[1] "ofn"        "-oTKIRP-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRP-TP/15081779/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/15087100/transformed.cor.cli.txt"

nPatients in clinical file=271, in cluster file=288, common to both=269
[1]  31 269
[1] "AMP PEAK 1(2P23.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                          42                          227 
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                          42                          227 
[1] "AMP PEAK 2(2Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                          51                          218 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                          51                          218 
[1] "AMP PEAK 3(3Q27.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                          93                          176 
  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                          93                          176 
[1] "AMP PEAK 4(5Q35.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                          35                          234 
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                          35                          234 
[1] "AMP PEAK 5(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                         165                          104 
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                         165                          104 
[1] "AMP PEAK 6(17Q25.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                          189                            80 
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                          189                            80 
[1] "AMP PEAK 7(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                           30                           239 
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                           30                           239 
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            50                            219 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            50                            219 
[1] "DEL PEAK  2(2P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          6                         263 
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          6                         263 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            9                           260 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            9                           260 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           11                           258 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           11                           258 
[1] "DEL PEAK  5(3P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                           23                           246 
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                           23                           246 
[1] "DEL PEAK  6(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           30                           239 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           30                           239 
[1] "DEL PEAK  7(5P15.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                            13                            256 
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                            13                            256 
[1] "DEL PEAK  8(5Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                           11                           258 
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                           11                           258 
[1] "DEL PEAK  9(6P12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                           23                           246 
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                           23                           246 
[1] "DEL PEAK 10(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                            27                            242 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                            27                            242 
[1] "DEL PEAK 11(6Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                           29                           240 
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                           29                           240 
[1] "DEL PEAK 12(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           38                           231 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           38                           231 
[1] "DEL PEAK 13(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                            17                            252 
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                            17                            252 
[1] "DEL PEAK 14(11Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                            30                            239 
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                            30                            239 
[1] "DEL PEAK 15(11Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                            28                            241 
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                            28                            241 
[1] "DEL PEAK 16(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                            48                            221 
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                            48                            221 
[1] "DEL PEAK 17(14Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                            47                            222 
  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                            47                            222 
[1] "DEL PEAK 18(15Q13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                            33                            236 
  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                            33                            236 
[1] "DEL PEAK 19(16Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                            11                            258 
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                            11                            258 
[1] "DEL PEAK 20(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                            20                            249 
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                            20                            249 
[1] "DEL PEAK 21(19Q13.42) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                             19                             250 
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                             19                             250 
[1] "DEL PEAK 22(22Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                            60                            209 
  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                            60                            209 
[1] "DEL PEAK 23(XP11.4) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                           30                           239 
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                           30                           239 
[1] "DEL PEAK 24(XQ28) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                         25                         244 
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                         25                         244 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 269 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=35,	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=219,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'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 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'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 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=26,	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] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 269 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "NEOPLASM_DISEASESTAGE"        
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "KARNOFSKY_PERFORMANCE_SCORE"   "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RACE"                         
[11] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=54, 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 
176  29  54   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  176    29    56 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
176  29  54   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  176    29    56 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
45 22  4 
[1] "table(vv)"
vv
N0 N1 N2 
45 22  4 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
45 22  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
45 22  4 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=6, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=34, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=33, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 1(2P23.2) MUTATION ANALYSIS
D1V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 1(2P23.2) MUTATED    35   6
  AMP PEAK 1(2P23.2) WILD-TYPE 187  28
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                          41                          215 
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                           6                           28 
$`AMP PEAK 1(2P23.2) MUTATED`
TCGA-2Z-A9J5 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3466 
      100.27        16.96        16.31        15.75         8.28         9.63 
TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-A44B 
       13.55         2.20         7.33        10.16         0.46         2.10 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7046 TCGA-DW-5561 TCGA-DZ-6133 
       11.97         7.92         2.76        96.92        13.61        51.19 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A8LC TCGA-G7-A8LD 
        1.18         4.01        51.78        39.25        17.33        16.90 
TCGA-GL-7966 TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40Y 
        3.68        17.95        68.12        11.84        16.80         2.04 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5E8 TCGA-P4-A5EB 
       11.97        29.10        11.41        34.29        42.94        84.95 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SQ TCGA-UZ-A9PK 
       17.75        14.07        28.80        41.62        60.03 

$`AMP PEAK 1(2P23.2) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        75.55        59.01        58.22        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5Y1 
       19.63        19.73        14.33        12.46         8.48        12.99 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46        58.45        76.64        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       49.25        19.56        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
        1.15        15.12        43.99        22.06        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
       10.88         7.66         0.95       123.62        48.26        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
       14.63         3.02        40.77        79.86        80.88        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       54.90        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 
        2.40         0.43        48.62        11.05        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 
       13.68        25.84         6.38        17.98        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92        27.65         1.05        12.43         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X 
        4.60        13.41        56.75        73.25         5.49        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       12.36         0.13        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
        0.36        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       87.22         6.61        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL 
       78.90        12.85        47.90        47.44        33.04        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        38.63        16.31        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       43.76        18.02        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                        0.46                         0.10 
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                      100.27                       194.79 
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                       15.75                        22.92 
[1] "0.5 - 100.3 (15.8)" "0.1 - 194.8 (22.9)"
[1] "hr=" "1.3"
D1V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 1(2P23.2) MUTATED        25        3         8        5
  AMP PEAK 1(2P23.2) WILD-TYPE     142       18        41        9
D1V3, multiclass
           clus
vv          AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  STAGE I                           25                          142
  STAGE II                           3                           18
  STAGE III                          8                           41
  STAGE IV                           5                            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 1(2P23.2) MUTATED    25   5    12
  AMP PEAK 1(2P23.2) WILD-TYPE 151  24    44
D1V4, multiclass
       clus
vv      AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  T1                            25                          151
  T2                             5                           24
  T3+T4                         12                           44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2
  AMP PEAK 1(2P23.2) MUTATED    4  8  1
  AMP PEAK 1(2P23.2) WILD-TYPE 41 14  3
D1V5, multiclass
    clus
vv   AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  N0                          4                           41
  N1                          8                           14
  N2                          1                            3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                              cls
clus                            0  1
  AMP PEAK 1(2P23.2) MUTATED   11  4
  AMP PEAK 1(2P23.2) WILD-TYPE 79  5
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(2P23.2) MUTATED     11    4
  AMP PEAK 1(2P23.2) WILD-TYPE   79    5
   clus
vv  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  0                         11                           79
  1                          4                            5
[1] 2 2
[1] FALSE
D1V7, binary
                              cls
clus                             0   1
  AMP PEAK 1(2P23.2) MUTATED    14  28
  AMP PEAK 1(2P23.2) WILD-TYPE  58 169
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(2P23.2) MUTATED     14   28
  AMP PEAK 1(2P23.2) WILD-TYPE   58  169
        clus
vv       AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  FEMALE                         14                           58
  MALE                           28                          169
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
D1V10, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 1(2P23.2) MUTATED                                  0     1
  AMP PEAK 1(2P23.2) WILD-TYPE                                2     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 1(2P23.2) MUTATED                           7    30
  AMP PEAK 1(2P23.2) WILD-TYPE                        53   157
D1V11, multiclass
                                  clus
vv                                 AMP PEAK 1(2P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 7
  WHITE                                                    30
                                  clus
vv                                 AMP PEAK 1(2P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  53
  WHITE                                                     157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
                              cls
clus                             0   1
  AMP PEAK 1(2P23.2) MUTATED     2  35
  AMP PEAK 1(2P23.2) WILD-TYPE  10 185
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(2P23.2) MUTATED      2   35
  AMP PEAK 1(2P23.2) WILD-TYPE   10  185
                        clus
vv                       AMP PEAK 1(2P23.2) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         35
                        clus
vv                       AMP PEAK 1(2P23.2) WILD-TYPE
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          185
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK 2(2Q32.1) MUTATION ANALYSIS
D2V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 2(2Q32.1) MUTATED    43   8
  AMP PEAK 2(2Q32.1) WILD-TYPE 179  26
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                          51                          205 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                           8                           26 
$`AMP PEAK 2(2Q32.1) MUTATED`
TCGA-2Z-A9J5 TCGA-2Z-A9JR TCGA-A4-7585 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
      100.27         5.29        35.18        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3471 TCGA-AL-7173 TCGA-AT-A5NU 
       15.75         8.28         9.63        13.55        44.61         2.20 
TCGA-B1-7332 TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-A44B TCGA-B9-A69E 
        7.33         6.58        10.16         0.46         2.10        14.86 
TCGA-BQ-5878 TCGA-BQ-5885 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7046 
       63.72        30.28        11.97         7.92         2.76        96.92 
TCGA-DW-5561 TCGA-DZ-6131 TCGA-DZ-6133 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
       13.61        79.86        51.19         1.18         4.01        51.78 
TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-GL-A59T TCGA-HE-A5NF 
       39.25        25.84        17.33         3.68        17.95        68.12 
TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       11.84        16.80         2.04        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71V 
       34.29        42.94        84.95        17.75        14.07        28.80 
TCGA-SX-A7SQ TCGA-UZ-A9PK TCGA-UZ-A9PQ 
       41.62        60.03        86.27 

$`AMP PEAK 2(2Q32.1) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        75.55        59.01        58.22        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       29.36        25.58        16.18        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
       11.57        18.21        19.63        61.05         0.10        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
       14.33        12.46        12.99        12.46        58.45        76.64 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       30.35        25.08        49.25        19.56        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       16.87         3.55        16.77         0.46        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 
       20.61         1.15        15.12        43.99        22.06        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        6.81         0.16        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       26.04        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
        0.95       123.62        48.26        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 
        7.04         7.17         3.81        11.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       40.77        80.88        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6792 
       24.89        10.68        13.08         2.40         0.43        48.62 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
       11.05        34.82        25.15        13.68         6.38        17.98 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       16.90        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ 
       12.43         0.89        11.21         4.60        13.41        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       73.25         5.49        19.99        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55Z 
       22.26        21.34        16.34        12.36         0.13        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5ED 
       21.44        15.48        99.78        87.22         6.61        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        12.85        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       47.44        33.04        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PM 
       16.31        26.47        48.30        43.76        18.02        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       21.93         0.53        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                        0.46                         0.10 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                      100.27                       194.79 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                       16.31                        22.26 
[1] "0.5 - 100.3 (16.3)" "0.1 - 194.8 (22.3)"
[1] "hr=" "1.3"
D2V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 2(2Q32.1) MUTATED        28        3        12        7
  AMP PEAK 2(2Q32.1) WILD-TYPE     139       18        37        7
D2V3, multiclass
           clus
vv          AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  STAGE I                           28                          139
  STAGE II                           3                           18
  STAGE III                         12                           37
  STAGE IV                           7                            7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2 T3+T4
  AMP PEAK 2(2Q32.1) MUTATED    28   7    16
  AMP PEAK 2(2Q32.1) WILD-TYPE 148  22    40
D2V4, multiclass
       clus
vv      AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  T1                            28                          148
  T2                             7                           22
  T3+T4                         16                           40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2
  AMP PEAK 2(2Q32.1) MUTATED    9  9  2
  AMP PEAK 2(2Q32.1) WILD-TYPE 36 13  2
D2V5, multiclass
    clus
vv   AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  N0                          9                           36
  N1                          9                           13
  N2                          2                            2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                              cls
clus                            0  1
  AMP PEAK 2(2Q32.1) MUTATED   15  5
  AMP PEAK 2(2Q32.1) WILD-TYPE 75  4
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(2Q32.1) MUTATED     15    5
  AMP PEAK 2(2Q32.1) WILD-TYPE   75    4
   clus
vv  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  0                         15                           75
  1                          5                            4
[1] 2 2
[1] FALSE
D2V7, binary
                              cls
clus                             0   1
  AMP PEAK 2(2Q32.1) MUTATED    15  36
  AMP PEAK 2(2Q32.1) WILD-TYPE  57 161
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(2Q32.1) MUTATED     15   36
  AMP PEAK 2(2Q32.1) WILD-TYPE   57  161
        clus
vv       AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  FEMALE                         15                           57
  MALE                           36                          161
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
D2V10, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 2(2Q32.1) MUTATED                                  0     1
  AMP PEAK 2(2Q32.1) WILD-TYPE                                2     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 2(2Q32.1) MUTATED                           8    39
  AMP PEAK 2(2Q32.1) WILD-TYPE                        52   148
D2V11, multiclass
                                  clus
vv                                 AMP PEAK 2(2Q32.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 8
  WHITE                                                    39
                                  clus
vv                                 AMP PEAK 2(2Q32.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  52
  WHITE                                                     148
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
                              cls
clus                             0   1
  AMP PEAK 2(2Q32.1) MUTATED     2  43
  AMP PEAK 2(2Q32.1) WILD-TYPE  10 177
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(2Q32.1) MUTATED      2   43
  AMP PEAK 2(2Q32.1) WILD-TYPE   10  177
                        clus
vv                       AMP PEAK 2(2Q32.1) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         43
                        clus
vv                       AMP PEAK 2(2Q32.1) WILD-TYPE
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          177
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK 3(3Q27.1) MUTATION ANALYSIS
D3V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 3(3Q27.1) MUTATED    74  12
  AMP PEAK 3(3Q27.1) WILD-TYPE 148  22
  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                          86                          170 
  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                          12                           22 
$`AMP PEAK 3(3Q27.1) MUTATED`
TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-A4-7287 
        7.04        59.01        58.22       100.27        56.91        19.63 
TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       30.48        23.97        23.31        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU 
       16.96        16.31        15.75        76.64        13.55         2.20 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4114 
        7.33        21.67         6.58        30.58        10.16        28.18 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-7045 TCGA-BQ-7046 
       17.49        47.80        26.04         7.66        48.26        96.92 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7963 
        7.04         3.81        35.93        37.55        24.46        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-F9-A7Q0 TCGA-F9-A7VF 
       80.88        51.19        54.90        34.19        13.08         2.40 
TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-A8LB TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-A59T 
       51.78        11.05        17.98        16.90       194.79        17.95 
TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A40Y TCGA-IA-A83S 
       11.21        68.12        11.84         5.49         2.04        85.78 
TCGA-IA-A83W TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5E6 
       67.17        11.97        29.10        11.41        34.29        99.78 
TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-P4-AAVM TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       87.22         6.61        16.01        50.60        17.75        14.07 
TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-UZ-A9PK 
       28.80        19.00        16.31        41.62        48.30        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9Q0 
       14.83        21.93        52.11        30.67        25.68        12.99 
TCGA-Y8-A895 TCGA-Y8-A8RZ 
       15.91         6.74 

$`AMP PEAK 3(3Q27.1) WILD-TYPE`
TCGA-2Z-A9J1 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       75.55         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       54.64        51.52        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       24.33        31.20        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 
       22.49         0.13        12.82        11.57        18.21        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-A57E 
       29.46        25.64        23.28         0.76        19.63         8.48 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        58.45        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A47O 
       25.08        44.61        49.25        19.56        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 
        3.55        16.77         0.46        33.83        10.09        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A5W7 TCGA-B9-A5W8 
       12.46        50.50        26.40        20.61        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        0.16        14.86        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 
       30.28        25.35        13.25        10.88         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
        7.92         2.76       123.62        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7840 
        7.17        11.61        13.61       129.86        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 
       14.63         3.02        79.86        61.02        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6795 
       10.68         1.18         0.43         4.01        48.62        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LC 
       34.82        25.15        13.68        25.84         6.38        17.33 
TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A40U 
        0.89         4.60        13.41        56.75        73.25        16.80 
TCGA-IA-A40X TCGA-IA-A83T TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99        88.24        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        0.13        27.78        30.38        27.65        20.25         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E8 TCGA-P4-A5EB 
       12.13        25.97        21.44        15.48        42.94        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A71R TCGA-SX-A71S 
       92.58        52.27        78.90        12.85        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SU 
       33.04        27.06        11.93        38.63        26.47        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PX TCGA-WN-A9G9 
       18.02         0.53        86.27        38.86        27.39        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       29.00        18.64        18.64        18.05        15.62        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                        0.46                         0.10 
  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                      194.79                       129.86 
  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                       20.70                        21.39 
[1] "0.5 - 194.8 (20.7)" "0.1 - 129.9 (21.4)"
[1] "hr=" "1.1"
D3V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 3(3Q27.1) MUTATED        60       10        14        3
  AMP PEAK 3(3Q27.1) WILD-TYPE     107       11        35       11
D3V3, multiclass
           clus
vv          AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE
  STAGE I                           60                          107
  STAGE II                          10                           11
  STAGE III                         14                           35
  STAGE IV                           3                           11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2 T3+T4
  AMP PEAK 3(3Q27.1) MUTATED    62  13    15
  AMP PEAK 3(3Q27.1) WILD-TYPE 114  16    41
D3V4, multiclass
       clus
vv      AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE
  T1                            62                          114
  T2                            13                           16
  T3+T4                         15                           41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2
  AMP PEAK 3(3Q27.1) MUTATED   11  6  1
  AMP PEAK 3(3Q27.1) WILD-TYPE 34 16  3
D3V5, multiclass
    clus
vv   AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE
  N0                         11                           34
  N1                          6                           16
  N2                          1                            3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                              cls
clus                            0  1
  AMP PEAK 3(3Q27.1) MUTATED   29  0
  AMP PEAK 3(3Q27.1) WILD-TYPE 61  9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(3Q27.1) MUTATED     29    0
  AMP PEAK 3(3Q27.1) WILD-TYPE   61    9
   clus
vv  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE
  0                         29                           61
  1                          0                            9
[1] 2 2
[1] FALSE
D3V7, binary
                              cls
clus                             0   1
  AMP PEAK 3(3Q27.1) MUTATED    22  71
  AMP PEAK 3(3Q27.1) WILD-TYPE  50 126
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(3Q27.1) MUTATED     22   71
  AMP PEAK 3(3Q27.1) WILD-TYPE   50  126
        clus
vv       AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE
  FEMALE                         22                           50
  MALE                           71                          126
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
D3V10, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 3(3Q27.1) MUTATED                                  2     1
  AMP PEAK 3(3Q27.1) WILD-TYPE                                0     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 3(3Q27.1) MUTATED                          17    65
  AMP PEAK 3(3Q27.1) WILD-TYPE                        43   122
D3V11, multiclass
                                  clus
vv                                 AMP PEAK 3(3Q27.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          2
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                17
  WHITE                                                    65
                                  clus
vv                                 AMP PEAK 3(3Q27.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  43
  WHITE                                                     122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                              cls
clus                             0   1
  AMP PEAK 3(3Q27.1) MUTATED     4  76
  AMP PEAK 3(3Q27.1) WILD-TYPE   8 144
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(3Q27.1) MUTATED      4   76
  AMP PEAK 3(3Q27.1) WILD-TYPE    8  144
                        clus
vv                       AMP PEAK 3(3Q27.1) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                         76
                        clus
vv                       AMP PEAK 3(3Q27.1) WILD-TYPE
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          144
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK 4(5Q35.2) MUTATION ANALYSIS
D4V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 4(5Q35.2) MUTATED    31   3
  AMP PEAK 4(5Q35.2) WILD-TYPE 191  31
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                          34                          222 
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                           3                           31 
$`AMP PEAK 4(5Q35.2) MUTATED`
TCGA-2K-A9WE TCGA-2Z-A9JK TCGA-2Z-A9JR TCGA-4A-A93X TCGA-A4-8098 TCGA-A4-8516 
        7.04        38.99         5.29        12.82        29.46         0.76 
TCGA-A4-A48D TCGA-A4-A57E TCGA-AL-3466 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-A656 
       12.46         8.48         9.63        25.08        19.56         0.46 
TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5878 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
        0.46         0.16        63.72        25.35         7.66         0.95 
TCGA-BQ-5892 TCGA-DW-7838 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 
       11.97        24.46        19.00        13.08         0.43         4.01 
TCGA-G7-A8LC TCGA-GL-A4EM TCGA-HE-A5NK TCGA-IA-A40X TCGA-IA-A40Y TCGA-KV-A6GD 
       17.33         1.05        73.25        19.99         2.04        11.97 
TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SQ 
       99.78        84.95        14.07        41.62 

$`AMP PEAK 4(5Q35.2) WILD-TYPE`
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       35.67        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 
       25.58        16.18        22.49         0.13        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
        0.23        16.64        30.48        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU 
       23.31        19.63        19.73        14.33        16.96        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
       15.75         8.28        12.99        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 
       13.55        30.35        44.61        49.25         2.20         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 
       21.67        24.56        16.87         3.55        16.77         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 
       50.50        28.18        26.40        20.61         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E 
       43.99        22.06         2.10        19.23         6.81        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 
       17.49        12.30        86.76        19.27         8.88        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       26.04        13.25        10.88         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       37.55        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 
       24.89        10.68         2.40         1.18        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
        6.38        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
        4.60        68.12        13.41        11.84        56.75         5.49 
TCGA-IA-A40U TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       16.80        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       16.34        12.36         0.13        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       25.97        21.44        15.48        87.22        42.94         6.61 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        38.63        16.31        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                        0.16                         0.10 
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                       99.78                       194.79 
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                      12.640                       22.705 
[1] "0.2 - 99.8 (12.6)"  "0.1 - 194.8 (22.7)"
[1] "hr=" "1.1"
D4V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 4(5Q35.2) MUTATED        16        2        11        3
  AMP PEAK 4(5Q35.2) WILD-TYPE     151       19        38       11
D4V3, multiclass
           clus
vv          AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  STAGE I                           16                          151
  STAGE II                           2                           19
  STAGE III                         11                           38
  STAGE IV                           3                           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 4(5Q35.2) MUTATED    18   4    12
  AMP PEAK 4(5Q35.2) WILD-TYPE 158  25    44
D4V4, multiclass
       clus
vv      AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  T1                            18                          158
  T2                             4                           25
  T3+T4                         12                           44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2
  AMP PEAK 4(5Q35.2) MUTATED    9  4  1
  AMP PEAK 4(5Q35.2) WILD-TYPE 36 18  3
D4V5, multiclass
    clus
vv   AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  N0                          9                           36
  N1                          4                           18
  N2                          1                            3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                              cls
clus                            0  1
  AMP PEAK 4(5Q35.2) MUTATED   15  2
  AMP PEAK 4(5Q35.2) WILD-TYPE 75  7
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q35.2) MUTATED     15    2
  AMP PEAK 4(5Q35.2) WILD-TYPE   75    7
   clus
vv  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  0                         15                           75
  1                          2                            7
[1] 2 2
[1] FALSE
D4V7, binary
                              cls
clus                             0   1
  AMP PEAK 4(5Q35.2) MUTATED     8  27
  AMP PEAK 4(5Q35.2) WILD-TYPE  64 170
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q35.2) MUTATED      8   27
  AMP PEAK 4(5Q35.2) WILD-TYPE   64  170
        clus
vv       AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  FEMALE                          8                           64
  MALE                           27                          170
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
D4V10, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 4(5Q35.2) MUTATED                                  0     2
  AMP PEAK 4(5Q35.2) WILD-TYPE                                2     3
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 4(5Q35.2) MUTATED                           6    25
  AMP PEAK 4(5Q35.2) WILD-TYPE                        54   162
D4V11, multiclass
                                  clus
vv                                 AMP PEAK 4(5Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 6
  WHITE                                                    25
                                  clus
vv                                 AMP PEAK 4(5Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  54
  WHITE                                                     162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
                              cls
clus                             0   1
  AMP PEAK 4(5Q35.2) MUTATED     0  30
  AMP PEAK 4(5Q35.2) WILD-TYPE  12 190
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q35.2) MUTATED      0   30
  AMP PEAK 4(5Q35.2) WILD-TYPE   12  190
                        clus
vv                       AMP PEAK 4(5Q35.2) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         30
                        clus
vv                       AMP PEAK 4(5Q35.2) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          190
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK 5(7Q31.2) MUTATION ANALYSIS
D5V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 5(7Q31.2) MUTATED   137  16
  AMP PEAK 5(7Q31.2) WILD-TYPE  85  18
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                         153                          103 
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                          16                           18 
$`AMP PEAK 5(7Q31.2) MUTATED`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        75.55        58.22       100.27        56.91         4.57 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       34.85        56.81        26.43        30.71        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-A4-7288 
        5.29        16.18        22.49         0.13        12.82        61.05 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
       19.13         0.89        16.64        30.48        25.64        23.97 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A57E 
       23.31         0.76        19.63        14.33        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       16.31        15.75        12.46        76.64        13.55        30.35 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       44.61        49.25         2.20        21.67        24.56         3.55 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 
        0.46         6.58        33.83        30.58        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-5881 
       15.12        43.99        22.06        19.23        17.49        47.80 
TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
       26.04        25.35        10.88         0.95        11.97         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 
      123.62        48.26        96.92        50.40         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       37.55        24.46         3.75        14.63         3.02        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 
       80.88        51.19        61.02        34.19        24.89        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 
        2.40         1.18         4.01        51.78        11.05        39.25 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 
       25.84         6.38        17.98        17.33        80.65       194.79 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DD TCGA-HE-A5NF 
        3.68        27.65        12.43        17.95        11.21        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40Y TCGA-IA-A83T 
       13.41        11.84        56.75         5.49         2.04        88.24 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       21.34        16.34        12.36        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVK 
       34.29        27.78        20.25        15.48        87.22        52.27 
TCGA-P4-AAVL TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       28.80        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PR 
       48.30        43.76        60.03        14.83        21.93        38.86 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A895 TCGA-Y8-A896 
       30.67        25.68        27.39        12.99        15.91        18.64 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       15.62        25.28         6.02 

$`AMP PEAK 5(7Q31.2) WILD-TYPE`
TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       59.01        67.30        75.42        54.64        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 
       38.99        24.33        31.20        11.57        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-8518 
        0.10        35.18         0.23        29.46        23.28        19.73 
TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 
       12.46         8.28        12.99         9.63        58.45        25.08 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47O TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4104 
       19.56         7.33        16.87        16.77        10.09        34.49 
TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
        2.10         6.81         0.16        14.86        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 
       19.27         8.88        63.72        22.92        43.20        21.63 
TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5893 
       40.83        30.28        26.04        13.25         7.66         7.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       93.34        44.84        61.28        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-7839 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ 
       11.28        13.78        79.86        54.90        19.00        10.68 
TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD 
        0.43        48.62        34.82        25.15        13.68        16.90 
TCGA-GL-7773 TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40U 
       12.92         1.05         0.89         4.60        73.25        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83W TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A560 
       19.99        85.78        67.17        22.26         0.13        30.38 
TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E6 
       27.65         0.36        12.13        25.97        21.44        99.78 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO 
       42.94         6.61        84.95        92.58        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-SX-A7SL TCGA-SX-A7SO TCGA-UN-AAZ9 TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       12.85        27.06        38.63        18.02         0.53        86.27 
TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RZ 
       52.11        26.01        29.00        18.64        18.05         6.74 
TCGA-Y8-A8S1 
       13.28 

  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                        0.13                         0.10 
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                      194.79                        99.78 
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                       20.61                        21.63 
[1] "0.1 - 194.8 (20.6)" "0.1 - 99.8 (21.6)" 
[1] "hr=" "1.5"
D5V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 5(7Q31.2) MUTATED       113       11        18       11
  AMP PEAK 5(7Q31.2) WILD-TYPE      54       10        31        3
D5V3, multiclass
           clus
vv          AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  STAGE I                          113                           54
  STAGE II                          11                           10
  STAGE III                         18                           31
  STAGE IV                          11                            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 5(7Q31.2) MUTATED   116  19    26
  AMP PEAK 5(7Q31.2) WILD-TYPE  60  10    30
D5V4, multiclass
       clus
vv      AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  T1                           116                           60
  T2                            19                           10
  T3+T4                         26                           30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2
  AMP PEAK 5(7Q31.2) MUTATED   22  8  3
  AMP PEAK 5(7Q31.2) WILD-TYPE 23 14  1
D5V5, multiclass
    clus
vv   AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  N0                         22                           23
  N1                          8                           14
  N2                          3                            1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                              cls
clus                            0  1
  AMP PEAK 5(7Q31.2) MUTATED   50  6
  AMP PEAK 5(7Q31.2) WILD-TYPE 40  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(7Q31.2) MUTATED     50    6
  AMP PEAK 5(7Q31.2) WILD-TYPE   40    3
   clus
vv  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  0                         50                           40
  1                          6                            3
[1] 2 2
[1] FALSE
D5V7, binary
                              cls
clus                             0   1
  AMP PEAK 5(7Q31.2) MUTATED    34 131
  AMP PEAK 5(7Q31.2) WILD-TYPE  38  66
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(7Q31.2) MUTATED     34  131
  AMP PEAK 5(7Q31.2) WILD-TYPE   38   66
        clus
vv       AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  FEMALE                         34                           38
  MALE                          131                           66
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
D5V10, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 5(7Q31.2) MUTATED                                  2     3
  AMP PEAK 5(7Q31.2) WILD-TYPE                                0     2
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 5(7Q31.2) MUTATED                          31   118
  AMP PEAK 5(7Q31.2) WILD-TYPE                        29    69
D5V11, multiclass
                                  clus
vv                                 AMP PEAK 5(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          2
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                31
  WHITE                                                   118
                                  clus
vv                                 AMP PEAK 5(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  29
  WHITE                                                      69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                              cls
clus                             0   1
  AMP PEAK 5(7Q31.2) MUTATED     6 140
  AMP PEAK 5(7Q31.2) WILD-TYPE   6  80
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(7Q31.2) MUTATED      6  140
  AMP PEAK 5(7Q31.2) WILD-TYPE    6   80
                        clus
vv                       AMP PEAK 5(7Q31.2) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                        140
                        clus
vv                       AMP PEAK 5(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           80
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK 6(17Q25.2) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 6(17Q25.2) MUTATED   156  23
  AMP PEAK 6(17Q25.2) WILD-TYPE  66  11
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                          179                            77 
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                           23                            11 
$`AMP PEAK 6(17Q25.2) MUTATED`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JM TCGA-2Z-A9JP 
        4.57        34.85        56.81        51.52        30.71        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-A4-7286 
       25.58         5.29        16.18        22.49         0.13        18.21 
TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
       61.05        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       29.46        25.64        23.97        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.73        14.33        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 
        8.28        12.99        12.46         9.63        76.64        13.55 
TCGA-AL-3472 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       30.35        49.25         2.20         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 
       16.87         3.55        16.77         6.58        33.83        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5880 
       19.23         0.16        17.49        86.76         8.88        43.20 
TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
       47.80        26.04        25.35        13.25         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7053 
       11.97         7.92        48.26        96.92        50.40        49.84 
TCGA-BQ-7058 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       11.28         7.04         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 
       34.19        24.89        13.08         2.40         1.18         4.01 
TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM 
       51.78        11.05        39.25        34.82        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 
       17.98        17.33        16.90        80.65       194.79         3.68 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF 
        1.05        12.43        17.95         0.89        11.21        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y 
       13.41        11.84        56.75         5.49        16.80         2.04 
TCGA-IA-A83T TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       88.24        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB 
       27.65        20.25        15.48        87.22         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       33.04        28.80        27.06        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP 
       26.47        48.30        43.76        60.03        14.83         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-AB4C TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       29.00        15.91        15.62        25.28         6.02 

$`AMP PEAK 6(17Q25.2) WILD-TYPE`
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JG TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       67.30        75.42        54.64        35.67        38.99        26.43 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7583 
       24.33        31.20        12.82        11.57        19.63         0.10 
TCGA-A4-7997 TCGA-A4-8312 TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3473 TCGA-AL-7173 
       30.48        23.28        12.46        58.45        25.08        44.61 
TCGA-B1-5398 TCGA-B1-A656 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E 
       19.56         0.46        10.09        20.61         6.81        14.86 
TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5883 
       12.30        19.27        63.72        22.92        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 
       26.04        30.28        10.88         2.76       123.62        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 
       44.84        61.28        26.27        20.12         7.63         7.17 
TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6797 
       54.90        19.00        10.68         0.43        48.62        25.15 
TCGA-G7-7501 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40X 
       13.68        12.92        27.65         4.60        73.25        19.99 
TCGA-IA-A83S TCGA-IA-A83W TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       85.78        67.17         0.36        12.13        25.97        21.44 
TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       99.78        42.94        52.27        50.60        78.90        12.85 
TCGA-SX-A7SM TCGA-SX-A7SO TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-A9G9 
       11.93        38.63        18.02        21.93        86.27        26.01 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       18.64        18.64        18.05         6.74        13.28 

  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                         0.13                          0.10 
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                       194.79                        123.62 
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                        19.63                         22.92 
[1] "0.1 - 194.8 (19.6)" "0.1 - 123.6 (22.9)"
[1] "hr=" "1.1"
D6V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 6(17Q25.2) MUTATED       124       16        29       10
  AMP PEAK 6(17Q25.2) WILD-TYPE      43        5        20        4
D6V3, multiclass
           clus
vv          AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  STAGE I                           124                            43
  STAGE II                           16                             5
  STAGE III                          29                            20
  STAGE IV                           10                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  AMP PEAK 6(17Q25.2) MUTATED   128  23    36
  AMP PEAK 6(17Q25.2) WILD-TYPE  48   6    20
D6V4, multiclass
       clus
vv      AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  T1                            128                            48
  T2                             23                             6
  T3+T4                          36                            20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  AMP PEAK 6(17Q25.2) MUTATED   30 13  3
  AMP PEAK 6(17Q25.2) WILD-TYPE 15  9  1
D6V5, multiclass
    clus
vv   AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  N0                          30                            15
  N1                          13                             9
  N2                           3                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                               cls
clus                             0  1
  AMP PEAK 6(17Q25.2) MUTATED   54  6
  AMP PEAK 6(17Q25.2) WILD-TYPE 36  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(17Q25.2) MUTATED     54    6
  AMP PEAK 6(17Q25.2) WILD-TYPE   36    3
   clus
vv  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  0                          54                            36
  1                           6                             3
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK 6(17Q25.2) MUTATED    43 146
  AMP PEAK 6(17Q25.2) WILD-TYPE  29  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(17Q25.2) MUTATED     43  146
  AMP PEAK 6(17Q25.2) WILD-TYPE   29   51
        clus
vv       AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  FEMALE                          43                            29
  MALE                           146                            51
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
D6V10, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 6(17Q25.2) MUTATED                                  2     4
  AMP PEAK 6(17Q25.2) WILD-TYPE                                0     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 6(17Q25.2) MUTATED                          34   139
  AMP PEAK 6(17Q25.2) WILD-TYPE                        26    48
D6V11, multiclass
                                  clus
vv                                 AMP PEAK 6(17Q25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 34
  WHITE                                                    139
                                  clus
vv                                 AMP PEAK 6(17Q25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                       48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
                               cls
clus                              0   1
  AMP PEAK 6(17Q25.2) MUTATED     7 159
  AMP PEAK 6(17Q25.2) WILD-TYPE   5  61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(17Q25.2) MUTATED      7  159
  AMP PEAK 6(17Q25.2) WILD-TYPE    5   61
                        clus
vv                       AMP PEAK 6(17Q25.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         159
                        clus
vv                       AMP PEAK 6(17Q25.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            61
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK 7(19P13.2) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 7(19P13.2) MUTATED    24   4
  AMP PEAK 7(19P13.2) WILD-TYPE 198  30
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                           28                           228 
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                            4                            30 
$`AMP PEAK 7(19P13.2) MUTATED`
TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JR TCGA-A4-7732 TCGA-A4-A5DU 
       58.22         4.57        56.81         5.29        19.13        16.31 
TCGA-A4-A5XZ TCGA-AL-3472 TCGA-B9-4113 TCGA-B9-4116 TCGA-B9-4617 TCGA-BQ-5885 
       15.75        30.35        50.50        20.61         1.15        30.28 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-DW-5561 TCGA-DW-7840 TCGA-EV-5901 TCGA-F9-A7Q0 
        0.95        11.97        13.61         3.75        34.19        13.08 
TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-A5NJ TCGA-IZ-8196 
       39.25         6.38        17.33         3.68        56.75        21.34 
TCGA-P4-A5E7 TCGA-P4-AAVL TCGA-SX-A7SU TCGA-UZ-A9PX 
       87.22        16.01        43.76        27.39 

$`AMP PEAK 7(19P13.2) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J8 
        7.04        75.55        59.01       100.27        56.91        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK 
       75.42        34.85        54.64        51.52        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 
       16.18        22.49         0.13        12.82        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7734 TCGA-A4-7915 
       19.63        61.05         0.10        35.18         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.96         8.48         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       58.45        76.64        13.55        25.08        44.61        49.25 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
        2.20        19.56         7.33        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        10.16        28.18        26.40 
TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        0.46        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       21.63        40.83        26.04        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       10.88         7.66         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
        3.81        11.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
       13.78        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        61.02        54.90        19.00        24.89        10.68 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LB 
       11.05        34.82        25.15        13.68        25.84        17.98 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       16.90        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       13.41        11.84        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-A6M8 
        2.04        85.78        88.24        67.17        22.26        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA 
       25.97        21.44        15.48        99.78        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       84.95        92.58        52.27        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       26.47        48.30        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                         0.95                          0.10 
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                        87.22                        194.79 
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                        18.23                         21.80 
[1] "0.9 - 87.2 (18.2)"  "0.1 - 194.8 (21.8)"
[1] "hr=" "1.3"
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 7(19P13.2) MUTATED        17        2         4        1
  AMP PEAK 7(19P13.2) WILD-TYPE     150       19        45       13
D7V3, multiclass
           clus
vv          AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  STAGE I                            17                           150
  STAGE II                            2                            19
  STAGE III                           4                            45
  STAGE IV                            1                            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 7(19P13.2) MUTATED    18   7     4
  AMP PEAK 7(19P13.2) WILD-TYPE 158  22    52
D7V4, multiclass
       clus
vv      AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  T1                             18                           158
  T2                              7                            22
  T3+T4                           4                            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"
                               vv
clus                            N0 N1 N2
  AMP PEAK 7(19P13.2) MUTATED    6  2  0
  AMP PEAK 7(19P13.2) WILD-TYPE 39 20  4
D7V5, multiclass
    clus
vv   AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  N0                           6                            39
  N1                           2                            20
  N2                           0                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                               cls
clus                             0  1
  AMP PEAK 7(19P13.2) MUTATED   11  1
  AMP PEAK 7(19P13.2) WILD-TYPE 79  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(19P13.2) MUTATED     11    1
  AMP PEAK 7(19P13.2) WILD-TYPE   79    8
   clus
vv  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  0                          11                            79
  1                           1                             8
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK 7(19P13.2) MUTATED     8  22
  AMP PEAK 7(19P13.2) WILD-TYPE  64 175
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(19P13.2) MUTATED      8   22
  AMP PEAK 7(19P13.2) WILD-TYPE   64  175
        clus
vv       AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  FEMALE                           8                            64
  MALE                            22                           175
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
D7V10, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 7(19P13.2) MUTATED                                  0     1
  AMP PEAK 7(19P13.2) WILD-TYPE                                2     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 7(19P13.2) MUTATED                           8    18
  AMP PEAK 7(19P13.2) WILD-TYPE                        52   169
D7V11, multiclass
                                  clus
vv                                 AMP PEAK 7(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     18
                                  clus
vv                                 AMP PEAK 7(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   52
  WHITE                                                      169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                               cls
clus                              0   1
  AMP PEAK 7(19P13.2) MUTATED     2  25
  AMP PEAK 7(19P13.2) WILD-TYPE  10 195
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(19P13.2) MUTATED      2   25
  AMP PEAK 7(19P13.2) WILD-TYPE   10  195
                        clus
vv                       AMP PEAK 7(19P13.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          25
                        clus
vv                       AMP PEAK 7(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           195
[1] 2 2
[1] FALSE

Clustering(8) Variable = DEL PEAK  1(1P36.31) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.31) MUTATED    39  11
  DEL PEAK  1(1P36.31) WILD-TYPE 183  23
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            50                            206 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            11                             23 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7583 
       67.30        54.64        51.52        12.82        18.21         0.10 
TCGA-A4-8098 TCGA-A4-A5XZ TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B1-7332 
       29.46        15.75        12.99         9.63        49.25         7.33 
TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A69E TCGA-BQ-5875 
       10.09        20.61         2.10         6.81        14.86        86.76 
TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5890 
        8.88        22.92        21.63        30.28        13.25         7.66 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7055 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 
        2.76       123.62        26.27        19.00        10.68        13.08 
TCGA-G7-6789 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD 
        4.01        25.15        13.68        25.84        17.33        16.90 
TCGA-GL-7966 TCGA-GL-8500 TCGA-HE-A5NK TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EA 
        3.68        27.65        73.25         2.04         0.13         6.61 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ 
       78.90        12.85        14.07        18.02        21.93        86.27 
TCGA-WN-A9G9 TCGA-Y8-A8RZ 
       26.01         6.74 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JK 
        4.57        75.42        34.85        56.81        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7287 
        5.29        16.18        22.49         0.13        11.57        19.63 
TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
       61.05        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       30.48        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       16.31         8.28        12.46        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       33.83        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       28.18        26.40         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 
       22.06        19.23         0.16        17.49        12.30        19.27 
TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 
       63.72        43.20        47.80        40.83        26.04        26.04 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 
       25.35        10.88         0.95        11.97         7.92        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
       80.88        51.19        61.02        54.90        34.19        24.89 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 
       39.25        34.82         6.38        17.98        80.65       194.79 
TCGA-GL-7773 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
        4.60        68.12        13.41        11.84        56.75         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       21.34        16.34        12.36        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94        84.95        92.58        52.27        16.01        50.60 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PR 
       48.30        43.76        60.03        14.83         0.53        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-AB4C 
       52.11        30.67        25.68        27.39        12.99        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          0.10                           0.13 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        123.62                         194.79 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        16.325                         23.295 
[1] "0.1 - 123.6 (16.3)" "0.1 - 194.8 (23.3)"
[1] "hr=" "2.3"
D8V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  1(1P36.31) MUTATED        16        3        22        4
  DEL PEAK  1(1P36.31) WILD-TYPE     151       18        27       10
D8V3, multiclass
           clus
vv          DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  STAGE I                             16                            151
  STAGE II                             3                             18
  STAGE III                           22                             27
  STAGE IV                             4                             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  1(1P36.31) MUTATED    19   5    24
  DEL PEAK  1(1P36.31) WILD-TYPE 157  24    32
D8V4, multiclass
       clus
vv      DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T1                              19                            157
  T2                               5                             24
  T3+T4                           24                             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK  1(1P36.31) MUTATED    7 12  1
  DEL PEAK  1(1P36.31) WILD-TYPE 38 10  3
D8V5, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  N0                            7                             38
  N1                           12                             10
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED   16  3
  DEL PEAK  1(1P36.31) WILD-TYPE 74  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     16    3
  DEL PEAK  1(1P36.31) WILD-TYPE   74    6
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                           16                             74
  1                            3                              6
[1] 2 2
[1] FALSE
D8V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    19  31
  DEL PEAK  1(1P36.31) WILD-TYPE  53 166
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     19   31
  DEL PEAK  1(1P36.31) WILD-TYPE   53  166
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                           19                             53
  MALE                             31                            166
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
D8V10, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.31) MUTATED                                  0     2
  DEL PEAK  1(1P36.31) WILD-TYPE                                2     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.31) MUTATED                          12    33
  DEL PEAK  1(1P36.31) WILD-TYPE                        48   154
D8V11, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      33
                                  clus
vv                                 DEL PEAK  1(1P36.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    48
  WHITE                                                       154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED     1  39
  DEL PEAK  1(1P36.31) WILD-TYPE  11 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      1   39
  DEL PEAK  1(1P36.31) WILD-TYPE   11  181
                        clus
vv                       DEL PEAK  1(1P36.31) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           39
                        clus
vv                       DEL PEAK  1(1P36.31) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            181
[1] 2 2
[1] FALSE

Clustering(9) Variable = DEL PEAK  2(2P12) MUTATION ANALYSIS
D9V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  2(2P12) MUTATED     4   2
  DEL PEAK  2(2P12) WILD-TYPE 218  32
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          6                         250 
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          2                          32 
$`DEL PEAK  2(2P12) MUTATED`
TCGA-4A-A93X TCGA-A4-A57E TCGA-BQ-5875 TCGA-BQ-5885 TCGA-G7-6792 TCGA-UZ-A9PQ 
       12.82         8.48        86.76        30.28        48.62        86.27 

$`DEL PEAK  2(2P12) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        0.13        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU 
       19.63        19.73        14.33        12.46        16.96        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       76.64        13.55        30.35        25.08        44.61        49.25 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
        2.20        19.56         7.33        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        12.30        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 
       43.20        47.80        21.63        40.83        26.04        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.78        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84         6.38        17.98        17.33        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       16.34        12.36         0.13        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
       50.60        78.90        12.85        17.75        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR 
       18.02        60.03        14.83        21.93         0.53        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                       8.48                        0.10 
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                      86.76                      194.79 
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                     39.450                      20.975 
[1] "8.5 - 86.8 (39.5)"  "0.1 - 194.8 (21.0)"
[1] "hr=" "1.5"
D9V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  2(2P12) MUTATED         1        0         3        1
  DEL PEAK  2(2P12) WILD-TYPE     166       21        46       13
D9V3, multiclass
           clus
vv          DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  STAGE I                           1                         166
  STAGE II                          0                          21
  STAGE III                         3                          46
  STAGE IV                          1                          13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2 T3+T4
  DEL PEAK  2(2P12) MUTATED     1   2     2
  DEL PEAK  2(2P12) WILD-TYPE 175  27    54
D9V4, multiclass
       clus
vv      DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  T1                            1                         175
  T2                            2                          27
  T3+T4                         2                          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"
                             vv
clus                          N0 N1 N2
  DEL PEAK  2(2P12) MUTATED    2  1  0
  DEL PEAK  2(2P12) WILD-TYPE 43 21  4
D9V5, multiclass
    clus
vv   DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  N0                         2                          43
  N1                         1                          21
  N2                         0                           4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                             cls
clus                           0  1
  DEL PEAK  2(2P12) MUTATED    2  1
  DEL PEAK  2(2P12) WILD-TYPE 88  8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(2P12) MUTATED      2    1
  DEL PEAK  2(2P12) WILD-TYPE   88    8
   clus
vv  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  0                         2                          88
  1                         1                           8
[1] 2 2
[1] FALSE
D9V7, binary
                             cls
clus                            0   1
  DEL PEAK  2(2P12) MUTATED     1   5
  DEL PEAK  2(2P12) WILD-TYPE  71 192
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(2P12) MUTATED      1    5
  DEL PEAK  2(2P12) WILD-TYPE   71  192
        clus
vv       DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  FEMALE                         1                          71
  MALE                           5                         192
[1] 2 2
[1] FALSE
D9V8, continuous
[1] "Remove cluster labels:"    "DEL PEAK  2(2P12) MUTATED"
clus
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          2                          58 
                 TCGA-2Z-A9JK                  TCGA-4A-A93Y 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-A4-7286                  TCGA-A4-7828 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-A4-8310                  TCGA-A4-8311 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-A4-8312                  TCGA-A4-8518 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-A4-8630                  TCGA-A4-A4ZT 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-A4-A5DU                  TCGA-A4-A5XZ 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-A4-A6HP                  TCGA-AL-3466 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-DW-5560                  TCGA-DW-5561 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-DW-7834                  TCGA-DW-7836 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-DW-7837                  TCGA-DW-7838 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-DW-7839                  TCGA-DW-7840 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-DW-7841                  TCGA-DW-7842 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-DW-7963                  TCGA-EV-5901 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-EV-5902                  TCGA-EV-5903 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-6790                  TCGA-G7-6793 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-6796                  TCGA-G7-6797 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-7501                  TCGA-G7-7502 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-A4TM                  TCGA-G7-A8LB 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-A8LC                  TCGA-G7-A8LD 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-A8LE                  TCGA-IA-A40U 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-IA-A40X                  TCGA-IA-A40Y 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-J7-8537                  TCGA-P4-AAVK 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-Q2-A5QZ                  TCGA-SX-A71R 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A71S                  TCGA-SX-A71U 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A71V                  TCGA-SX-A7SL 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SM                  TCGA-SX-A7SN 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SO                  TCGA-SX-A7SP 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SQ                  TCGA-SX-A7SR 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SS                  TCGA-SX-A7SU 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
D9V9, continuous
[1] "Remove cluster labels:"    "DEL PEAK  2(2P12) MUTATED"
clus
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          1                          64 
                 TCGA-2Z-A9J2                  TCGA-2Z-A9J5 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-2Z-A9J7                  TCGA-2Z-A9J8 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-2Z-A9JD                  TCGA-2Z-A9JI 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-2Z-A9JK                  TCGA-2Z-A9JM 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-2Z-A9JN                  TCGA-2Z-A9JO 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-2Z-A9JQ                  TCGA-4A-A93W 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-4A-A93Y                  TCGA-A4-8310 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-A4-A48D                  TCGA-A4-A5Y0 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-AL-3466                  TCGA-AL-3472 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-AL-7173                  TCGA-B1-A654 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-B9-4115                  TCGA-B9-4117 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-B9-7268                  TCGA-B9-A44B 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-B9-A69E                  TCGA-DW-5561 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-DW-7834                  TCGA-DW-7963 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-F9-A97G                  TCGA-G7-7501 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-A8LB                  TCGA-G7-A8LD 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-A8LE                  TCGA-GL-7773 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-GL-A59T                  TCGA-GL-A9DD 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-HE-A5NI                  TCGA-HE-A5NJ 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-HE-A5NK                  TCGA-IA-A40U 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-IA-A83S                  TCGA-IZ-A6M8 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-MH-A854                  TCGA-MH-A856 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-P4-A5E7                  TCGA-P4-A5EB 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-PJ-A5Z9                  TCGA-Q2-A5QZ 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A71S                  TCGA-SX-A71U 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SL                  TCGA-SX-A7SM 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SR                  TCGA-SX-A7SS 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-UZ-A9PM                  TCGA-UZ-A9PO 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-UZ-A9PR                  TCGA-UZ-A9PS 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-UZ-A9PX                  TCGA-WN-A9G9 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-Y8-A894                  TCGA-Y8-A896 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-Y8-A8RY                  TCGA-Y8-A8RZ 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
D9V10, continuous
[1] "Remove cluster labels:"    "DEL PEAK  2(2P12) MUTATED"
clus
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          1                          50 
                 TCGA-2Z-A9J3                  TCGA-2Z-A9J7 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-2Z-A9J8                  TCGA-2Z-A9JD 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-2Z-A9JI                  TCGA-2Z-A9JN 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-2Z-A9JO                  TCGA-4A-A93W 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-4A-A93Y                  TCGA-A4-A48D 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-A4-A5Y0                  TCGA-AL-3472 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-AL-7173                  TCGA-B1-A654 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-B9-4117                  TCGA-B9-A69E 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-DW-5561                  TCGA-DW-7963 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-F9-A97G                  TCGA-G7-7501 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-A8LB                  TCGA-G7-A8LD 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-A8LE                  TCGA-GL-7773 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-GL-A9DD                  TCGA-HE-A5NI 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-IA-A40U                  TCGA-MH-A854 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-MH-A856                  TCGA-P4-A5E6 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-P4-AAVK                  TCGA-PJ-A5Z9 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-Q2-A5QZ                  TCGA-SX-A71S 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A71U                  TCGA-SX-A7SL 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SM                  TCGA-SX-A7SR 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SS                  TCGA-UZ-A9PM 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-UZ-A9PO                  TCGA-UZ-A9PR 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-UZ-A9PS                  TCGA-UZ-A9PX 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-WN-A9G9                  TCGA-WN-AB4C 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-Y8-A894                  TCGA-Y8-A896 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-Y8-A8RY                  TCGA-Y8-A8RZ 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(2P12) MUTATED                                  0     0
  DEL PEAK  2(2P12) WILD-TYPE                                2     5
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(2P12) MUTATED                           2     4
  DEL PEAK  2(2P12) WILD-TYPE                        58   183
D9V11, multiclass
                                  clus
vv                                 DEL PEAK  2(2P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                    4
                                  clus
vv                                 DEL PEAK  2(2P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 58
  WHITE                                                    183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
                             cls
clus                            0   1
  DEL PEAK  2(2P12) MUTATED     0   5
  DEL PEAK  2(2P12) WILD-TYPE  12 215
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(2P12) MUTATED      0    5
  DEL PEAK  2(2P12) WILD-TYPE   12  215
                        clus
vv                       DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  HISPANIC OR LATINO                             0                          12
  NOT HISPANIC OR LATINO                         5                         215
[1] 2 2
[1] FALSE

Clustering(10) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED     6   2
  DEL PEAK  3(2Q22.1) WILD-TYPE 216  32
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            8                           248 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            2                            32 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B9-A69E TCGA-BQ-5878 
       51.52        12.82        12.99         9.63        14.86        63.72 
TCGA-BQ-5888 TCGA-Q2-A5QZ 
       13.25        14.07 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       11.57        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       15.75         8.28        12.46        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       30.35        25.08        44.61        49.25         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       19.23         6.81         0.16        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
       19.27         8.88        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5889 
       40.83        26.04        30.28        26.04        25.35        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        17.33        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                         9.63                          0.10 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                        63.72                        194.79 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                        13.66                         21.65 
[1] "9.6 - 63.7 (13.7)"  "0.1 - 194.8 (21.6)"
[1] "hr=" "2.3"
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  3(2Q22.1) MUTATED         1        0         6        1
  DEL PEAK  3(2Q22.1) WILD-TYPE     166       21        43       13
D10V3, multiclass
           clus
vv          DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE I                             1                           166
  STAGE II                            0                            21
  STAGE III                           6                            43
  STAGE IV                            1                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  DEL PEAK  3(2Q22.1) MUTATED     2   0     6
  DEL PEAK  3(2Q22.1) WILD-TYPE 174  29    50
D10V4, multiclass
       clus
vv      DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1                              2                           174
  T2                              0                            29
  T3+T4                           6                            50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  3(2Q22.1) MUTATED    1  3  0
  DEL PEAK  3(2Q22.1) WILD-TYPE 44 19  4
D10V5, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  N0                           1                            44
  N1                           3                            19
  N2                           0                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED    3  1
  DEL PEAK  3(2Q22.1) WILD-TYPE 87  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      3    1
  DEL PEAK  3(2Q22.1) WILD-TYPE   87    8
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                           3                            87
  1                           1                             8
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     4   5
  DEL PEAK  3(2Q22.1) WILD-TYPE  68 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      4    5
  DEL PEAK  3(2Q22.1) WILD-TYPE   68  192
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                           4                            68
  MALE                             5                           192
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
D10V10, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(2Q22.1) MUTATED                                  0     0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                2     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q22.1) MUTATED                           1     7
  DEL PEAK  3(2Q22.1) WILD-TYPE                        59   180
D10V11, multiclass
                                  clus
vv                                 DEL PEAK  3(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                      7
                                  clus
vv                                 DEL PEAK  3(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   59
  WHITE                                                      180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     0   6
  DEL PEAK  3(2Q22.1) WILD-TYPE  12 214
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      0    6
  DEL PEAK  3(2Q22.1) WILD-TYPE   12  214
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           6
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           214
[1] 2 2
[1] FALSE

Clustering(11) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.3) MUTATED     9   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 213  33
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           10                           246 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            1                            33 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-4A-A93X TCGA-A4-7585 TCGA-A4-A5Y0 TCGA-B3-4104 TCGA-B9-4117 TCGA-B9-A69E 
       12.82        35.18         8.28        34.49         0.46        14.86 
TCGA-BQ-5878 TCGA-MH-A855 TCGA-Q2-A5QZ TCGA-Y8-A8RZ 
       63.72        12.13        14.07         6.74 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        0.13        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
       15.75        12.99        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        6.81         0.16        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        17.33        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-MH-A857 
       30.38        27.65        20.25         0.36        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       48.30        43.76        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        15.62        25.28         6.02        13.28 

  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         0.46                          0.10 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                        63.72                        194.79 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       13.445                        21.650 
[1] "0.5 - 63.7 (13.4)"  "0.1 - 194.8 (21.6)"
[1] "hr=" "1.2"
D11V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  4(2Q37.3) MUTATED         2        2         5        0
  DEL PEAK  4(2Q37.3) WILD-TYPE     165       19        44       14
D11V3, multiclass
           clus
vv          DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  STAGE I                             2                           165
  STAGE II                            2                            19
  STAGE III                           5                            44
  STAGE IV                            0                            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  4(2Q37.3) MUTATED     2   3     5
  DEL PEAK  4(2Q37.3) WILD-TYPE 174  26    51
D11V4, multiclass
       clus
vv      DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  T1                              2                           174
  T2                              3                            26
  T3+T4                           5                            51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  4(2Q37.3) MUTATED    2  1  0
  DEL PEAK  4(2Q37.3) WILD-TYPE 43 21  4
D11V5, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  N0                           2                            43
  N1                           1                            21
  N2                           0                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.3) MUTATED    4  0
  DEL PEAK  4(2Q37.3) WILD-TYPE 86  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      4    0
  DEL PEAK  4(2Q37.3) WILD-TYPE   86    9
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                           4                            86
  1                           0                             9
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     6   5
  DEL PEAK  4(2Q37.3) WILD-TYPE  66 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      6    5
  DEL PEAK  4(2Q37.3) WILD-TYPE   66  192
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                           6                            66
  MALE                             5                           192
[1] 2 2
[1] FALSE
D11V8, continuous
[1] "Remove cluster labels:"      "DEL PEAK  4(2Q37.3) MUTATED"
clus
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            2                            58 
                   TCGA-2Z-A9JK                    TCGA-4A-A93Y 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-7286                    TCGA-A4-7828 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-8310                    TCGA-A4-8311 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-8312                    TCGA-A4-8518 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-8630                    TCGA-A4-A4ZT 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-A57E                    TCGA-A4-A5DU 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-A5XZ                    TCGA-A4-A6HP 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-AL-3466                    TCGA-DW-5560 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DW-5561                    TCGA-DW-7834 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7836                    TCGA-DW-7837 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7838                    TCGA-DW-7839 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7840                    TCGA-DW-7841 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7842                    TCGA-DW-7963 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-EV-5901                    TCGA-EV-5902 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-EV-5903                    TCGA-G7-6790 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-6793                    TCGA-G7-6796 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-6797                    TCGA-G7-7501 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-7502                    TCGA-G7-A4TM 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-A8LB                    TCGA-G7-A8LC 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-A8LD                    TCGA-G7-A8LE 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-IA-A40U                    TCGA-IA-A40X 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-IA-A40Y                    TCGA-J7-8537 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-P4-AAVK                    TCGA-SX-A71R 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A71S                    TCGA-SX-A71U 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A71V                    TCGA-SX-A7SL 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SM                    TCGA-SX-A7SN 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SO                    TCGA-SX-A7SP 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SQ                    TCGA-SX-A7SR 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SS                    TCGA-SX-A7SU 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
D11V9, continuous
D11V10, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2Q37.3) MUTATED                                  0     0
  DEL PEAK  4(2Q37.3) WILD-TYPE                                2     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED                           3     7
  DEL PEAK  4(2Q37.3) WILD-TYPE                        57   180
D11V11, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                      7
                                  clus
vv                                 DEL PEAK  4(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   57
  WHITE                                                      180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     0   9
  DEL PEAK  4(2Q37.3) WILD-TYPE  12 211
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      0    9
  DEL PEAK  4(2Q37.3) WILD-TYPE   12  211
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           211
[1] 2 2
[1] FALSE

Clustering(12) Variable = DEL PEAK  5(3P22.1) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(3P22.1) MUTATED    16   7
  DEL PEAK  5(3P22.1) WILD-TYPE 206  27
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                           23                           233 
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                            7                            27 
$`DEL PEAK  5(3P22.1) MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3473 
       54.64        51.52        38.99         8.48        12.99        25.08 
TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5892 TCGA-DZ-6131 
        2.10        14.86         8.88        21.63        11.97        79.86 
TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y 
        4.01        13.68        17.33        16.90         3.68         2.04 
TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UZ-A9PQ TCGA-WN-A9G9 TCGA-Y8-A8RZ 
        0.13        14.07        86.27        26.01         6.74 

$`DEL PEAK  5(3P22.1) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ 
        4.57        67.30        75.42        34.85        56.81        35.67 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
        5.29        16.18        22.49         0.13        12.82        11.57 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       14.33        12.46        16.96        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       15.12        43.99        22.06        19.23         6.81         0.16 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        12.30        86.76        19.27        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       43.20        47.80        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       25.35        13.25        10.88         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        40.77        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       54.90        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       39.25        34.82        25.15        25.84         6.38        17.98 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65       194.79        12.92        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       21.93         0.53        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       27.39        12.99        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.02        13.28 

  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                         0.13                          0.10 
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                        86.27                        194.79 
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                        14.07                         22.06 
[1] "0.1 - 86.3 (14.1)"  "0.1 - 194.8 (22.1)"
[1] "hr=" "3.4"
D12V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  5(3P22.1) MUTATED         5        1        14        3
  DEL PEAK  5(3P22.1) WILD-TYPE     162       20        35       11
D12V3, multiclass
           clus
vv          DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  STAGE I                             5                           162
  STAGE II                            1                            20
  STAGE III                          14                            35
  STAGE IV                            3                            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(3P22.1) MUTATED     6   3    14
  DEL PEAK  5(3P22.1) WILD-TYPE 170  26    42
D12V4, multiclass
       clus
vv      DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  T1                              6                           170
  T2                              3                            26
  T3+T4                          14                            42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  5(3P22.1) MUTATED    6  8  1
  DEL PEAK  5(3P22.1) WILD-TYPE 39 14  3
D12V5, multiclass
    clus
vv   DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  N0                           6                            39
  N1                           8                            14
  N2                           1                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P22.1) MUTATED    4  2
  DEL PEAK  5(3P22.1) WILD-TYPE 86  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED      4    2
  DEL PEAK  5(3P22.1) WILD-TYPE   86    7
   clus
vv  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  0                           4                            86
  1                           2                             7
[1] 2 2
[1] FALSE
D12V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P22.1) MUTATED     6  17
  DEL PEAK  5(3P22.1) WILD-TYPE  66 180
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED      6   17
  DEL PEAK  5(3P22.1) WILD-TYPE   66  180
        clus
vv       DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  FEMALE                           6                            66
  MALE                            17                           180
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
D12V10, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(3P22.1) MUTATED                                  0     1
  DEL PEAK  5(3P22.1) WILD-TYPE                                2     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P22.1) MUTATED                           5    16
  DEL PEAK  5(3P22.1) WILD-TYPE                        55   171
D12V11, multiclass
                                  clus
vv                                 DEL PEAK  5(3P22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     16
                                  clus
vv                                 DEL PEAK  5(3P22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   55
  WHITE                                                      171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P22.1) MUTATED     0  20
  DEL PEAK  5(3P22.1) WILD-TYPE  12 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED      0   20
  DEL PEAK  5(3P22.1) WILD-TYPE   12  200
                        clus
vv                       DEL PEAK  5(3P22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          20
                        clus
vv                       DEL PEAK  5(3P22.1) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           200
[1] 2 2
[1] FALSE

Clustering(13) Variable = DEL PEAK  6(4Q34.3) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(4Q34.3) MUTATED    21   8
  DEL PEAK  6(4Q34.3) WILD-TYPE 201  26
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           29                           227 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                            8                            26 
$`DEL PEAK  6(4Q34.3) MUTATED`
TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7287 TCGA-A4-8098 TCGA-A4-A57E TCGA-A4-A5Y1 
       51.52        12.82        19.63        29.46         8.48        12.99 
TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-3926 TCGA-B3-4104 TCGA-BQ-5876 TCGA-BQ-5882 
       49.25         7.33        10.09        34.49        19.27        21.63 
TCGA-BQ-5890 TCGA-BQ-5894 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G 
        7.66         2.76        79.86        10.68        13.08         0.43 
TCGA-G7-7501 TCGA-GL-7966 TCGA-HE-A5NK TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5E8 
       13.68         3.68        73.25         2.04         0.13        42.94 
TCGA-P4-A5EA TCGA-P4-AAVK TCGA-Q2-A5QZ TCGA-SX-A7SS TCGA-UN-AAZ9 
        6.61        52.27        14.07        48.30        18.02 

$`DEL PEAK  6(4Q34.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       11.57        18.21        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23        16.64        30.48        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       12.46        16.96        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       44.61         2.20        19.56        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 
        3.55        16.77         0.46         6.58        33.83        30.58 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23         6.81         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 
       10.88         0.95        11.97         7.92       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       24.89         2.40         1.18         4.01        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM 
       11.05        39.25        34.82        25.15        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        17.33        16.90        80.65       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
        4.60        68.12        13.41        11.84        56.75         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       21.34        16.34        12.36        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       84.95        92.58        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       43.76        60.03        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                         0.13                          0.10 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                        79.86                        194.79 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                        13.68                         22.26 
[1] "0.1 - 79.9 (13.7)"  "0.1 - 194.8 (22.3)"
[1] "hr=" "3.4"
D13V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  6(4Q34.3) MUTATED         7        2        16        2
  DEL PEAK  6(4Q34.3) WILD-TYPE     160       19        33       12
D13V3, multiclass
           clus
vv          DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  STAGE I                             7                           160
  STAGE II                            2                            19
  STAGE III                          16                            33
  STAGE IV                            2                            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  6(4Q34.3) MUTATED     9   4    15
  DEL PEAK  6(4Q34.3) WILD-TYPE 167  25    41
D13V4, multiclass
       clus
vv      DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  T1                              9                           167
  T2                              4                            25
  T3+T4                          15                            41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  6(4Q34.3) MUTATED    7  8  0
  DEL PEAK  6(4Q34.3) WILD-TYPE 38 14  4
D13V5, multiclass
    clus
vv   DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  N0                           7                            38
  N1                           8                            14
  N2                           0                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED   12  2
  DEL PEAK  6(4Q34.3) WILD-TYPE 78  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     12    2
  DEL PEAK  6(4Q34.3) WILD-TYPE   78    7
   clus
vv  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  0                          12                            78
  1                           2                             7
[1] 2 2
[1] FALSE
D13V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(4Q34.3) MUTATED    14  16
  DEL PEAK  6(4Q34.3) WILD-TYPE  58 181
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     14   16
  DEL PEAK  6(4Q34.3) WILD-TYPE   58  181
        clus
vv       DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  FEMALE                          14                            58
  MALE                            16                           181
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
D13V10, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(4Q34.3) MUTATED                                  0     3
  DEL PEAK  6(4Q34.3) WILD-TYPE                                2     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4Q34.3) MUTATED                           6    17
  DEL PEAK  6(4Q34.3) WILD-TYPE                        54   170
D13V11, multiclass
                                  clus
vv                                 DEL PEAK  6(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     17
                                  clus
vv                                 DEL PEAK  6(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   54
  WHITE                                                      170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, binary
                               cls
clus                              0   1
  DEL PEAK  6(4Q34.3) MUTATED     2  22
  DEL PEAK  6(4Q34.3) WILD-TYPE  10 198
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED      2   22
  DEL PEAK  6(4Q34.3) WILD-TYPE   10  198
                        clus
vv                       DEL PEAK  6(4Q34.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          22
                        clus
vv                       DEL PEAK  6(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           198
[1] 2 2
[1] FALSE

Clustering(14) Variable = DEL PEAK  7(5P15.33) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  7(5P15.33) MUTATED     8   4
  DEL PEAK  7(5P15.33) WILD-TYPE 214  30
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                            12                            244 
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                             4                             30 
$`DEL PEAK  7(5P15.33) MUTATED`
TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9JJ TCGA-A4-7286 TCGA-BQ-5878 TCGA-BQ-5879 
       59.01        67.30        35.67        18.21        63.72        22.92 
TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-G7-6793 TCGA-GL-7773 TCGA-P4-A5E6 TCGA-P4-A5EA 
        2.76        10.68        11.05        12.92        99.78         6.61 

$`DEL PEAK  7(5P15.33) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        75.55        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
       75.42        34.85        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
        5.29        16.18        22.49         0.13        12.82        11.57 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       12.99        12.46         9.63        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       30.35        25.08        44.61        49.25         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23         6.81         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
       86.76        19.27         8.88        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 
       10.88         7.66         0.95        11.97         7.92       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       34.19        19.00        24.89        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        0.43         4.01        51.78        48.62        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        13.68        25.84         6.38        17.98        17.33 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       16.90        80.65       194.79         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E7 
        0.36        12.13        25.97        21.44        15.48        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       78.90        12.85        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                          2.76                           0.10 
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                         99.78                         194.79 
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                        20.565                         21.390 
[1] "2.8 - 99.8 (20.6)"  "0.1 - 194.8 (21.4)"
[1] "hr=" "2.1"
D14V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  7(5P15.33) MUTATED         5        0         5        2
  DEL PEAK  7(5P15.33) WILD-TYPE     162       21        44       12
D14V3, multiclass
           clus
vv          DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE
  STAGE I                              5                            162
  STAGE II                             0                             21
  STAGE III                            5                             44
  STAGE IV                             2                             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  7(5P15.33) MUTATED     5   1     7
  DEL PEAK  7(5P15.33) WILD-TYPE 171  28    49
D14V4, multiclass
       clus
vv      DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE
  T1                               5                            171
  T2                               1                             28
  T3+T4                            7                             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK  7(5P15.33) MUTATED    0  5  1
  DEL PEAK  7(5P15.33) WILD-TYPE 45 17  3
D14V5, multiclass
    clus
vv   DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE
  N0                            0                             45
  N1                            5                             17
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                                cls
clus                              0  1
  DEL PEAK  7(5P15.33) MUTATED    4  1
  DEL PEAK  7(5P15.33) WILD-TYPE 86  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(5P15.33) MUTATED      4    1
  DEL PEAK  7(5P15.33) WILD-TYPE   86    8
   clus
vv  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE
  0                            4                             86
  1                            1                              8
[1] 2 2
[1] FALSE
D14V7, binary
                                cls
clus                               0   1
  DEL PEAK  7(5P15.33) MUTATED     7   6
  DEL PEAK  7(5P15.33) WILD-TYPE  65 191
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(5P15.33) MUTATED      7    6
  DEL PEAK  7(5P15.33) WILD-TYPE   65  191
        clus
vv       DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE
  FEMALE                            7                             65
  MALE                              6                            191
[1] 2 2
[1] FALSE
D14V8, continuous
[1] "Remove cluster labels:"       "DEL PEAK  7(5P15.33) MUTATED"
clus
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                             2                             58 
                    TCGA-2Z-A9JK                     TCGA-4A-A93X 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-4A-A93Y                     TCGA-A4-7828 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-8310                     TCGA-A4-8311 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-8312                     TCGA-A4-8518 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-8630                     TCGA-A4-A4ZT 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-A57E                     TCGA-A4-A5DU 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-A5XZ                     TCGA-A4-A6HP 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-AL-3466                     TCGA-DW-5560 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-5561                     TCGA-DW-7834 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-7836                     TCGA-DW-7837 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-7838                     TCGA-DW-7839 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-7840                     TCGA-DW-7841 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-7842                     TCGA-DW-7963 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-EV-5901                     TCGA-EV-5902 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-EV-5903                     TCGA-G7-6790 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-6796                     TCGA-G7-6797 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-7501                     TCGA-G7-7502 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-A4TM                     TCGA-G7-A8LB 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-A8LC                     TCGA-G7-A8LD 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-A8LE                     TCGA-IA-A40U 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-IA-A40X                     TCGA-IA-A40Y 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-J7-8537                     TCGA-P4-AAVK 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-Q2-A5QZ                     TCGA-SX-A71R 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A71S                     TCGA-SX-A71U 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A71V                     TCGA-SX-A7SL 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A7SM                     TCGA-SX-A7SN 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A7SO                     TCGA-SX-A7SP 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A7SQ                     TCGA-SX-A7SR 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A7SS                     TCGA-SX-A7SU 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
D14V9, continuous
D14V10, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(5P15.33) MUTATED                                  0     0
  DEL PEAK  7(5P15.33) WILD-TYPE                                2     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(5P15.33) MUTATED                           2     9
  DEL PEAK  7(5P15.33) WILD-TYPE                        58   178
D14V11, multiclass
                                  clus
vv                                 DEL PEAK  7(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                       9
                                  clus
vv                                 DEL PEAK  7(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    58
  WHITE                                                       178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                                cls
clus                               0   1
  DEL PEAK  7(5P15.33) MUTATED     1   8
  DEL PEAK  7(5P15.33) WILD-TYPE  11 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(5P15.33) MUTATED      1    8
  DEL PEAK  7(5P15.33) WILD-TYPE   11  212
                        clus
vv                       DEL PEAK  7(5P15.33) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            8
                        clus
vv                       DEL PEAK  7(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            212
[1] 2 2
[1] FALSE

Clustering(15) Variable = DEL PEAK  8(5Q35.2) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(5Q35.2) MUTATED     5   5
  DEL PEAK  8(5Q35.2) WILD-TYPE 217  29
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                           10                           246 
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                            5                            29 
$`DEL PEAK  8(5Q35.2) MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-AL-A5DJ TCGA-B3-4104 TCGA-BQ-5879 TCGA-BQ-5894 
       18.21        19.63        49.25        34.49        22.92         2.76 
TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-GL-7966 TCGA-P4-A5EA 
       79.86        10.68         3.68         6.61 

$`DEL PEAK  8(5Q35.2) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
        0.13        12.82        11.57        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       76.64        13.55        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23         6.81         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76        19.27         8.88        63.72        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        40.77        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       34.19        19.00        24.89        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       17.33        16.90        80.65       194.79        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       16.80        19.99         2.04        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.22        42.94        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       16.01        50.60        78.90        12.85        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                         2.76                          0.10 
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                        79.86                        194.79 
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                       18.920                        21.535 
[1] "2.8 - 79.9 (18.9)"  "0.1 - 194.8 (21.5)"
[1] "hr=" "5.5"
D15V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  8(5Q35.2) MUTATED         1        1         7        1
  DEL PEAK  8(5Q35.2) WILD-TYPE     166       20        42       13
D15V3, multiclass
           clus
vv          DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  STAGE I                             1                           166
  STAGE II                            1                            20
  STAGE III                           7                            42
  STAGE IV                            1                            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  8(5Q35.2) MUTATED     1   1     9
  DEL PEAK  8(5Q35.2) WILD-TYPE 175  28    47
D15V4, multiclass
       clus
vv      DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  T1                              1                           175
  T2                              1                            28
  T3+T4                           9                            47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  8(5Q35.2) MUTATED    1  4  0
  DEL PEAK  8(5Q35.2) WILD-TYPE 44 18  4
D15V5, multiclass
    clus
vv   DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  N0                           1                            44
  N1                           4                            18
  N2                           0                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                               cls
clus                             0  1
  DEL PEAK  8(5Q35.2) MUTATED    3  1
  DEL PEAK  8(5Q35.2) WILD-TYPE 87  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5Q35.2) MUTATED      3    1
  DEL PEAK  8(5Q35.2) WILD-TYPE   87    8
   clus
vv  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  0                           3                            87
  1                           1                             8
[1] 2 2
[1] FALSE
D15V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(5Q35.2) MUTATED     7   4
  DEL PEAK  8(5Q35.2) WILD-TYPE  65 193
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5Q35.2) MUTATED      7    4
  DEL PEAK  8(5Q35.2) WILD-TYPE   65  193
        clus
vv       DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  FEMALE                           7                            65
  MALE                             4                           193
[1] 2 2
[1] FALSE
D15V8, continuous
[1] "Remove cluster labels:"      "DEL PEAK  8(5Q35.2) MUTATED"
clus
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                            1                            59 
                   TCGA-2Z-A9JK                    TCGA-4A-A93X 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-4A-A93Y                    TCGA-A4-7828 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-8310                    TCGA-A4-8311 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-8312                    TCGA-A4-8518 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-8630                    TCGA-A4-A4ZT 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-A57E                    TCGA-A4-A5DU 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-A5XZ                    TCGA-A4-A6HP 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-AL-3466                    TCGA-DW-5560 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-5561                    TCGA-DW-7834 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7836                    TCGA-DW-7837 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7838                    TCGA-DW-7839 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7840                    TCGA-DW-7841 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7842                    TCGA-DW-7963 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-EV-5901                    TCGA-EV-5902 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-EV-5903                    TCGA-G7-6790 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-6793                    TCGA-G7-6796 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-6797                    TCGA-G7-7501 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-7502                    TCGA-G7-A4TM 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-A8LB                    TCGA-G7-A8LC 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-A8LD                    TCGA-G7-A8LE 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-IA-A40U                    TCGA-IA-A40X 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-IA-A40Y                    TCGA-J7-8537 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-P4-AAVK                    TCGA-Q2-A5QZ 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A71R                    TCGA-SX-A71S 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A71U                    TCGA-SX-A71V 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SL                    TCGA-SX-A7SM 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SN                    TCGA-SX-A7SO 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SP                    TCGA-SX-A7SQ 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SR                    TCGA-SX-A7SS 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SU 
"DEL PEAK  8(5Q35.2) WILD-TYPE" 
D15V9, continuous
D15V10, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(5Q35.2) MUTATED                                  0     0
  DEL PEAK  8(5Q35.2) WILD-TYPE                                2     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(5Q35.2) MUTATED                           1     8
  DEL PEAK  8(5Q35.2) WILD-TYPE                        59   179
D15V11, multiclass
                                  clus
vv                                 DEL PEAK  8(5Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                      8
                                  clus
vv                                 DEL PEAK  8(5Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   59
  WHITE                                                      179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                               cls
clus                              0   1
  DEL PEAK  8(5Q35.2) MUTATED     1   6
  DEL PEAK  8(5Q35.2) WILD-TYPE  11 214
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5Q35.2) MUTATED      1    6
  DEL PEAK  8(5Q35.2) WILD-TYPE   11  214
                        clus
vv                       DEL PEAK  8(5Q35.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           6
                        clus
vv                       DEL PEAK  8(5Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           214
[1] 2 2
[1] FALSE

Clustering(16) Variable = DEL PEAK  9(6P12.3) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(6P12.3) MUTATED    17   5
  DEL PEAK  9(6P12.3) WILD-TYPE 205  29
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                           22                           234 
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                            5                            29 
$`DEL PEAK  9(6P12.3) MUTATED`
TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-A4-7286 TCGA-AL-A5DJ TCGA-B3-3926 
       67.30        54.64        51.52        18.21        49.25        10.09 
TCGA-B9-A44B TCGA-BQ-5882 TCGA-BQ-5890 TCGA-BQ-7048 TCGA-BQ-7056 TCGA-EV-5902 
        2.10        21.63         7.66        93.34        20.12        19.00 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A8LC 
       13.08         4.01        11.05        25.15        25.84        17.33 
TCGA-P4-A5E8 TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-Y8-A896 
       42.94        27.06        18.02        18.64 

$`DEL PEAK  9(6P12.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JK 
        4.57        75.42        34.85        56.81        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
        5.29        16.18        22.49         0.13        12.82        11.57 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       12.99        12.46         9.63        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       30.35        25.08        44.61         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        6.58        33.83        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       15.12        43.99        22.06        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5891 
       30.28        26.04        25.35        13.25        10.88         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       44.84        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
       61.02        54.90        34.19        24.89        10.68         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        1.18         0.43        51.78        48.62        39.25        34.82 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       13.68         6.38        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA 
       25.97        21.44        15.48        99.78        87.22         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       12.85        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       26.47        48.30        43.76        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                          2.1                           0.1 
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                        93.34                        194.79 
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                       19.560                        21.555 
[1] "2.1 - 93.3 (19.6)"  "0.1 - 194.8 (21.6)"
[1] "hr=" "1.8"
D16V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  9(6P12.3) MUTATED         9        0        11        2
  DEL PEAK  9(6P12.3) WILD-TYPE     158       21        38       12
D16V3, multiclass
           clus
vv          DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  STAGE I                             9                           158
  STAGE II                            0                            21
  STAGE III                          11                            38
  STAGE IV                            2                            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  9(6P12.3) MUTATED    10   1    12
  DEL PEAK  9(6P12.3) WILD-TYPE 166  28    44
D16V4, multiclass
       clus
vv      DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  T1                             10                           166
  T2                              1                            28
  T3+T4                          12                            44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  9(6P12.3) MUTATED    5  1  2
  DEL PEAK  9(6P12.3) WILD-TYPE 40 21  2
D16V5, multiclass
    clus
vv   DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  N0                           5                            40
  N1                           1                            21
  N2                           2                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                               cls
clus                             0  1
  DEL PEAK  9(6P12.3) MUTATED   10  0
  DEL PEAK  9(6P12.3) WILD-TYPE 80  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6P12.3) MUTATED     10    0
  DEL PEAK  9(6P12.3) WILD-TYPE   80    9
   clus
vv  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  0                          10                            80
  1                           0                             9
[1] 2 2
[1] FALSE
D16V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(6P12.3) MUTATED     8  15
  DEL PEAK  9(6P12.3) WILD-TYPE  64 182
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6P12.3) MUTATED      8   15
  DEL PEAK  9(6P12.3) WILD-TYPE   64  182
        clus
vv       DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  FEMALE                           8                            64
  MALE                            15                           182
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
D16V10, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(6P12.3) MUTATED                                  0     1
  DEL PEAK  9(6P12.3) WILD-TYPE                                2     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(6P12.3) MUTATED                           2    17
  DEL PEAK  9(6P12.3) WILD-TYPE                        58   170
D16V11, multiclass
                                  clus
vv                                 DEL PEAK  9(6P12.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     17
                                  clus
vv                                 DEL PEAK  9(6P12.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   58
  WHITE                                                      170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, binary
                               cls
clus                              0   1
  DEL PEAK  9(6P12.3) MUTATED     0  19
  DEL PEAK  9(6P12.3) WILD-TYPE  12 201
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6P12.3) MUTATED      0   19
  DEL PEAK  9(6P12.3) WILD-TYPE   12  201
                        clus
vv                       DEL PEAK  9(6P12.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          19
                        clus
vv                       DEL PEAK  9(6P12.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           201
[1] 2 2
[1] FALSE

Clustering(17) Variable = DEL PEAK 10(6Q22.31) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 10(6Q22.31) MUTATED    21   5
  DEL PEAK 10(6Q22.31) WILD-TYPE 201  29
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                            26                            230 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                             5                             29 
$`DEL PEAK 10(6Q22.31) MUTATED`
TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-A4-7286 TCGA-B3-3926 
       67.30        54.64        51.52        35.67        18.21        10.09 
TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5882 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-7056 
        2.10        86.76        21.63        13.25        10.88        20.12 
TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LC 
       19.00        13.08         4.01        11.05        25.84        17.33 
TCGA-GL-7966 TCGA-J7-8537 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SL TCGA-UN-AAZ9 
        3.68         0.13        84.95        14.07        27.06        18.02 
TCGA-UZ-A9PQ TCGA-Y8-A896 
       86.27        18.64 

$`DEL PEAK 10(6Q22.31) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JL 
        4.57        75.42        34.85        56.81        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 
       16.18        22.49         0.13        12.82        11.57        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       25.08        44.61        49.25         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        6.58        33.83        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       15.12        43.99        22.06        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       14.86        17.49        12.30        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.20        47.80        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       26.04        25.35         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY 
       54.90        34.19        24.89        10.68         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        0.43        51.78        48.62        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       13.68         6.38        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
       12.92        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94         6.61        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        47.44        33.04        28.80        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS 
       60.03        14.83        21.93         0.53        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       18.64        15.91        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                         86.76                         194.79 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                        18.425                         21.995 
[1] "0.1 - 86.8 (18.4)"  "0.1 - 194.8 (22.0)"
[1] "hr=" "1.5"
D17V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 10(6Q22.31) MUTATED        12        0        11        3
  DEL PEAK 10(6Q22.31) WILD-TYPE     155       21        38       11
D17V3, multiclass
           clus
vv          DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  STAGE I                             12                            155
  STAGE II                             0                             21
  STAGE III                           11                             38
  STAGE IV                             3                             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 10(6Q22.31) MUTATED    12   1    14
  DEL PEAK 10(6Q22.31) WILD-TYPE 164  28    42
D17V4, multiclass
       clus
vv      DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  T1                              12                            164
  T2                               1                             28
  T3+T4                           14                             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 10(6Q22.31) MUTATED    4  4  2
  DEL PEAK 10(6Q22.31) WILD-TYPE 41 18  2
D17V5, multiclass
    clus
vv   DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  N0                            4                             41
  N1                            4                             18
  N2                            2                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                                cls
clus                              0  1
  DEL PEAK 10(6Q22.31) MUTATED   11  1
  DEL PEAK 10(6Q22.31) WILD-TYPE 79  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.31) MUTATED     11    1
  DEL PEAK 10(6Q22.31) WILD-TYPE   79    8
   clus
vv  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  0                           11                             79
  1                            1                              8
[1] 2 2
[1] FALSE
D17V7, binary
                                cls
clus                               0   1
  DEL PEAK 10(6Q22.31) MUTATED    13  14
  DEL PEAK 10(6Q22.31) WILD-TYPE  59 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.31) MUTATED     13   14
  DEL PEAK 10(6Q22.31) WILD-TYPE   59  183
        clus
vv       DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  FEMALE                           13                             59
  MALE                             14                            183
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
D17V10, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(6Q22.31) MUTATED                                  0     2
  DEL PEAK 10(6Q22.31) WILD-TYPE                                2     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6Q22.31) MUTATED                           4    18
  DEL PEAK 10(6Q22.31) WILD-TYPE                        56   169
D17V11, multiclass
                                  clus
vv                                 DEL PEAK 10(6Q22.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      18
                                  clus
vv                                 DEL PEAK 10(6Q22.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    56
  WHITE                                                       169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                                cls
clus                               0   1
  DEL PEAK 10(6Q22.31) MUTATED     0  21
  DEL PEAK 10(6Q22.31) WILD-TYPE  12 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.31) MUTATED      0   21
  DEL PEAK 10(6Q22.31) WILD-TYPE   12  199
                        clus
vv                       DEL PEAK 10(6Q22.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           21
                        clus
vv                       DEL PEAK 10(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            199
[1] 2 2
[1] FALSE

Clustering(18) Variable = DEL PEAK 11(6Q25.3) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(6Q25.3) MUTATED    23   5
  DEL PEAK 11(6Q25.3) WILD-TYPE 199  29
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                           28                           228 
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                            5                            29 
$`DEL PEAK 11(6Q25.3) MUTATED`
TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-A4-7286 TCGA-AL-A5DJ 
       67.30        54.64        51.52        35.67        18.21        49.25 
TCGA-B3-3926 TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5882 TCGA-BQ-5888 TCGA-BQ-5890 
       10.09         2.10        86.76        21.63        13.25         7.66 
TCGA-BQ-7056 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 
       20.12        19.00        13.08         4.01        11.05        25.84 
TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EB TCGA-Q2-A5QZ 
       17.33         3.68         2.04         0.13        84.95        14.07 
TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-UZ-A9PQ TCGA-Y8-A896 
       27.06        18.02        86.27        18.64 

$`DEL PEAK 11(6Q25.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JL 
        4.57        75.42        34.85        56.81        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 
       16.18        22.49         0.13        12.82        11.57        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       25.08        44.61         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       33.83        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       43.99        22.06        19.23         6.81         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        12.30        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       43.20        47.80        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.88         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       34.19        24.89        10.68         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.78        48.62        39.25        34.82        25.15        13.68 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
        6.38        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
        5.49        16.80        19.99        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
       22.26        21.34        16.34        12.36        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
        0.36        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       87.22        42.94         6.61        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
       50.60        78.90        12.85        17.75        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       33.04        28.80        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM 
       41.62        26.47        48.30        43.76        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       21.93         0.53        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                         0.13                          0.10 
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                        86.76                        194.79 
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                       18.425                        21.995 
[1] "0.1 - 86.8 (18.4)"  "0.1 - 194.8 (22.0)"
[1] "hr=" "1.4"
D18V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 11(6Q25.3) MUTATED        12        0        14        2
  DEL PEAK 11(6Q25.3) WILD-TYPE     155       21        35       12
D18V3, multiclass
           clus
vv          DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE
  STAGE I                            12                           155
  STAGE II                            0                            21
  STAGE III                          14                            35
  STAGE IV                            2                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  DEL PEAK 11(6Q25.3) MUTATED    12   1    16
  DEL PEAK 11(6Q25.3) WILD-TYPE 164  28    40
D18V4, multiclass
       clus
vv      DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE
  T1                             12                           164
  T2                              1                            28
  T3+T4                          16                            40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK 11(6Q25.3) MUTATED    5  4  2
  DEL PEAK 11(6Q25.3) WILD-TYPE 40 18  2
D18V5, multiclass
    clus
vv   DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE
  N0                           5                            40
  N1                           4                            18
  N2                           2                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                               cls
clus                             0  1
  DEL PEAK 11(6Q25.3) MUTATED   12  0
  DEL PEAK 11(6Q25.3) WILD-TYPE 78  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q25.3) MUTATED     12    0
  DEL PEAK 11(6Q25.3) WILD-TYPE   78    9
   clus
vv  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE
  0                          12                            78
  1                           0                             9
[1] 2 2
[1] FALSE
D18V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(6Q25.3) MUTATED    15  14
  DEL PEAK 11(6Q25.3) WILD-TYPE  57 183
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q25.3) MUTATED     15   14
  DEL PEAK 11(6Q25.3) WILD-TYPE   57  183
        clus
vv       DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE
  FEMALE                          15                            57
  MALE                            14                           183
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
D18V10, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(6Q25.3) MUTATED                                  0     2
  DEL PEAK 11(6Q25.3) WILD-TYPE                                2     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q25.3) MUTATED                           4    20
  DEL PEAK 11(6Q25.3) WILD-TYPE                        56   167
D18V11, multiclass
                                  clus
vv                                 DEL PEAK 11(6Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     20
                                  clus
vv                                 DEL PEAK 11(6Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   56
  WHITE                                                      167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, binary
                               cls
clus                              0   1
  DEL PEAK 11(6Q25.3) MUTATED     0  23
  DEL PEAK 11(6Q25.3) WILD-TYPE  12 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q25.3) MUTATED      0   23
  DEL PEAK 11(6Q25.3) WILD-TYPE   12  197
                        clus
vv                       DEL PEAK 11(6Q25.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          23
                        clus
vv                       DEL PEAK 11(6Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           197
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEL PEAK 12(9P21.3) MUTATION ANALYSIS
D19V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(9P21.3) MUTATED    22  14
  DEL PEAK 12(9P21.3) WILD-TYPE 200  20
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           36                           220 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           14                            20 
$`DEL PEAK 12(9P21.3) MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7287 
       54.64        51.52        35.67        12.82        18.21        19.63 
TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B9-4116 
        8.48        12.99         9.63        49.25        10.09        20.61 
TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-7048 
       14.86         8.88        22.92        13.25        10.88        93.34 
TCGA-BQ-7056 TCGA-DZ-6131 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 
       20.12        79.86        13.08         4.01        11.05        34.82 
TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 
       13.68        17.33        16.90         3.68         2.04         0.13 
TCGA-P4-A5EA TCGA-P4-AAVL TCGA-SX-A71V TCGA-UN-AAZ9 TCGA-UZ-A9PQ TCGA-Y8-A896 
        6.61        16.01        28.80        18.02        86.27        18.64 

$`DEL PEAK 12(9P21.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JK 
        4.57        67.30        75.42        34.85        56.81        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7288 
        5.29        16.18        22.49         0.13        11.57        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
       16.31        15.75         8.28        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       13.55        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        0.46         6.58        33.83        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
       10.16        50.50        28.18        26.40         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
        0.16        17.49        12.30        86.76        19.27        63.72 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       26.04        25.35         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       19.00        24.89        10.68         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM 
       51.78        48.62        39.25        25.15        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       17.98        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       16.34        12.36        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       84.95        92.58        52.27        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL 
       17.75        14.07        47.90        47.44        33.04        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       48.30        43.76        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 
       26.01        29.00        18.64        15.91        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                         0.13                          0.10 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                        93.34                        194.79 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                       16.455                        23.295 
[1] "0.1 - 93.3 (16.5)"  "0.1 - 194.8 (23.3)"
[1] "hr=" "5.1"
D19V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 12(9P21.3) MUTATED        10        0        18        6
  DEL PEAK 12(9P21.3) WILD-TYPE     157       21        31        8
D19V3, multiclass
           clus
vv          DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  STAGE I                            10                           157
  STAGE II                            0                            21
  STAGE III                          18                            31
  STAGE IV                            6                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  DEL PEAK 12(9P21.3) MUTATED    11   3    22
  DEL PEAK 12(9P21.3) WILD-TYPE 165  26    34
D19V4, multiclass
       clus
vv      DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  T1                             11                           165
  T2                              3                            26
  T3+T4                          22                            34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK 12(9P21.3) MUTATED    6 13  2
  DEL PEAK 12(9P21.3) WILD-TYPE 39  9  2
D19V5, multiclass
    clus
vv   DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  N0                           6                            39
  N1                          13                             9
  N2                           2                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                               cls
clus                             0  1
  DEL PEAK 12(9P21.3) MUTATED   10  4
  DEL PEAK 12(9P21.3) WILD-TYPE 80  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED     10    4
  DEL PEAK 12(9P21.3) WILD-TYPE   80    5
   clus
vv  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  0                          10                            80
  1                           4                             5
[1] 2 2
[1] FALSE
D19V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(9P21.3) MUTATED    18  20
  DEL PEAK 12(9P21.3) WILD-TYPE  54 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED     18   20
  DEL PEAK 12(9P21.3) WILD-TYPE   54  177
        clus
vv       DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  FEMALE                          18                            54
  MALE                            20                           177
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
D19V10, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(9P21.3) MUTATED                                  0     2
  DEL PEAK 12(9P21.3) WILD-TYPE                                2     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(9P21.3) MUTATED                           5    30
  DEL PEAK 12(9P21.3) WILD-TYPE                        55   157
D19V11, multiclass
                                  clus
vv                                 DEL PEAK 12(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     30
                                  clus
vv                                 DEL PEAK 12(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   55
  WHITE                                                      157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                               cls
clus                              0   1
  DEL PEAK 12(9P21.3) MUTATED     1  32
  DEL PEAK 12(9P21.3) WILD-TYPE  11 188
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED      1   32
  DEL PEAK 12(9P21.3) WILD-TYPE   11  188
                        clus
vv                       DEL PEAK 12(9P21.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          32
                        clus
vv                       DEL PEAK 12(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           188
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK 13(10Q21.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 13(10Q21.1) MUTATED    12   4
  DEL PEAK 13(10Q21.1) WILD-TYPE 210  30
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                            16                            240 
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                             4                             30 
$`DEL PEAK 13(10Q21.1) MUTATED`
TCGA-2Z-A9J8 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5882 
       67.30        12.99        49.25         2.10        19.27        21.63 
TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 
       79.86         4.01        13.68        25.84        17.33         3.68 
TCGA-J7-8537 TCGA-P4-A5E6 TCGA-P4-AAVO TCGA-Q2-A5QZ 
        0.13        99.78        78.90        14.07 

$`DEL PEAK 13(10Q21.1) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
        4.57        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       76.64        13.55        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23         6.81         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        40.77        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        1.18         0.43        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       34.82        25.15         6.38        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       21.44        15.48        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       92.58        52.27        16.01        50.60        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                         99.78                         194.79 
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                        18.300                         21.555 
[1] "0.1 - 99.8 (18.3)"  "0.1 - 194.8 (21.6)"
[1] "hr=" "1.7"
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 13(10Q21.1) MUTATED         4        0        11        1
  DEL PEAK 13(10Q21.1) WILD-TYPE     163       21        38       13
D20V3, multiclass
           clus
vv          DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE
  STAGE I                              4                            163
  STAGE II                             0                             21
  STAGE III                           11                             38
  STAGE IV                             1                             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(10Q21.1) MUTATED     6   0    10
  DEL PEAK 13(10Q21.1) WILD-TYPE 170  29    46
D20V4, multiclass
       clus
vv      DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE
  T1                               6                            170
  T2                               0                             29
  T3+T4                           10                             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"
                                vv
clus                             N0 N1 N2
  DEL PEAK 13(10Q21.1) MUTATED    2  5  1
  DEL PEAK 13(10Q21.1) WILD-TYPE 43 17  3
D20V5, multiclass
    clus
vv   DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE
  N0                            2                             43
  N1                            5                             17
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q21.1) MUTATED    4  0
  DEL PEAK 13(10Q21.1) WILD-TYPE 86  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q21.1) MUTATED      4    0
  DEL PEAK 13(10Q21.1) WILD-TYPE   86    9
   clus
vv  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE
  0                            4                             86
  1                            0                              9
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                               0   1
  DEL PEAK 13(10Q21.1) MUTATED     7  10
  DEL PEAK 13(10Q21.1) WILD-TYPE  65 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q21.1) MUTATED      7   10
  DEL PEAK 13(10Q21.1) WILD-TYPE   65  187
        clus
vv       DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE
  FEMALE                            7                             65
  MALE                             10                            187
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
D20V10, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(10Q21.1) MUTATED                                  0     1
  DEL PEAK 13(10Q21.1) WILD-TYPE                                2     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(10Q21.1) MUTATED                           4    10
  DEL PEAK 13(10Q21.1) WILD-TYPE                        56   177
D20V11, multiclass
                                  clus
vv                                 DEL PEAK 13(10Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      10
                                  clus
vv                                 DEL PEAK 13(10Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    56
  WHITE                                                       177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, binary
                                cls
clus                               0   1
  DEL PEAK 13(10Q21.1) MUTATED     0  13
  DEL PEAK 13(10Q21.1) WILD-TYPE  12 207
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q21.1) MUTATED      0   13
  DEL PEAK 13(10Q21.1) WILD-TYPE   12  207
                        clus
vv                       DEL PEAK 13(10Q21.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           13
                        clus
vv                       DEL PEAK 13(10Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            207
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK 14(11Q22.3) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 14(11Q22.3) MUTATED    19   9
  DEL PEAK 14(11Q22.3) WILD-TYPE 203  25
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                            28                            228 
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                             9                             25 
$`DEL PEAK 14(11Q22.3) MUTATED`
TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-A5Y1 
        4.57        56.81        54.64        51.52        12.82        12.99 
TCGA-B1-7332 TCGA-B3-4104 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5882 
        7.33        34.49         2.10        19.27         8.88        21.63 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6793 
       10.88         7.66       123.62         0.43         4.01        11.05 
TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-J7-8537 TCGA-PJ-A5Z8 TCGA-UZ-A9PQ 
       25.84        16.90         2.04         0.13        12.85        86.27 
TCGA-UZ-A9PS TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8S1 
       52.11        18.64        18.64        13.28 

$`DEL PEAK 14(11Q22.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       67.30        75.42        34.85        35.67        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 
       16.18        22.49         0.13        11.57        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       44.61        49.25         2.20        19.56        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       22.06        19.23         6.81         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       12.30        86.76        63.72        22.92        43.20        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         7.92         2.76        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 
       24.89        10.68        13.08         2.40         1.18        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
       48.62        39.25        34.82        25.15        13.68         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.98        17.33        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
        5.49        16.80        19.99        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
       22.26        21.34        16.34        12.36        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
        0.36        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.22        42.94         6.61        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
       16.01        50.60        78.90        17.75        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR 
       18.02        60.03        14.83        21.93         0.53        38.86 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       15.91        18.05        15.62        25.28         6.74         6.02 

  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                        123.62                         194.79 
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                        13.135                         22.375 
[1] "0.1 - 123.6 (13.1)" "0.1 - 194.8 (22.4)"
[1] "hr=" "3.4"
D21V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 14(11Q22.3) MUTATED         7        3        14        5
  DEL PEAK 14(11Q22.3) WILD-TYPE     160       18        35        9
D21V3, multiclass
           clus
vv          DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  STAGE I                              7                            160
  STAGE II                             3                             18
  STAGE III                           14                             35
  STAGE IV                             5                              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 14(11Q22.3) MUTATED     8   5    16
  DEL PEAK 14(11Q22.3) WILD-TYPE 168  24    40
D21V4, multiclass
       clus
vv      DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  T1                               8                            168
  T2                               5                             24
  T3+T4                           16                             40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 14(11Q22.3) MUTATED    3  8  2
  DEL PEAK 14(11Q22.3) WILD-TYPE 42 14  2
D21V5, multiclass
    clus
vv   DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  N0                            3                             42
  N1                            8                             14
  N2                            2                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                                cls
clus                              0  1
  DEL PEAK 14(11Q22.3) MUTATED    9  3
  DEL PEAK 14(11Q22.3) WILD-TYPE 81  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q22.3) MUTATED      9    3
  DEL PEAK 14(11Q22.3) WILD-TYPE   81    6
   clus
vv  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  0                            9                             81
  1                            3                              6
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                               0   1
  DEL PEAK 14(11Q22.3) MUTATED     9  21
  DEL PEAK 14(11Q22.3) WILD-TYPE  63 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q22.3) MUTATED      9   21
  DEL PEAK 14(11Q22.3) WILD-TYPE   63  176
        clus
vv       DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  FEMALE                            9                             63
  MALE                             21                            176
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
D21V10, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(11Q22.3) MUTATED                                  0     2
  DEL PEAK 14(11Q22.3) WILD-TYPE                                2     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(11Q22.3) MUTATED                           5    21
  DEL PEAK 14(11Q22.3) WILD-TYPE                        55   166
D21V11, multiclass
                                  clus
vv                                 DEL PEAK 14(11Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      21
                                  clus
vv                                 DEL PEAK 14(11Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    55
  WHITE                                                       166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                                cls
clus                               0   1
  DEL PEAK 14(11Q22.3) MUTATED     0  25
  DEL PEAK 14(11Q22.3) WILD-TYPE  12 195
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q22.3) MUTATED      0   25
  DEL PEAK 14(11Q22.3) WILD-TYPE   12  195
                        clus
vv                       DEL PEAK 14(11Q22.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           25
                        clus
vv                       DEL PEAK 14(11Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            195
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK 15(11Q23.3) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 15(11Q23.3) MUTATED    16  10
  DEL PEAK 15(11Q23.3) WILD-TYPE 206  24
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                            26                            230 
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                            10                             24 
$`DEL PEAK 15(11Q23.3) MUTATED`
TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-A5Y1 
        4.57        56.81        54.64        51.52        12.82        12.99 
TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-4104 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 
       49.25         7.33        34.49         2.10        19.27         8.88 
TCGA-BQ-5882 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-F9-A97G TCGA-G7-6789 
       21.63        10.88         7.66       123.62         0.43         4.01 
TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-J7-8537 TCGA-UZ-A9PQ 
       11.05        25.84        16.90         2.04         0.13        86.27 
TCGA-Y8-A896 TCGA-Y8-A8S1 
       18.64        13.28 

$`DEL PEAK 15(11Q23.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       67.30        75.42        34.85        35.67        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 
       16.18        22.49         0.13        11.57        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       44.61         2.20        19.56        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23         6.81         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       86.76        63.72        22.92        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 
       26.04        30.28        26.04        25.35        13.25         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
       11.97         7.92         2.76        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 
       10.68        13.08         2.40         1.18        51.78        48.62 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
       39.25        34.82        25.15        13.68         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       17.33        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       21.34        16.34        12.36        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
       50.60        78.90        12.85        17.75        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR 
       18.02        60.03        14.83        21.93         0.53        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       29.00        18.64        15.91        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 
        6.74         6.02 

  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                        123.62                         194.79 
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                        13.135                         22.160 
[1] "0.1 - 123.6 (13.1)" "0.1 - 194.8 (22.2)"
[1] "hr=" "4.2"
D22V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 15(11Q23.3) MUTATED         5        2        15        5
  DEL PEAK 15(11Q23.3) WILD-TYPE     162       19        34        9
D22V3, multiclass
           clus
vv          DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  STAGE I                              5                            162
  STAGE II                             2                             19
  STAGE III                           15                             34
  STAGE IV                             5                              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 15(11Q23.3) MUTATED     6   4    17
  DEL PEAK 15(11Q23.3) WILD-TYPE 170  25    39
D22V4, multiclass
       clus
vv      DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  T1                               6                            170
  T2                               4                             25
  T3+T4                           17                             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 15(11Q23.3) MUTATED    3  8  2
  DEL PEAK 15(11Q23.3) WILD-TYPE 42 14  2
D22V5, multiclass
    clus
vv   DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  N0                            3                             42
  N1                            8                             14
  N2                            2                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                                cls
clus                              0  1
  DEL PEAK 15(11Q23.3) MUTATED    8  3
  DEL PEAK 15(11Q23.3) WILD-TYPE 82  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q23.3) MUTATED      8    3
  DEL PEAK 15(11Q23.3) WILD-TYPE   82    6
   clus
vv  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  0                            8                             82
  1                            3                              6
[1] 2 2
[1] FALSE
D22V7, binary
                                cls
clus                               0   1
  DEL PEAK 15(11Q23.3) MUTATED     7  21
  DEL PEAK 15(11Q23.3) WILD-TYPE  65 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q23.3) MUTATED      7   21
  DEL PEAK 15(11Q23.3) WILD-TYPE   65  176
        clus
vv       DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  FEMALE                            7                             65
  MALE                             21                            176
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
D22V10, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(11Q23.3) MUTATED                                  0     2
  DEL PEAK 15(11Q23.3) WILD-TYPE                                2     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(11Q23.3) MUTATED                           4    20
  DEL PEAK 15(11Q23.3) WILD-TYPE                        56   167
D22V11, multiclass
                                  clus
vv                                 DEL PEAK 15(11Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      20
                                  clus
vv                                 DEL PEAK 15(11Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    56
  WHITE                                                       167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                                cls
clus                               0   1
  DEL PEAK 15(11Q23.3) MUTATED     0  23
  DEL PEAK 15(11Q23.3) WILD-TYPE  12 197
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q23.3) MUTATED      0   23
  DEL PEAK 15(11Q23.3) WILD-TYPE   12  197
                        clus
vv                       DEL PEAK 15(11Q23.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           23
                        clus
vv                       DEL PEAK 15(11Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            197
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK 16(14Q11.2) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 16(14Q11.2) MUTATED    37  10
  DEL PEAK 16(14Q11.2) WILD-TYPE 185  24
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                            47                            209 
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                            10                             24 
$`DEL PEAK 16(14Q11.2) MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JK TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7997 
       54.64        38.99        18.21         0.10        35.18        30.48 
TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       29.46        12.99         9.63        25.08        44.61        49.25 
TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4103 TCGA-B9-4116 TCGA-B9-A5W8 
        7.33        16.77        10.09        30.58        20.61         6.81 
TCGA-BQ-5876 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-DW-5560 
       19.27        30.28        13.25        10.88         2.76        11.61 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 
       79.86        80.88        10.68        13.08         4.01        11.05 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-8500 
       34.82        13.68        25.84        17.33        16.90        27.65 
TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40Y TCGA-MH-A854 TCGA-P4-A5EA 
        4.60        73.25        16.80         2.04         0.36         6.61 
TCGA-PJ-A5Z8 TCGA-SX-A71V TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-WN-A9G9 
       12.85        28.80        18.02        21.93        26.01 

$`DEL PEAK 16(14Q11.2) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI 
        4.57        67.30        75.42        34.85        56.81        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       35.67        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       25.58         5.29        16.18        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       11.57        19.63        61.05        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       16.64        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
       16.31        15.75         8.28        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       13.55        30.35         2.20        19.56        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4104 
       16.87         3.55         0.46         6.58        33.83        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       12.46        10.16        50.50        28.18        26.40         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 
        0.16        14.86        17.49        12.30        86.76         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        26.04        25.35         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        7.92       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7834 
        7.63         7.04         7.17         3.81        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        3.02        40.77        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       19.00        24.89         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE 
       48.62        39.25        25.15         6.38        17.98        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92         3.68         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
        0.89        11.21        68.12        13.41        11.84        56.75 
TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
        5.49        19.99        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       78.90        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP 
       26.47        48.30        43.76        60.03        14.83         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       12.99        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                          0.10                           0.13 
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                         80.88                         194.79 
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                         17.33                          22.26 
[1] "0.1 - 80.9 (17.3)"  "0.1 - 194.8 (22.3)"
[1] "hr=" "2.8"
D23V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 16(14Q11.2) MUTATED        22        3        14        6
  DEL PEAK 16(14Q11.2) WILD-TYPE     145       18        35        8
D23V3, multiclass
           clus
vv          DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  STAGE I                             22                            145
  STAGE II                             3                             18
  STAGE III                           14                             35
  STAGE IV                             6                              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 16(14Q11.2) MUTATED    24   4    20
  DEL PEAK 16(14Q11.2) WILD-TYPE 152  25    36
D23V4, multiclass
       clus
vv      DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  T1                              24                            152
  T2                               4                             25
  T3+T4                           20                             36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 16(14Q11.2) MUTATED    9  8  3
  DEL PEAK 16(14Q11.2) WILD-TYPE 36 14  1
D23V5, multiclass
    clus
vv   DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  N0                            9                             36
  N1                            8                             14
  N2                            3                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                                cls
clus                              0  1
  DEL PEAK 16(14Q11.2) MUTATED   18  3
  DEL PEAK 16(14Q11.2) WILD-TYPE 72  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(14Q11.2) MUTATED     18    3
  DEL PEAK 16(14Q11.2) WILD-TYPE   72    6
   clus
vv  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  0                           18                             72
  1                            3                              6
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                               0   1
  DEL PEAK 16(14Q11.2) MUTATED    19  29
  DEL PEAK 16(14Q11.2) WILD-TYPE  53 168
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(14Q11.2) MUTATED     19   29
  DEL PEAK 16(14Q11.2) WILD-TYPE   53  168
        clus
vv       DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  FEMALE                           19                             53
  MALE                             29                            168
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
D23V10, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(14Q11.2) MUTATED                                  0     1
  DEL PEAK 16(14Q11.2) WILD-TYPE                                2     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(14Q11.2) MUTATED                          10    33
  DEL PEAK 16(14Q11.2) WILD-TYPE                        50   154
D23V11, multiclass
                                  clus
vv                                 DEL PEAK 16(14Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      33
                                  clus
vv                                 DEL PEAK 16(14Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    50
  WHITE                                                       154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                                cls
clus                               0   1
  DEL PEAK 16(14Q11.2) MUTATED     1  40
  DEL PEAK 16(14Q11.2) WILD-TYPE  11 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(14Q11.2) MUTATED      1   40
  DEL PEAK 16(14Q11.2) WILD-TYPE   11  180
                        clus
vv                       DEL PEAK 16(14Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           40
                        clus
vv                       DEL PEAK 16(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            180
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK 17(14Q24.2) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(14Q24.2) MUTATED    36  11
  DEL PEAK 17(14Q24.2) WILD-TYPE 186  23
  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                            47                            209 
  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                            11                             23 
$`DEL PEAK 17(14Q24.2) MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       54.64        51.52        38.99        18.21        19.63         0.10 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3473 TCGA-AL-7173 
       30.48        29.46        12.99         9.63        25.08        44.61 
TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A5W8 
       49.25         7.33        16.77        10.09        20.61         6.81 
TCGA-BQ-5876 TCGA-BQ-5880 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5894 
       19.27        43.20        30.28        13.25        10.88         2.76 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 
       79.86        80.88        10.68        13.08         4.01        11.05 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-8500 
       34.82        13.68        25.84        17.33        16.90        27.65 
TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40Y TCGA-MH-A854 TCGA-P4-A5EA 
        4.60        73.25        16.80         2.04         0.36         6.61 
TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-WN-A9G9 
       12.85        14.07        18.02        21.93        26.01 

$`DEL PEAK 17(14Q24.2) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ 
        4.57        67.30        75.42        34.85        56.81        35.67 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
        5.29        16.18        22.49         0.13        12.82        11.57 
TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
       61.05        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       15.75         8.28        12.46        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       30.35         2.20        19.56        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
        3.55         0.46         6.58        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       12.46        10.16        50.50        28.18        26.40         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 
        0.16        14.86        17.49        12.30        86.76         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        47.80        21.63        40.83        26.04 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       26.04        25.35         7.66         0.95        11.97         7.92 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        3.02        40.77        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       19.00        24.89         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE 
       48.62        39.25        25.15         6.38        17.98        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92         3.68         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
        0.89        11.21        68.12        13.41        11.84        56.75 
TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
        5.49        19.99        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       78.90        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP 
       26.47        48.30        43.76        60.03        14.83         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       12.99        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                          0.10                           0.13 
  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                         80.88                         194.79 
  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                         17.33                          22.49 
[1] "0.1 - 80.9 (17.3)"  "0.1 - 194.8 (22.5)"
[1] "hr=" "3.1"
D24V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 17(14Q24.2) MUTATED        20        3        15        6
  DEL PEAK 17(14Q24.2) WILD-TYPE     147       18        34        8
D24V3, multiclass
           clus
vv          DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE
  STAGE I                             20                            147
  STAGE II                             3                             18
  STAGE III                           15                             34
  STAGE IV                             6                              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 17(14Q24.2) MUTATED    22   4    21
  DEL PEAK 17(14Q24.2) WILD-TYPE 154  25    35
D24V4, multiclass
       clus
vv      DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE
  T1                              22                            154
  T2                               4                             25
  T3+T4                           21                             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 17(14Q24.2) MUTATED    8  9  3
  DEL PEAK 17(14Q24.2) WILD-TYPE 37 13  1
D24V5, multiclass
    clus
vv   DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE
  N0                            8                             37
  N1                            9                             13
  N2                            3                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                                cls
clus                              0  1
  DEL PEAK 17(14Q24.2) MUTATED   14  3
  DEL PEAK 17(14Q24.2) WILD-TYPE 76  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(14Q24.2) MUTATED     14    3
  DEL PEAK 17(14Q24.2) WILD-TYPE   76    6
   clus
vv  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE
  0                           14                             76
  1                            3                              6
[1] 2 2
[1] FALSE
D24V7, binary
                                cls
clus                               0   1
  DEL PEAK 17(14Q24.2) MUTATED    19  28
  DEL PEAK 17(14Q24.2) WILD-TYPE  53 169
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(14Q24.2) MUTATED     19   28
  DEL PEAK 17(14Q24.2) WILD-TYPE   53  169
        clus
vv       DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE
  FEMALE                           19                             53
  MALE                             28                            169
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
D24V10, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(14Q24.2) MUTATED                                  0     1
  DEL PEAK 17(14Q24.2) WILD-TYPE                                2     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(14Q24.2) MUTATED                          11    32
  DEL PEAK 17(14Q24.2) WILD-TYPE                        49   155
D24V11, multiclass
                                  clus
vv                                 DEL PEAK 17(14Q24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      32
                                  clus
vv                                 DEL PEAK 17(14Q24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    49
  WHITE                                                       155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, binary
                                cls
clus                               0   1
  DEL PEAK 17(14Q24.2) MUTATED     1  39
  DEL PEAK 17(14Q24.2) WILD-TYPE  11 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(14Q24.2) MUTATED      1   39
  DEL PEAK 17(14Q24.2) WILD-TYPE   11  181
                        clus
vv                       DEL PEAK 17(14Q24.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           39
                        clus
vv                       DEL PEAK 17(14Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            181
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK 18(15Q13.3) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(15Q13.3) MUTATED    23   9
  DEL PEAK 18(15Q13.3) WILD-TYPE 199  25
  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                            32                            224 
  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                             9                             25 
$`DEL PEAK 18(15Q13.3) MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-A5Y1 
       54.64        51.52        12.82        18.21         0.10        12.99 
TCGA-AL-3466 TCGA-B1-5398 TCGA-B3-3926 TCGA-B9-A5W8 TCGA-B9-A8YI TCGA-BQ-5879 
        9.63        19.56        10.09         6.81        12.30        22.92 
TCGA-BQ-5882 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 
       21.63        10.88         2.76        10.68        13.08         4.01 
TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 
       34.82        25.84        17.33        16.90       194.79         3.68 
TCGA-HE-A5NK TCGA-IA-A40Y TCGA-P4-A5EA TCGA-PJ-A5Z8 TCGA-UN-AAZ9 TCGA-UZ-A9PP 
       73.25         2.04         6.61        12.85        18.02         0.53 
TCGA-Y8-A896 TCGA-Y8-A8S1 
       18.64        13.28 

$`DEL PEAK 18(15Q13.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ 
        4.57        67.30        75.42        34.85        56.81        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y 
       25.58         5.29        16.18        22.49         0.13        11.57 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       19.63        61.05        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       49.25         2.20         7.33        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 
        3.55        16.77         0.46         6.58        33.83        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-BQ-5875 
        2.10        19.23         0.16        14.86        17.49        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       19.27         8.88        63.72        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 
       26.04        30.28        26.04        25.35        13.25         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         7.92       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
       24.89         2.40         1.18         0.43        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
       11.05        39.25        25.15        13.68         6.38        17.98 
TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       80.65        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       56.75         5.49        16.80        19.99        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       52.27        16.01        50.60        78.90        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       43.76        60.03        14.83        21.93        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       29.00        18.64        15.91        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 
        6.74         6.02 

  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                          0.10                           0.13 
  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                        194.79                         129.86 
  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                        13.035                         23.640 
[1] "0.1 - 194.8 (13.0)" "0.1 - 129.9 (23.6)"
[1] "hr=" "3.7"
D25V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 18(15Q13.3) MUTATED        12        1        12        5
  DEL PEAK 18(15Q13.3) WILD-TYPE     155       20        37        9
D25V3, multiclass
           clus
vv          DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE
  STAGE I                             12                            155
  STAGE II                             1                             20
  STAGE III                           12                             37
  STAGE IV                             5                              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 18(15Q13.3) MUTATED    14   1    17
  DEL PEAK 18(15Q13.3) WILD-TYPE 162  28    39
D25V4, multiclass
       clus
vv      DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE
  T1                              14                            162
  T2                               1                             28
  T3+T4                           17                             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 18(15Q13.3) MUTATED    4 10  1
  DEL PEAK 18(15Q13.3) WILD-TYPE 41 12  3
D25V5, multiclass
    clus
vv   DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE
  N0                            4                             41
  N1                           10                             12
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                                cls
clus                              0  1
  DEL PEAK 18(15Q13.3) MUTATED   10  3
  DEL PEAK 18(15Q13.3) WILD-TYPE 80  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(15Q13.3) MUTATED     10    3
  DEL PEAK 18(15Q13.3) WILD-TYPE   80    6
   clus
vv  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE
  0                           10                             80
  1                            3                              6
[1] 2 2
[1] FALSE
D25V7, binary
                                cls
clus                               0   1
  DEL PEAK 18(15Q13.3) MUTATED    11  22
  DEL PEAK 18(15Q13.3) WILD-TYPE  61 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(15Q13.3) MUTATED     11   22
  DEL PEAK 18(15Q13.3) WILD-TYPE   61  175
        clus
vv       DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE
  FEMALE                           11                             61
  MALE                             22                            175
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
D25V10, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(15Q13.3) MUTATED                                  0     1
  DEL PEAK 18(15Q13.3) WILD-TYPE                                2     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(15Q13.3) MUTATED                           5    23
  DEL PEAK 18(15Q13.3) WILD-TYPE                        55   164
D25V11, multiclass
                                  clus
vv                                 DEL PEAK 18(15Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      23
                                  clus
vv                                 DEL PEAK 18(15Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    55
  WHITE                                                       164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, binary
                                cls
clus                               0   1
  DEL PEAK 18(15Q13.3) MUTATED     1  27
  DEL PEAK 18(15Q13.3) WILD-TYPE  11 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(15Q13.3) MUTATED      1   27
  DEL PEAK 18(15Q13.3) WILD-TYPE   11  193
                        clus
vv                       DEL PEAK 18(15Q13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           27
                        clus
vv                       DEL PEAK 18(15Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            193
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK 19(16Q24.1) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(16Q24.1) MUTATED     4   6
  DEL PEAK 19(16Q24.1) WILD-TYPE 218  28
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                            10                            246 
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                             6                             28 
$`DEL PEAK 19(16Q24.1) MUTATED`
TCGA-2Z-A9JI TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-B9-A8YI TCGA-BQ-5882 TCGA-BQ-5893 
       51.52        19.63        12.99        12.30        21.63         7.92 
TCGA-F9-A97G TCGA-G7-6793 TCGA-G7-A8LD TCGA-IA-A40X 
        0.43        11.05        16.90        19.99 

$`DEL PEAK 19(16Q24.1) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       12.82        11.57        18.21        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
       15.75         8.28        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        2.10        19.23         6.81         0.16        14.86        17.49 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
       13.25        10.88         7.66         0.95        11.97         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       54.90        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
        2.40         1.18         4.01        51.78        48.62        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       17.33        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       16.80         2.04        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
        0.36        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.22        42.94         6.61        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       16.01        50.60        78.90        12.85        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                         51.52                         194.79 
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                        14.945                         21.995 
[1] "0.4 - 51.5 (14.9)"  "0.1 - 194.8 (22.0)"
[1] "hr=" "9"  
D26V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 19(16Q24.1) MUTATED         3        0         6        2
  DEL PEAK 19(16Q24.1) WILD-TYPE     164       21        43       12
D26V3, multiclass
           clus
vv          DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE
  STAGE I                              3                            164
  STAGE II                             0                             21
  STAGE III                            6                             43
  STAGE IV                             2                             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 19(16Q24.1) MUTATED     4   0     7
  DEL PEAK 19(16Q24.1) WILD-TYPE 172  29    49
D26V4, multiclass
       clus
vv      DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE
  T1                               4                            172
  T2                               0                             29
  T3+T4                            7                             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 19(16Q24.1) MUTATED    2  3  1
  DEL PEAK 19(16Q24.1) WILD-TYPE 43 19  3
D26V5, multiclass
    clus
vv   DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE
  N0                            2                             43
  N1                            3                             19
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                                cls
clus                              0  1
  DEL PEAK 19(16Q24.1) MUTATED    3  1
  DEL PEAK 19(16Q24.1) WILD-TYPE 87  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16Q24.1) MUTATED      3    1
  DEL PEAK 19(16Q24.1) WILD-TYPE   87    8
   clus
vv  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE
  0                            3                             87
  1                            1                              8
[1] 2 2
[1] FALSE
D26V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(16Q24.1) MUTATED     4   7
  DEL PEAK 19(16Q24.1) WILD-TYPE  68 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16Q24.1) MUTATED      4    7
  DEL PEAK 19(16Q24.1) WILD-TYPE   68  190
        clus
vv       DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE
  FEMALE                            4                             68
  MALE                              7                            190
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
D26V10, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(16Q24.1) MUTATED                                  0     1
  DEL PEAK 19(16Q24.1) WILD-TYPE                                2     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(16Q24.1) MUTATED                           2     6
  DEL PEAK 19(16Q24.1) WILD-TYPE                        58   181
D26V11, multiclass
                                  clus
vv                                 DEL PEAK 19(16Q24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                       6
                                  clus
vv                                 DEL PEAK 19(16Q24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    58
  WHITE                                                       181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                                cls
clus                               0   1
  DEL PEAK 19(16Q24.1) MUTATED     0   9
  DEL PEAK 19(16Q24.1) WILD-TYPE  12 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16Q24.1) MUTATED      0    9
  DEL PEAK 19(16Q24.1) WILD-TYPE   12  211
                        clus
vv                       DEL PEAK 19(16Q24.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            9
                        clus
vv                       DEL PEAK 19(16Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            211
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK 20(19P13.3) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(19P13.3) MUTATED    16   4
  DEL PEAK 20(19P13.3) WILD-TYPE 206  30
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                            20                            236 
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                             4                             30 
$`DEL PEAK 20(19P13.3) MUTATED`
TCGA-2Z-A9JG TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-8517 TCGA-A4-A5Y1 TCGA-AL-3466 
       54.64        18.21        25.64        19.63        12.99         9.63 
TCGA-B1-7332 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5876 TCGA-BQ-5890 TCGA-BQ-5891 
        7.33         2.10        19.23        19.27         7.66         0.95 
TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ 
        4.01        25.84        16.90         2.04         0.13        14.07 
TCGA-UZ-A9PN TCGA-UZ-A9PP 
       21.93         0.53 

$`DEL PEAK 20(19P13.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI 
        4.57        67.30        75.42        34.85        56.81        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       12.82        11.57        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31         0.76        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       44.61        49.25         2.20        19.56        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06         6.81         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       12.30        86.76         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        13.25        10.88        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       54.90        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
       39.25        34.82        25.15        13.68         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       17.33        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       21.34        16.34        12.36        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
       50.60        78.90        12.85        17.75        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       60.03        14.83        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                         54.64                         194.79 
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                        13.530                         22.705 
[1] "0.1 - 54.6 (13.5)"  "0.1 - 194.8 (22.7)"
[1] "hr=" "3.7"
D27V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 20(19P13.3) MUTATED         6        1        10        2
  DEL PEAK 20(19P13.3) WILD-TYPE     161       20        39       12
D27V3, multiclass
           clus
vv          DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  STAGE I                              6                            161
  STAGE II                             1                             20
  STAGE III                           10                             39
  STAGE IV                             2                             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 20(19P13.3) MUTATED     7   1    12
  DEL PEAK 20(19P13.3) WILD-TYPE 169  28    44
D27V4, multiclass
       clus
vv      DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  T1                               7                            169
  T2                               1                             28
  T3+T4                           12                             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 20(19P13.3) MUTATED    2  5  1
  DEL PEAK 20(19P13.3) WILD-TYPE 43 17  3
D27V5, multiclass
    clus
vv   DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  N0                            2                             43
  N1                            5                             17
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                                cls
clus                              0  1
  DEL PEAK 20(19P13.3) MUTATED    4  1
  DEL PEAK 20(19P13.3) WILD-TYPE 86  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(19P13.3) MUTATED      4    1
  DEL PEAK 20(19P13.3) WILD-TYPE   86    8
   clus
vv  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  0                            4                             86
  1                            1                              8
[1] 2 2
[1] FALSE
D27V7, binary
                                cls
clus                               0   1
  DEL PEAK 20(19P13.3) MUTATED     6  14
  DEL PEAK 20(19P13.3) WILD-TYPE  66 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(19P13.3) MUTATED      6   14
  DEL PEAK 20(19P13.3) WILD-TYPE   66  183
        clus
vv       DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  FEMALE                            6                             66
  MALE                             14                            183
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
D27V10, continuous
[1] "Remove cluster labels:"       "DEL PEAK 20(19P13.3) MUTATED"
clus
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                             2                             49 
                    TCGA-2Z-A9J3                     TCGA-2Z-A9J7 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-2Z-A9J8                     TCGA-2Z-A9JD 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-2Z-A9JI                     TCGA-2Z-A9JN 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-2Z-A9JO                     TCGA-4A-A93W 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-4A-A93Y                     TCGA-A4-A48D 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-A4-A57E                     TCGA-A4-A5Y0 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-AL-3472                     TCGA-AL-7173 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-B1-A654                     TCGA-B9-4117 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-B9-A69E                     TCGA-DW-5561 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-DW-7963                     TCGA-F9-A97G 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-G7-7501                     TCGA-G7-A8LB 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-G7-A8LE                     TCGA-GL-7773 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-GL-A9DD                     TCGA-HE-A5NI 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-IA-A40U                     TCGA-MH-A854 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-MH-A856                     TCGA-P4-A5E6 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-P4-AAVK                     TCGA-PJ-A5Z9 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-SX-A71S                     TCGA-SX-A71U 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-SX-A7SL                     TCGA-SX-A7SM 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-SX-A7SR                     TCGA-SX-A7SS 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-UZ-A9PM                     TCGA-UZ-A9PO 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-UZ-A9PR                     TCGA-UZ-A9PS 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-UZ-A9PX                     TCGA-WN-A9G9 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-WN-AB4C                     TCGA-Y8-A894 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-Y8-A896                     TCGA-Y8-A8RY 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-Y8-A8RZ 
"DEL PEAK 20(19P13.3) WILD-TYPE" 
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(19P13.3) MUTATED                                  0     1
  DEL PEAK 20(19P13.3) WILD-TYPE                                2     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(19P13.3) MUTATED                           4    15
  DEL PEAK 20(19P13.3) WILD-TYPE                        56   172
D27V11, multiclass
                                  clus
vv                                 DEL PEAK 20(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      15
                                  clus
vv                                 DEL PEAK 20(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    56
  WHITE                                                       172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, binary
                                cls
clus                               0   1
  DEL PEAK 20(19P13.3) MUTATED     0  19
  DEL PEAK 20(19P13.3) WILD-TYPE  12 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(19P13.3) MUTATED      0   19
  DEL PEAK 20(19P13.3) WILD-TYPE   12  201
                        clus
vv                       DEL PEAK 20(19P13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           19
                        clus
vv                       DEL PEAK 20(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            201
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK 21(19Q13.42) MUTATION ANALYSIS
D28V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 21(19Q13.42) MUTATED    15   4
  DEL PEAK 21(19Q13.42) WILD-TYPE 207  30
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                             19                             237 
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                              4                              30 
$`DEL PEAK 21(19Q13.42) MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-A4-7286 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8517 
       54.64        51.52        18.21        29.46        25.64        19.63 
TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-BQ-5885 TCGA-BQ-5891 TCGA-BQ-7048 TCGA-BQ-7060 
       12.99         7.33        30.28         0.95        93.34         7.04 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-Q2-A5QZ 
       10.68         4.01        25.84        16.90         2.04        14.07 
TCGA-UZ-A9PN 
       21.93 

$`DEL PEAK 21(19Q13.42) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ 
        4.57        67.30        75.42        34.85        56.81        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       25.58         5.29        16.18        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       11.57        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8312 
        0.89         0.23        16.64        30.48        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31         0.76        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       49.25         2.20        19.56        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 
       26.04        25.35        13.25        10.88         7.66        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 
        7.92         2.76       123.62        48.26        96.92        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.63         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF 
       54.90        34.19        19.00        24.89        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        1.18         0.43        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       34.82        25.15        13.68         6.38        17.98        17.33 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       16.34        12.36         0.13        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
       50.60        78.90        12.85        17.75        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       60.03        14.83         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                           0.95                            0.10 
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                          93.34                          194.79 
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                          18.21                           21.63 
[1] "0.9 - 93.3 (18.2)"  "0.1 - 194.8 (21.6)"
[1] "hr=" "2"  
D28V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 21(19Q13.42) MUTATED         5        1        11        1
  DEL PEAK 21(19Q13.42) WILD-TYPE     162       20        38       13
D28V3, multiclass
           clus
vv          DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE
  STAGE I                               5                             162
  STAGE II                              1                              20
  STAGE III                            11                              38
  STAGE IV                              1                              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 21(19Q13.42) MUTATED     6   1    12
  DEL PEAK 21(19Q13.42) WILD-TYPE 170  28    44
D28V4, multiclass
       clus
vv      DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE
  T1                                6                             170
  T2                                1                              28
  T3+T4                            12                              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2
  DEL PEAK 21(19Q13.42) MUTATED    3  3  1
  DEL PEAK 21(19Q13.42) WILD-TYPE 42 19  3
D28V5, multiclass
    clus
vv   DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE
  N0                             3                              42
  N1                             3                              19
  N2                             1                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                                 cls
clus                               0  1
  DEL PEAK 21(19Q13.42) MUTATED    4  0
  DEL PEAK 21(19Q13.42) WILD-TYPE 86  9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(19Q13.42) MUTATED      4    0
  DEL PEAK 21(19Q13.42) WILD-TYPE   86    9
   clus
vv  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE
  0                             4                              86
  1                             0                               9
[1] 2 2
[1] FALSE
D28V7, binary
                                 cls
clus                                0   1
  DEL PEAK 21(19Q13.42) MUTATED     6  13
  DEL PEAK 21(19Q13.42) WILD-TYPE  66 184
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(19Q13.42) MUTATED      6   13
  DEL PEAK 21(19Q13.42) WILD-TYPE   66  184
        clus
vv       DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE
  FEMALE                             6                              66
  MALE                              13                             184
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
D28V10, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(19Q13.42) MUTATED                                  1     0
  DEL PEAK 21(19Q13.42) WILD-TYPE                                1     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(19Q13.42) MUTATED                           4    14
  DEL PEAK 21(19Q13.42) WILD-TYPE                        56   173
D28V11, multiclass
                                  clus
vv                                 DEL PEAK 21(19Q13.42) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       14
                                  clus
vv                                 DEL PEAK 21(19Q13.42) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     56
  WHITE                                                        173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, binary
                                 cls
clus                                0   1
  DEL PEAK 21(19Q13.42) MUTATED     0  18
  DEL PEAK 21(19Q13.42) WILD-TYPE  12 202
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(19Q13.42) MUTATED      0   18
  DEL PEAK 21(19Q13.42) WILD-TYPE   12  202
                        clus
vv                       DEL PEAK 21(19Q13.42) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            18
                        clus
vv                       DEL PEAK 21(19Q13.42) WILD-TYPE
  HISPANIC OR LATINO                                  12
  NOT HISPANIC OR LATINO                             202
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK 22(22Q12.2) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(22Q12.2) MUTATED    47  12
  DEL PEAK 22(22Q12.2) WILD-TYPE 175  22
  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                            59                            197 
  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                            12                             22 
$`DEL PEAK 22(22Q12.2) MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-8098 
       54.64        51.52        12.82        18.21        61.05        29.46 
TCGA-A4-8517 TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B1-7332 
       19.63         8.28        12.99         9.63        49.25         7.33 
TCGA-B1-A47O TCGA-B3-3925 TCGA-B3-3926 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 
       16.87        33.83        10.09         2.10         6.81        86.76 
TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5891 
        8.88        22.92        26.04        30.28         7.66         0.95 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7055 TCGA-BQ-7056 
        2.76       123.62        61.28        50.40        26.27        20.12 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY 
        7.17        79.86        19.00        10.68        13.08         1.18 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC 
        4.01        11.05        25.15        13.68        25.84        17.33 
TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-MH-A856 TCGA-P4-A5E8 TCGA-P4-A5EA 
        3.68         2.04         0.13        25.97        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A7SL TCGA-SX-A7SM TCGA-UN-AAZ9 
       84.95        78.90        14.07        27.06        11.93        18.02 
TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-AB4C TCGA-Y8-A896 TCGA-Y8-A8RZ 
       21.93        86.27        29.00        18.64         6.74 

$`DEL PEAK 22(22Q12.2) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ 
        4.57        67.30        75.42        34.85        56.81        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y 
       25.58         5.29        16.18        22.49         0.13        11.57 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       16.64        30.48        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
        0.76        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       16.31        15.75        12.46        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-4103 
       24.56         3.55        16.77         0.46         6.58        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 
       19.23         0.16        14.86        17.49        12.30        19.27 
TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5886 
       63.72        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 
       25.35        13.25        10.88        11.97         7.92        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7053 TCGA-BQ-7058 TCGA-BQ-7059 
       96.92        93.34        44.84        49.84        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.04         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
       24.89         2.40         0.43        51.78        48.62        39.25 
TCGA-G7-6796 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       34.82         6.38        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
       12.92        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25         5.49        16.80        19.99        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
       67.17        22.26        21.34        16.34        12.36        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
       20.25         0.36        12.13        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-PJ-A5Z8 
       87.22        92.58        52.27        16.01        50.60        12.85 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN 
       17.75        47.90        47.44        33.04        28.80        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       60.03        14.83         0.53        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A895 
       25.68        27.39        12.99        26.01        18.64        15.91 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.02        13.28 

  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                        123.62                         194.79 
  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                         18.21                          22.26 
[1] "0.1 - 123.6 (18.2)" "0.1 - 194.8 (22.3)"
[1] "hr=" "2.1"
D29V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 22(22Q12.2) MUTATED        21        3        25        7
  DEL PEAK 22(22Q12.2) WILD-TYPE     146       18        24        7
D29V3, multiclass
           clus
vv          DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE
  STAGE I                             21                            146
  STAGE II                             3                             18
  STAGE III                           25                             24
  STAGE IV                             7                              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 22(22Q12.2) MUTATED    23   6    29
  DEL PEAK 22(22Q12.2) WILD-TYPE 153  23    27
D29V4, multiclass
       clus
vv      DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE
  T1                              23                            153
  T2                               6                             23
  T3+T4                           29                             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"
                                vv
clus                             N0 N1 N2
  DEL PEAK 22(22Q12.2) MUTATED   10 14  2
  DEL PEAK 22(22Q12.2) WILD-TYPE 35  8  2
D29V5, multiclass
    clus
vv   DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE
  N0                           10                             35
  N1                           14                              8
  N2                            2                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                                cls
clus                              0  1
  DEL PEAK 22(22Q12.2) MUTATED   22  5
  DEL PEAK 22(22Q12.2) WILD-TYPE 68  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(22Q12.2) MUTATED     22    5
  DEL PEAK 22(22Q12.2) WILD-TYPE   68    4
   clus
vv  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE
  0                           22                             68
  1                            5                              4
[1] 2 2
[1] FALSE
D29V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(22Q12.2) MUTATED    26  34
  DEL PEAK 22(22Q12.2) WILD-TYPE  46 163
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(22Q12.2) MUTATED     26   34
  DEL PEAK 22(22Q12.2) WILD-TYPE   46  163
        clus
vv       DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE
  FEMALE                           26                             46
  MALE                             34                            163
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
D29V10, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(22Q12.2) MUTATED                                  0     3
  DEL PEAK 22(22Q12.2) WILD-TYPE                                2     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(22Q12.2) MUTATED                          12    42
  DEL PEAK 22(22Q12.2) WILD-TYPE                        48   145
D29V11, multiclass
                                  clus
vv                                 DEL PEAK 22(22Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      42
                                  clus
vv                                 DEL PEAK 22(22Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    48
  WHITE                                                       145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, binary
                                cls
clus                               0   1
  DEL PEAK 22(22Q12.2) MUTATED     3  44
  DEL PEAK 22(22Q12.2) WILD-TYPE   9 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(22Q12.2) MUTATED      3   44
  DEL PEAK 22(22Q12.2) WILD-TYPE    9  176
                        clus
vv                       DEL PEAK 22(22Q12.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           44
                        clus
vv                       DEL PEAK 22(22Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            176
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK 23(XP11.4) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 23(XP11.4) MUTATED    20   9
  DEL PEAK 23(XP11.4) WILD-TYPE 202  25
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                           29                           227 
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                            9                            25 
$`DEL PEAK 23(XP11.4) MUTATED`
TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7286 
       59.01        67.30        54.64        51.52        12.82        18.21 
TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A44B 
       19.63        12.99         7.33        10.09        20.61         2.10 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-DZ-6131 
       19.27         8.88        22.92        21.63        25.35        79.86 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6793 TCGA-G7-6797 TCGA-G7-7501 
       10.68        13.08         0.43        11.05        25.15        13.68 
TCGA-G7-A8LD TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       16.90         0.13        14.07        18.02        86.27 

$`DEL PEAK 23(XP11.4) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        75.55        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       75.42        34.85        56.81        35.67        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7288 TCGA-A4-7583 
       16.18        22.49         0.13        11.57        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       76.64        13.55        30.35        25.08        44.61        49.25 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
        2.20        19.56        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       16.77         0.46         6.58        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       12.46        10.16        50.50        28.18        26.40         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
        1.15        15.12        43.99        22.06        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 
        0.16        14.86        17.49        12.30        86.76        63.72 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       43.20        47.80        40.83        26.04        30.28        26.04 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        40.77        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
       54.90        34.19        19.00        24.89         2.40         1.18 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 
        4.01        51.78        48.62        39.25        34.82        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
        6.38        17.98        17.33        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       48.30        43.76        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                         0.13                          0.10 
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                        86.27                        194.79 
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                        18.02                         22.26 
[1] "0.1 - 86.3 (18.0)"  "0.1 - 194.8 (22.3)"
[1] "hr=" "3.2"
D30V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 23(XP11.4) MUTATED         8        1        16        2
  DEL PEAK 23(XP11.4) WILD-TYPE     159       20        33       12
D30V3, multiclass
           clus
vv          DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE
  STAGE I                             8                           159
  STAGE II                            1                            20
  STAGE III                          16                            33
  STAGE IV                            2                            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 23(XP11.4) MUTATED    10   3    16
  DEL PEAK 23(XP11.4) WILD-TYPE 166  26    40
D30V4, multiclass
       clus
vv      DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE
  T1                             10                           166
  T2                              3                            26
  T3+T4                          16                            40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK 23(XP11.4) MUTATED    5  7  1
  DEL PEAK 23(XP11.4) WILD-TYPE 40 15  3
D30V5, multiclass
    clus
vv   DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE
  N0                           5                            40
  N1                           7                            15
  N2                           1                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                               cls
clus                             0  1
  DEL PEAK 23(XP11.4) MUTATED    9  1
  DEL PEAK 23(XP11.4) WILD-TYPE 81  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(XP11.4) MUTATED      9    1
  DEL PEAK 23(XP11.4) WILD-TYPE   81    8
   clus
vv  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE
  0                           9                            81
  1                           1                             8
[1] 2 2
[1] FALSE
D30V7, binary
                               cls
clus                              0   1
  DEL PEAK 23(XP11.4) MUTATED    14  16
  DEL PEAK 23(XP11.4) WILD-TYPE  58 181
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(XP11.4) MUTATED     14   16
  DEL PEAK 23(XP11.4) WILD-TYPE   58  181
        clus
vv       DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE
  FEMALE                          14                            58
  MALE                            16                           181
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, continuous
D30V10, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(XP11.4) MUTATED                                  0     3
  DEL PEAK 23(XP11.4) WILD-TYPE                                2     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(XP11.4) MUTATED                           9    16
  DEL PEAK 23(XP11.4) WILD-TYPE                        51   171
D30V11, multiclass
                                  clus
vv                                 DEL PEAK 23(XP11.4) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     16
                                  clus
vv                                 DEL PEAK 23(XP11.4) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   51
  WHITE                                                      171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, binary
                               cls
clus                              0   1
  DEL PEAK 23(XP11.4) MUTATED     0  22
  DEL PEAK 23(XP11.4) WILD-TYPE  12 198
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(XP11.4) MUTATED      0   22
  DEL PEAK 23(XP11.4) WILD-TYPE   12  198
                        clus
vv                       DEL PEAK 23(XP11.4) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          22
                        clus
vv                       DEL PEAK 23(XP11.4) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           198
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK 24(XQ28) MUTATION ANALYSIS
D31V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 24(XQ28) MUTATED    15   9
  DEL PEAK 24(XQ28) WILD-TYPE 207  25
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                         24                         232 
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                          9                          25 
$`DEL PEAK 24(XQ28) MUTATED`
TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7287 
       67.30        54.64        51.52        12.82        18.21        19.63 
TCGA-A4-7583 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5876 
        0.10        12.99         9.63         7.33        10.09        19.27 
TCGA-BQ-5879 TCGA-BQ-5882 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6793 TCGA-G7-6797 
       22.92        21.63        10.68        13.08        11.05        25.15 
TCGA-G7-7501 TCGA-G7-A8LD TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       13.68        16.90         0.13        14.07        18.02        86.27 

$`DEL PEAK 24(XQ28) WILD-TYPE`
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JK 
        4.57        75.42        34.85        56.81        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7288 
        5.29        16.18        22.49         0.13        11.57        61.05 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
       16.31        15.75         8.28        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
       19.56        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        0.46         6.58        33.83        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
        8.88        63.72        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       19.00        24.89         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM 
       51.78        48.62        39.25        34.82        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.98        17.33        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
       67.17        22.26        21.34        16.34        12.36        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR 
       43.76        60.03        14.83        21.93         0.53        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                       0.10                        0.13 
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                      86.27                      194.79 
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                     15.485                      22.375 
[1] "0.1 - 86.3 (15.5)"  "0.1 - 194.8 (22.4)"
[1] "hr=" "4.3"
D31V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 24(XQ28) MUTATED         8        1        12        2
  DEL PEAK 24(XQ28) WILD-TYPE     159       20        37       12
D31V3, multiclass
           clus
vv          DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  STAGE I                           8                         159
  STAGE II                          1                          20
  STAGE III                        12                          37
  STAGE IV                          2                          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 24(XQ28) MUTATED    10   2    12
  DEL PEAK 24(XQ28) WILD-TYPE 166  27    44
D31V4, multiclass
       clus
vv      DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  T1                           10                         166
  T2                            2                          27
  T3+T4                        12                          44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2
  DEL PEAK 24(XQ28) MUTATED    3  7  1
  DEL PEAK 24(XQ28) WILD-TYPE 42 15  3
D31V5, multiclass
    clus
vv   DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  N0                         3                          42
  N1                         7                          15
  N2                         1                           3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                             cls
clus                           0  1
  DEL PEAK 24(XQ28) MUTATED    8  1
  DEL PEAK 24(XQ28) WILD-TYPE 82  8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 24(XQ28) MUTATED      8    1
  DEL PEAK 24(XQ28) WILD-TYPE   82    8
   clus
vv  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  0                         8                          82
  1                         1                           8
[1] 2 2
[1] FALSE
D31V7, binary
                             cls
clus                            0   1
  DEL PEAK 24(XQ28) MUTATED    12  13
  DEL PEAK 24(XQ28) WILD-TYPE  60 184
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 24(XQ28) MUTATED     12   13
  DEL PEAK 24(XQ28) WILD-TYPE   60  184
        clus
vv       DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  FEMALE                        12                          60
  MALE                          13                         184
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
D31V10, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(XQ28) MUTATED                                  0     2
  DEL PEAK 24(XQ28) WILD-TYPE                                2     3
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(XQ28) MUTATED                           7    14
  DEL PEAK 24(XQ28) WILD-TYPE                        53   173
D31V11, multiclass
                                  clus
vv                                 DEL PEAK 24(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                                7
  WHITE                                                   14
                                  clus
vv                                 DEL PEAK 24(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 53
  WHITE                                                    173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, binary
                             cls
clus                            0   1
  DEL PEAK 24(XQ28) MUTATED     0  20
  DEL PEAK 24(XQ28) WILD-TYPE  12 200
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 24(XQ28) MUTATED      0   20
  DEL PEAK 24(XQ28) WILD-TYPE   12  200
                        clus
vv                       DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             0                          12
  NOT HISPANIC OR LATINO                        20                         200
[1] 2 2
[1] FALSE
