(18Q21.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               28
                           clus
vv                          DEL PEAK 25(18Q21.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 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"
D44V8, binary
                                cls
clus                              0  1
  DEL PEAK 25(18Q21.2) MUTATED    2 10
  DEL PEAK 25(18Q21.2) WILD-TYPE  6 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(18Q21.2) MUTATED      2   10
  DEL PEAK 25(18Q21.2) WILD-TYPE    6   28
                        clus
vv                       DEL PEAK 25(18Q21.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           10
                        clus
vv                       DEL PEAK 25(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             28
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 26(20P12.1) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 26(20P12.1) MUTATED    6  6
  DEL PEAK 26(20P12.1) WILD-TYPE 52 26
  DEL PEAK 26(20P12.1) MUTATED DEL PEAK 26(20P12.1) WILD-TYPE 
                            12                             78 
  DEL PEAK 26(20P12.1) MUTATED DEL PEAK 26(20P12.1) WILD-TYPE 
                             6                             26 
$`DEL PEAK 26(20P12.1) MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JS 
       55.13        16.11        30.31        18.12        18.48        12.59 
TCGA-OR-A5K0 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-PK-A5HB TCGA-PK-A5HC 
       33.83        11.31        24.36        91.30        42.51        22.32 

$`DEL PEAK 26(20P12.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       44.55        68.75        13.91        12.00        88.87        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       44.45        57.53        91.46        69.21        66.25        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JO 
       69.37        46.82        16.11        49.22        22.03        29.23 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
       15.25        36.26       121.25        29.82         9.50        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 
       72.39        31.23        18.15        27.02        96.59        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KO 
      100.18        22.98        16.37        49.08        24.62        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        50.37 
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-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       31.79        43.30        28.31        29.10        28.64        23.64 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       39.58         5.23        39.35        21.76        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       78.41        14.33        36.33        73.05        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       62.99        69.11        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OG TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       38.50        12.59         0.00        24.85        20.25        39.48 

  DEL PEAK 26(20P12.1) MUTATED DEL PEAK 26(20P12.1) WILD-TYPE 
                         11.31                           0.00 
  DEL PEAK 26(20P12.1) MUTATED DEL PEAK 26(20P12.1) WILD-TYPE 
                         91.30                         153.63 
  DEL PEAK 26(20P12.1) MUTATED DEL PEAK 26(20P12.1) WILD-TYPE 
                        23.340                         39.415 
[1] "11.3 - 91.3 (23.3)" "0.0 - 153.6 (39.4)"
[1] "hr=" "2"  
D45V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 26(20P12.1) MUTATED         0        5         2        4
  DEL PEAK 26(20P12.1) WILD-TYPE       9       38        16       14
D45V3, multiclass
           clus
vv          DEL PEAK 26(20P12.1) MUTATED DEL PEAK 26(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 26(20P12.1) MUTATED    0  5  2  4
  DEL PEAK 26(20P12.1) WILD-TYPE  9 43  9 16
D45V4, multiclass
    clus
vv   DEL PEAK 26(20P12.1) MUTATED DEL PEAK 26(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"
D45V5, binary
                                cls
clus                              0  1
  DEL PEAK 26(20P12.1) MUTATED   11  0
  DEL PEAK 26(20P12.1) WILD-TYPE 67 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(20P12.1) MUTATED     11    0
  DEL PEAK 26(20P12.1) WILD-TYPE   67   10
   clus
vv  DEL PEAK 26(20P12.1) MUTATED DEL PEAK 26(20P12.1) WILD-TYPE
  0                           11                             67
  1                            0                             10
[1] 2 2
[1] FALSE
D45V6, binary
                                cls
clus                              0  1
  DEL PEAK 26(20P12.1) MUTATED   10  2
  DEL PEAK 26(20P12.1) WILD-TYPE 49 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(20P12.1) MUTATED     10    2
  DEL PEAK 26(20P12.1) WILD-TYPE   49   29
        clus
vv       DEL PEAK 26(20P12.1) MUTATED DEL PEAK 26(20P12.1) WILD-TYPE
  FEMALE                           10                             49
  MALE                              2                             29
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(20P12.1) MUTATED       1                         0    10
  DEL PEAK 26(20P12.1) WILD-TYPE     1                         1    66
D45V7, multiclass
                           clus
vv                          DEL PEAK 26(20P12.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               10
                           clus
vv                          DEL PEAK 26(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"
D45V8, binary
                                cls
clus                              0  1
  DEL PEAK 26(20P12.1) MUTATED    2  3
  DEL PEAK 26(20P12.1) WILD-TYPE  6 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(20P12.1) MUTATED      2    3
  DEL PEAK 26(20P12.1) WILD-TYPE    6   35
                        clus
vv                       DEL PEAK 26(20P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       DEL PEAK 26(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             35
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 27(22Q12.1) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 27(22Q12.1) MUTATED   28 22
  DEL PEAK 27(22Q12.1) WILD-TYPE 30 10
  DEL PEAK 27(22Q12.1) MUTATED DEL PEAK 27(22Q12.1) WILD-TYPE 
                            50                             40 
  DEL PEAK 27(22Q12.1) MUTATED DEL PEAK 27(22Q12.1) WILD-TYPE 
                            22                             10 
$`DEL PEAK 27(22Q12.1) MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 
       55.13        68.75        88.87        16.11        19.04        44.45 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JG 
       30.31        18.12        57.53        91.46        69.21        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       69.37        46.82        49.22        15.25        36.26       121.25 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
        9.50        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS 
       16.37        11.31        46.49        91.30        88.01        83.80 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LC 
       44.84        12.85         4.11        28.31        39.58         5.23 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       21.76        52.24        14.33        53.03        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-P6-A5OH 
       69.11        36.03        18.05        38.50        12.59         0.00 
TCGA-PK-A5H9 TCGA-PK-A5HA 
       20.25        39.48 

$`DEL PEAK 27(22Q12.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL 
       44.55        13.91        12.00        66.25        16.11        22.03 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JZ TCGA-OR-A5K0 
       18.48        29.23        12.59        29.82        27.02        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KB 
       96.59       100.18        22.98        49.08        24.62        24.36 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L1 TCGA-OR-A5L2 
       95.18       153.63       127.50        50.37        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        29.10        28.64        23.64 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LP 
       39.35        14.63        78.41        36.33        73.05        61.05 
TCGA-OR-A5LR TCGA-PA-A5YG TCGA-PK-A5HB TCGA-PK-A5HC 
       28.04        24.85        42.51        22.32 

  DEL PEAK 27(22Q12.1) MUTATED DEL PEAK 27(22Q12.1) WILD-TYPE 
                             0                             12 
  DEL PEAK 27(22Q12.1) MUTATED DEL PEAK 27(22Q12.1) WILD-TYPE 
                        121.25                         153.63 
  DEL PEAK 27(22Q12.1) MUTATED DEL PEAK 27(22Q12.1) WILD-TYPE 
                         38.99                          32.81 
[1] "0.0 - 121.2 (39.0)"  "12.0 - 153.6 (32.8)"
[1] "hr=" "1.9"
D46V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 27(22Q12.1) MUTATED         4       21        10       14
  DEL PEAK 27(22Q12.1) WILD-TYPE       5       22         8        4
D46V3, multiclass
           clus
vv          DEL PEAK 27(22Q12.1) MUTATED DEL PEAK 27(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 27(22Q12.1) MUTATED    4 23  9 13
  DEL PEAK 27(22Q12.1) WILD-TYPE  5 25  2  7
D46V4, multiclass
    clus
vv   DEL PEAK 27(22Q12.1) MUTATED DEL PEAK 27(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"
D46V5, binary
                                cls
clus                              0  1
  DEL PEAK 27(22Q12.1) MUTATED   44  5
  DEL PEAK 27(22Q12.1) WILD-TYPE 34  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(22Q12.1) MUTATED     44    5
  DEL PEAK 27(22Q12.1) WILD-TYPE   34    5
   clus
vv  DEL PEAK 27(22Q12.1) MUTATED DEL PEAK 27(22Q12.1) WILD-TYPE
  0                           44                             34
  1                            5                              5
[1] 2 2
[1] FALSE
D46V6, binary
                                cls
clus                              0  1
  DEL PEAK 27(22Q12.1) MUTATED   30 20
  DEL PEAK 27(22Q12.1) WILD-TYPE 29 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(22Q12.1) MUTATED     30   20
  DEL PEAK 27(22Q12.1) WILD-TYPE   29   11
        clus
vv       DEL PEAK 27(22Q12.1) MUTATED DEL PEAK 27(22Q12.1) WILD-TYPE
  FEMALE                           30                             29
  MALE                             20                             11
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(22Q12.1) MUTATED       1                         1    41
  DEL PEAK 27(22Q12.1) WILD-TYPE     1                         0    35
D46V7, multiclass
                           clus
vv                          DEL PEAK 27(22Q12.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               41
                           clus
vv                          DEL PEAK 27(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"
D46V8, binary
                                cls
clus                              0  1
  DEL PEAK 27(22Q12.1) MUTATED    6 17
  DEL PEAK 27(22Q12.1) WILD-TYPE  2 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(22Q12.1) MUTATED      6   17
  DEL PEAK 27(22Q12.1) WILD-TYPE    2   21
                        clus
vv                       DEL PEAK 27(22Q12.1) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           17
                        clus
vv                       DEL PEAK 27(22Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             21
[1] 2 2
[1] FALSE
