[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/19775272/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/19781624/transformed.cor.cli.txt"

nPatients in clinical file=290, in cluster file=288, common to both=287
[1]  31 287
[1] "AMP PEAK 1(2P23.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                          45                          242 
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                          45                          242 
[1] "AMP PEAK 2(2Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                          53                          234 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                          53                          234 
[1] "AMP PEAK 3(3Q27.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                         100                          187 
  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                         100                          187 
[1] "AMP PEAK 4(5Q35.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                          37                          250 
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                          37                          250 
[1] "AMP PEAK 5(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                         177                          110 
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                         177                          110 
[1] "AMP PEAK 6(17Q25.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                          200                            87 
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                          200                            87 
[1] "AMP PEAK 7(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                           31                           256 
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                           31                           256 
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            55                            232 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            55                            232 
[1] "DEL PEAK  2(2P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          8                         279 
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          8                         279 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           10                           277 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           10                           277 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           12                           275 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           12                           275 
[1] "DEL PEAK  5(3P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                           25                           262 
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                           25                           262 
[1] "DEL PEAK  6(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           32                           255 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           32                           255 
[1] "DEL PEAK  7(5P15.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                            13                            274 
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                            13                            274 
[1] "DEL PEAK  8(5Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                           11                           276 
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                           11                           276 
[1] "DEL PEAK  9(6P12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                           26                           261 
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                           26                           261 
[1] "DEL PEAK 10(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                            29                            258 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                            29                            258 
[1] "DEL PEAK 11(6Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                           32                           255 
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                           32                           255 
[1] "DEL PEAK 12(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           39                           248 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           39                           248 
[1] "DEL PEAK 13(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                            19                            268 
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                            19                            268 
[1] "DEL PEAK 14(11Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                            31                            256 
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                            31                            256 
[1] "DEL PEAK 15(11Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                            29                            258 
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                            29                            258 
[1] "DEL PEAK 16(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                            51                            236 
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                            51                            236 
[1] "DEL PEAK 17(14Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                            50                            237 
  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                            50                            237 
[1] "DEL PEAK 18(15Q13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                            35                            252 
  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                            35                            252 
[1] "DEL PEAK 19(16Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                            12                            275 
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                            12                            275 
[1] "DEL PEAK 20(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                            23                            264 
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                            23                            264 
[1] "DEL PEAK 21(19Q13.42) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                             19                             268 
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                             19                             268 
[1] "DEL PEAK 22(22Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                            63                            224 
  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                            63                            224 
[1] "DEL PEAK 23(XP11.4) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                           34                           253 
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                           34                           253 
[1] "DEL PEAK 24(XQ28) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                         28                         259 
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                         28                         259 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 287 columns.

[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=44,	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=235,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "200"   "1"    
freq.contrast "1"     "200"  
both >= 3     "FALSE" "FALSE"
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'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 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 287 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [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
PATHOLOGIC_STAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
190  33  60   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  190    33    62 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
190  33  60   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  190    33    62 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
48 24  5 
[1] "table(vv)"
vv
N0 N1 N2 
48 24  5 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
48 24  5 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
48 24  5 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=9, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=36, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=34, 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    36   8
  AMP PEAK 1(2P23.2) WILD-TYPE 202  36
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                          44                          238 
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                           8                           36 
$`AMP PEAK 1(2P23.2) MUTATED`
TCGA-2Z-A9J5 TCGA-5P-A9JV TCGA-5P-A9K9 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ 
      100.27        67.17        19.36        16.96        16.31        15.75 
TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B3-A6W5 
        8.28         9.63        49.32         2.20        37.51        10.16 
TCGA-B9-4117 TCGA-B9-A44B TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7046 
        0.46         2.10        11.97         7.92         2.76        96.92 
TCGA-DW-5561 TCGA-DZ-6133 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 
       13.61        51.19         1.18         4.01        51.78        39.25 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI 
       23.08        16.90         3.68        17.95        84.89        11.84 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       16.80         2.04        18.41        29.10        11.41        34.29 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SQ 
       42.94        99.12        17.75        14.07        28.80        41.62 
TCGA-UZ-A9PK TCGA-V9-A7HT 
      117.40        31.73 

$`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 
       91.73        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 
       39.88        38.99        33.07        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-5P-A9JU TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
       12.82        11.57        12.26       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       61.05         0.10        21.37        35.18        19.13         0.89 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         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-A57E TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
       14.33        12.46         8.48        12.99        12.46        70.19 
TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 
       76.64        66.71        62.66        67.73        49.25        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87        20.25        16.77        20.32 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       21.07        33.83        10.09        30.58        34.49        12.46 
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-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       43.99        22.06        19.23        17.23         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-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         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        48.85       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-6134 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        61.02        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G 
       19.00        24.89        10.68        13.08         2.40         0.43 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       90.90        11.05        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
        6.38        17.98        80.65       194.79        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH 
        1.05        12.43        12.89        11.21        16.31        26.01 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       56.75        73.25        25.22        19.99        85.78        88.24 
TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       96.69        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       12.76        10.55        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 
       17.62        12.13        31.13        29.26        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       87.09         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        19.73        47.90        49.45        44.61        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        41.33        16.31        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       43.76        18.02        26.20       103.63       125.29        37.35 
TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       62.83        98.96        86.27        86.37        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-WN-A9G9 
       47.47        65.13        21.60       110.73        51.35        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       39.06        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         3.68         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 
                      117.40                       194.79 
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                      17.355                       25.315 
[1] "0.5 - 117.4 (17.4)" "0.1 - 194.8 (25.3)"
[1] "hr=" "1.4"
D1V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 1(2P23.2) MUTATED        25        4         8        5
  AMP PEAK 1(2P23.2) WILD-TYPE     146       18        44       10
D1V3, multiclass
           clus
vv          AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  STAGE I                           25                          146
  STAGE II                           4                           18
  STAGE III                          8                           44
  STAGE IV                           5                           10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2 T3+T4
  AMP PEAK 1(2P23.2) MUTATED    26   6    13
  AMP PEAK 1(2P23.2) WILD-TYPE 164  27    49
D1V4, multiclass
       clus
vv      AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  T1                            26                          164
  T2                             6                           27
  T3+T4                         13                           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
  AMP PEAK 1(2P23.2) MUTATED    4  8  2
  AMP PEAK 1(2P23.2) WILD-TYPE 44 16  3
D1V5, multiclass
    clus
vv   AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  N0                          4                           44
  N1                          8                           16
  N2                          2                            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 82  5
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(2P23.2) MUTATED     11    4
  AMP PEAK 1(2P23.2) WILD-TYPE   82    5
   clus
vv  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  0                         11                           82
  1                          4                            5
[1] 2 2
[1] FALSE
D1V7, binary
                              cls
clus                             0   1
  AMP PEAK 1(2P23.2) MUTATED    15  30
  AMP PEAK 1(2P23.2) WILD-TYPE  61 181
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(2P23.2) MUTATED     15   30
  AMP PEAK 1(2P23.2) WILD-TYPE   61  181
        clus
vv       AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  FEMALE                         15                           61
  MALE                           30                          181
[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                           8    32
  AMP PEAK 1(2P23.2) WILD-TYPE                        53   172
D1V11, multiclass
                                  clus
vv                                 AMP PEAK 1(2P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 8
  WHITE                                                    32
                                  clus
vv                                 AMP PEAK 1(2P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  53
  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"
D1V12, binary
                              cls
clus                             0   1
  AMP PEAK 1(2P23.2) MUTATED     2  38
  AMP PEAK 1(2P23.2) WILD-TYPE  10 201
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(2P23.2) MUTATED      2   38
  AMP PEAK 1(2P23.2) WILD-TYPE   10  201
                        clus
vv                       AMP PEAK 1(2P23.2) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         38
                        clus
vv                       AMP PEAK 1(2P23.2) WILD-TYPE
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          201
[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  10
  AMP PEAK 2(2Q32.1) WILD-TYPE 195  34
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                          53                          229 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                          10                           34 
$`AMP PEAK 2(2Q32.1) MUTATED`
TCGA-2Z-A9J5 TCGA-2Z-A9JR TCGA-5P-A9K9 TCGA-A4-7585 TCGA-A4-A4ZT TCGA-A4-A57E 
      100.27         5.29        19.36        35.18        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3471 TCGA-AL-7173 
       16.31        15.75         8.28         9.63        49.32        67.73 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-A44B 
        2.20        37.51        21.07        10.16         0.46         2.10 
TCGA-B9-A69E TCGA-BQ-5878 TCGA-BQ-5885 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       14.86        63.72        30.28        11.97         7.92         2.76 
TCGA-BQ-7046 TCGA-DW-5561 TCGA-DZ-6131 TCGA-DZ-6133 TCGA-F9-A8NY TCGA-G7-6789 
       96.92        13.61        79.86        51.19         1.18         4.01 
TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-GL-A59T 
       51.78        39.25        25.84        23.08         3.68        17.95 
TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE 
       84.89        11.84        16.80         2.04        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       11.41        34.29        42.94        99.12        17.75        14.07 
TCGA-SX-A71V TCGA-SX-A7SQ TCGA-UZ-A9PK TCGA-UZ-A9PQ TCGA-V9-A7HT 
       28.80        41.62       117.40        86.27        31.73 

$`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 
       91.73        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 
       39.88        38.99        33.07        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-5P-A9JU TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
       11.57        12.26        67.17       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
       61.05         0.10        21.37        19.13         0.89         7.82 
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-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
       12.46        12.99        12.46        70.19        76.64        66.71 
TCGA-AL-3473 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       62.66        49.25        19.56        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        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        17.23 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        0.16        17.49        12.30        86.76        19.27         8.88 
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-5891 
       26.04        25.35        13.25        10.82         7.66         0.95 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        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-7834 TCGA-DW-7836 TCGA-DW-7837 
        7.17         3.81        48.85       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-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        61.02        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6793 
       10.68        13.08         2.40         0.43        90.90        11.05 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
       71.44        25.15        20.52         6.38        17.98        16.90 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK 
       12.89        11.21        16.31        26.01        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W 
       25.22        19.99        85.78        88.24        96.69        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       22.26        21.34        16.34        12.36        12.76        10.55 
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        17.62        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA 
       31.13        29.26        15.48        99.78        87.09         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        19.73 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        49.45        44.61        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       41.33        16.31        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9PP 
       26.20       103.63       125.29        37.35        62.83        98.96 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ 
       86.37        71.24        30.67        47.47        65.13        21.60 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
      110.73        51.35        26.01        39.06        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         3.68         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 
                      117.40                       194.79 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                       18.41                        25.22 
[1] "0.5 - 117.4 (18.4)" "0.1 - 194.8 (25.2)"
[1] "hr=" "1.4"
D2V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 2(2Q32.1) MUTATED        28        4        12        7
  AMP PEAK 2(2Q32.1) WILD-TYPE     143       18        40        8
D2V3, multiclass
           clus
vv          AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  STAGE I                           28                          143
  STAGE II                           4                           18
  STAGE III                         12                           40
  STAGE IV                           7                            8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2 T3+T4
  AMP PEAK 2(2Q32.1) MUTATED    28   8    17
  AMP PEAK 2(2Q32.1) WILD-TYPE 162  25    45
D2V4, multiclass
       clus
vv      AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  T1                            28                          162
  T2                             8                           25
  T3+T4                         17                           45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2
  AMP PEAK 2(2Q32.1) MUTATED    9  9  3
  AMP PEAK 2(2Q32.1) WILD-TYPE 39 15  2
D2V5, multiclass
    clus
vv   AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  N0                          9                           39
  N1                          9                           15
  N2                          3                            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 78  4
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(2Q32.1) MUTATED     15    5
  AMP PEAK 2(2Q32.1) WILD-TYPE   78    4
   clus
vv  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  0                         15                           78
  1                          5                            4
[1] 2 2
[1] FALSE
D2V7, binary
                              cls
clus                             0   1
  AMP PEAK 2(2Q32.1) MUTATED    16  37
  AMP PEAK 2(2Q32.1) WILD-TYPE  60 174
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(2Q32.1) MUTATED     16   37
  AMP PEAK 2(2Q32.1) WILD-TYPE   60  174
        clus
vv       AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  FEMALE                         16                           60
  MALE                           37                          174
[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                           9    40
  AMP PEAK 2(2Q32.1) WILD-TYPE                        52   164
D2V11, multiclass
                                  clus
vv                                 AMP PEAK 2(2Q32.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 9
  WHITE                                                    40
                                  clus
vv                                 AMP PEAK 2(2Q32.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  52
  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"
D2V12, binary
                              cls
clus                             0   1
  AMP PEAK 2(2Q32.1) MUTATED     2  45
  AMP PEAK 2(2Q32.1) WILD-TYPE  10 194
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(2Q32.1) MUTATED      2   45
  AMP PEAK 2(2Q32.1) WILD-TYPE   10  194
                        clus
vv                       AMP PEAK 2(2Q32.1) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         45
                        clus
vv                       AMP PEAK 2(2Q32.1) WILD-TYPE
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          194
[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    78  17
  AMP PEAK 3(3Q27.1) WILD-TYPE 160  27
  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                          95                          187 
  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                          17                           27 
$`AMP PEAK 3(3Q27.1) MUTATED`
TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-5P-A9JY 
        7.04        59.01        58.22       100.27        56.91        49.58 
TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-A4-7287 
       78.64        71.80        19.36        12.99        12.39        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        49.32         2.20 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4114 
       37.51        21.67        21.07        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        74.60        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        84.89        11.84        25.22         2.04        85.78 
TCGA-IA-A83W TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5E6 
       67.17        18.41        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 
       87.09         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        53.10       117.40 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PZ 
      125.29        37.35        71.24        30.67        47.47        21.60 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-Y8-A895 TCGA-Y8-A8RZ 
      110.73        51.35        31.73        15.91         3.68 

$`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        91.73        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        39.88        38.99        33.07        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-5P-A9JU TCGA-5P-A9JV 
       22.49         0.13        12.82        11.57        12.26        67.17 
TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
      106.55        90.21        22.26        15.48        62.93        43.04 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 
       27.09        67.43        18.21        61.05         0.10        21.37 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
       35.18        19.13         0.89         7.82         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        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A47O 
       62.66        67.73        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 
       20.25        16.77        20.32        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        17.23 
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        10.82         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        48.85        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        90.90        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LC 
       71.44        25.15        20.52        25.84         6.38        23.08 
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 
       12.89        16.31        26.01        56.75        73.25        16.80 
TCGA-IA-A40X TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       19.99        88.24        96.69        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       12.36        12.76        10.55        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        17.62        12.13        31.13        29.26        15.48 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVO TCGA-PJ-A5Z8 
       42.94        99.12        92.58        52.27        78.90        19.73 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO 
       47.90        49.45        44.61        27.06        11.93        41.33 
TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PO 
       26.47        43.76        18.02        26.20       103.63        62.83 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PX TCGA-WN-A9G9 TCGA-WN-AB4C 
       98.96        86.27        86.37        65.13        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       18.64        18.64        18.05        15.62        25.28         6.02 
TCGA-Y8-A8S1 
       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 
                       25.22                        24.33 
[1] "0.5 - 194.8 (25.2)" "0.1 - 129.9 (24.3)"
[1] "hr=" "1.1"
D3V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 3(3Q27.1) MUTATED        61       11        15        3
  AMP PEAK 3(3Q27.1) WILD-TYPE     110       11        37       12
D3V3, multiclass
           clus
vv          AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE
  STAGE I                           61                          110
  STAGE II                          11                           11
  STAGE III                         15                           37
  STAGE IV                           3                           12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2 T3+T4
  AMP PEAK 3(3Q27.1) MUTATED    67  15    17
  AMP PEAK 3(3Q27.1) WILD-TYPE 123  18    45
D3V4, multiclass
       clus
vv      AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE
  T1                            67                          123
  T2                            15                           18
  T3+T4                         17                           45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2
  AMP PEAK 3(3Q27.1) MUTATED   12  6  2
  AMP PEAK 3(3Q27.1) WILD-TYPE 36 18  3
D3V5, multiclass
    clus
vv   AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE
  N0                         12                           36
  N1                          6                           18
  N2                          2                            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 64  9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(3Q27.1) MUTATED     29    0
  AMP PEAK 3(3Q27.1) WILD-TYPE   64    9
   clus
vv  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE
  0                         29                           64
  1                          0                            9
[1] 2 2
[1] FALSE
D3V7, binary
                              cls
clus                             0   1
  AMP PEAK 3(3Q27.1) MUTATED    24  76
  AMP PEAK 3(3Q27.1) WILD-TYPE  52 135
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(3Q27.1) MUTATED     24   76
  AMP PEAK 3(3Q27.1) WILD-TYPE   52  135
        clus
vv       AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE
  FEMALE                         24                           52
  MALE                           76                          135
[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                          18    71
  AMP PEAK 3(3Q27.1) WILD-TYPE                        43   133
D3V11, multiclass
                                  clus
vv                                 AMP PEAK 3(3Q27.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          2
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                18
  WHITE                                                    71
                                  clus
vv                                 AMP PEAK 3(3Q27.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  43
  WHITE                                                     133
[1] 4 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  83
  AMP PEAK 3(3Q27.1) WILD-TYPE   8 156
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(3Q27.1) MUTATED      4   83
  AMP PEAK 3(3Q27.1) WILD-TYPE    8  156
                        clus
vv                       AMP PEAK 3(3Q27.1) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                         83
                        clus
vv                       AMP PEAK 3(3Q27.1) WILD-TYPE
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          156
[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   5
  AMP PEAK 4(5Q35.2) WILD-TYPE 207  39
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                          36                          246 
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                           5                           39 
$`AMP PEAK 4(5Q35.2) MUTATED`
TCGA-2K-A9WE TCGA-2Z-A9JK TCGA-2Z-A9JR TCGA-4A-A93X TCGA-5P-A9K3 TCGA-5P-A9K9 
        7.04        38.99         5.29        12.82        15.48        19.36 
TCGA-A4-8098 TCGA-A4-8516 TCGA-A4-A48D TCGA-A4-A57E TCGA-AL-3466 TCGA-AL-3473 
       29.46         0.76        12.46         8.48         9.63        62.66 
TCGA-B1-5398 TCGA-B1-A656 TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5878 TCGA-BQ-5887 
       19.56        20.32         0.46         0.16        63.72        25.35 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-DW-7838 TCGA-EV-5902 TCGA-F9-A7Q0 
        7.66         0.95        11.97        24.46        19.00        13.08 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-A4EM TCGA-HE-A5NK TCGA-IA-A40X 
        0.43         4.01        23.08         1.05        73.25        19.99 
TCGA-IA-A40Y TCGA-KV-A6GD TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SQ 
        2.04        18.41        99.78        99.12        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 
       91.73        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 
       39.88        33.07        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JU 
       25.58        16.18        22.49         0.13        11.57        12.26 
TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       67.17       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 
       67.43        18.21        19.63        61.05         0.10        21.37 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
       35.18        19.13         0.89         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       30.48        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       19.73        14.33        16.96        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.99        12.46        70.19        76.64        49.32        66.71 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       67.73        49.25         2.20        37.51        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       16.87        20.25        16.77        21.07        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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
        2.10        19.23        17.23        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76        19.27         8.88        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
       21.63        40.83        26.04        30.28        26.04        13.25 
TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       10.82         7.92         2.76       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-7839 
       48.85        13.61       129.86        35.93        37.55        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-5903 TCGA-F9-A4JJ 
       51.19        61.02        74.60        34.19        24.89        10.68 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        2.40         1.18        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84         6.38        17.98 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95        12.89        11.21        16.31        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A83S 
       26.01        11.84        56.75        25.22        16.80        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       88.24        96.69        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36        12.76        10.55        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        17.62        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        29.26        15.48        87.09        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        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        49.45        44.61        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        41.33        16.31        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       37.35        62.83        98.96        86.27        86.37        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       30.67        47.47        65.13        21.60       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       31.73        26.01        39.06        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         3.68         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 
                      14.775                       26.010 
[1] "0.2 - 99.8 (14.8)"  "0.1 - 194.8 (26.0)"
[1] "hr=" "1.4"
D4V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 4(5Q35.2) MUTATED        16        2        11        4
  AMP PEAK 4(5Q35.2) WILD-TYPE     155       20        41       11
D4V3, multiclass
           clus
vv          AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  STAGE I                           16                          155
  STAGE II                           2                           20
  STAGE III                         11                           41
  STAGE IV                           4                           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   5    14
  AMP PEAK 4(5Q35.2) WILD-TYPE 172  28    48
D4V4, multiclass
       clus
vv      AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  T1                            18                          172
  T2                             5                           28
  T3+T4                         14                           48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2
  AMP PEAK 4(5Q35.2) MUTATED    9  5  2
  AMP PEAK 4(5Q35.2) WILD-TYPE 39 19  3
D4V5, multiclass
    clus
vv   AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  N0                          9                           39
  N1                          5                           19
  N2                          2                            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 78  7
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q35.2) MUTATED     15    2
  AMP PEAK 4(5Q35.2) WILD-TYPE   78    7
   clus
vv  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  0                         15                           78
  1                          2                            7
[1] 2 2
[1] FALSE
D4V7, binary
                              cls
clus                             0   1
  AMP PEAK 4(5Q35.2) MUTATED     9  28
  AMP PEAK 4(5Q35.2) WILD-TYPE  67 183
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q35.2) MUTATED      9   28
  AMP PEAK 4(5Q35.2) WILD-TYPE   67  183
        clus
vv       AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  FEMALE                          9                           67
  MALE                           28                          183
[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    27
  AMP PEAK 4(5Q35.2) WILD-TYPE                        55   177
D4V11, multiclass
                                  clus
vv                                 AMP PEAK 4(5Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 6
  WHITE                                                    27
                                  clus
vv                                 AMP PEAK 4(5Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  55
  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"
D4V12, binary
                              cls
clus                             0   1
  AMP PEAK 4(5Q35.2) MUTATED     0  32
  AMP PEAK 4(5Q35.2) WILD-TYPE  12 207
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q35.2) MUTATED      0   32
  AMP PEAK 4(5Q35.2) WILD-TYPE   12  207
                        clus
vv                       AMP PEAK 4(5Q35.2) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         32
                        clus
vv                       AMP PEAK 4(5Q35.2) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          207
[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   149  23
  AMP PEAK 5(7Q31.2) WILD-TYPE  89  21
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                         172                          110 
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                          23                           21 
$`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        33.07        30.71        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-5P-A9JU 
        5.29        16.18        22.49         0.13        12.82        12.26 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        71.80        62.93 
TCGA-5P-A9K9 TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7732 
       19.36        12.39        27.09        61.05        21.37        19.13 
TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
        0.89        16.64        30.48        25.64        23.97        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
        0.76        19.63        14.33        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 
       15.75        12.46        76.64        49.32        66.71        67.73 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 
       49.25         2.20        21.67        24.56        20.25        20.32 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       21.07        33.83        30.58        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-A8YH TCGA-BQ-5881 TCGA-BQ-5884 
       43.99        22.06        19.23        17.49        47.80        26.04 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
       25.35        10.82         0.95        11.97         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       48.26        96.92        50.40         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        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 
       24.46         3.75        14.63         3.02        40.77        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF 
       51.19        61.02        34.19        24.89        13.08         2.40 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-7502 
        1.18         4.01        51.78        11.05        39.25        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 
        6.38        17.98        23.08        80.65       194.79         3.68 
TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65        12.43        17.95        11.21        84.89        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40Y TCGA-IA-A83T TCGA-IA-A83V 
       11.84        56.75        25.22         2.04        88.24        96.69 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36        12.76        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 
       11.41        34.29        27.78        20.25        15.48        87.09 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       52.27        16.01        17.75        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       44.61        28.80        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        53.10        43.76        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        62.83        86.37        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-Y8-A895 
       65.13        21.60       110.73        51.35        31.73        15.91 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       18.64        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        91.73        75.42        54.64        51.52        39.88 
TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-5P-A9JV TCGA-5P-A9JW 
       38.99        24.33        31.20        11.57        67.17       106.55 
TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       15.48        43.04        12.99        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 
        0.10        35.18         7.82         0.23        29.46        23.28 
TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 
       19.73        12.46         8.28        12.99         9.63        70.19 
TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47O TCGA-B1-A655 TCGA-B3-3926 
       62.66        19.56        37.51        16.87        16.77        10.09 
TCGA-B3-4104 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI 
       34.49         2.10        17.23         0.16        14.86        12.30 
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-5882 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 
       21.63        40.83        30.28        26.04        13.25         7.66 
TCGA-BQ-5893 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 
        7.92        93.34        44.84        61.28        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-7839 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 
       20.12        11.28        13.78        79.86        74.60        19.00 
TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       10.68         0.43        90.90        71.44        25.15        20.52 
TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NK 
       16.90        12.92         1.05        12.89        16.31        73.25 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83W TCGA-IZ-8195 TCGA-J7-8537 
       16.80        19.99        85.78        67.17        22.26        10.55 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       30.38        27.65        17.62        12.13        31.13        29.26 
TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVM 
       99.78        42.94         6.61        99.12        92.58        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A7SL TCGA-SX-A7SO TCGA-UN-AAZ9 TCGA-UZ-A9PP 
       78.90        19.73        27.06        41.33        18.02        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 
       86.27        71.24        26.01        39.06        18.64        18.05 
TCGA-Y8-A8RZ TCGA-Y8-A8S1 
        3.68        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                       106.55 
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                      24.725                       23.805 
[1] "0.1 - 194.8 (24.7)" "0.1 - 106.5 (23.8)"
[1] "hr=" "1.4"
D5V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 5(7Q31.2) MUTATED       114       12        21       12
  AMP PEAK 5(7Q31.2) WILD-TYPE      57       10        31        3
D5V3, multiclass
           clus
vv          AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  STAGE I                          114                           57
  STAGE II                          12                           10
  STAGE III                         21                           31
  STAGE IV                          12                            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   124  21    31
  AMP PEAK 5(7Q31.2) WILD-TYPE  66  12    31
D5V4, multiclass
       clus
vv      AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  T1                           124                           66
  T2                            21                           12
  T3+T4                         31                           31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2
  AMP PEAK 5(7Q31.2) MUTATED   24 10  4
  AMP PEAK 5(7Q31.2) WILD-TYPE 24 14  1
D5V5, multiclass
    clus
vv   AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  N0                         24                           24
  N1                         10                           14
  N2                          4                            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   52  6
  AMP PEAK 5(7Q31.2) WILD-TYPE 41  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(7Q31.2) MUTATED     52    6
  AMP PEAK 5(7Q31.2) WILD-TYPE   41    3
   clus
vv  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  0                         52                           41
  1                          6                            3
[1] 2 2
[1] FALSE
D5V7, binary
                              cls
clus                             0   1
  AMP PEAK 5(7Q31.2) MUTATED    37 140
  AMP PEAK 5(7Q31.2) WILD-TYPE  39  71
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(7Q31.2) MUTATED     37  140
  AMP PEAK 5(7Q31.2) WILD-TYPE   39   71
        clus
vv       AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  FEMALE                         37                           39
  MALE                          140                           71
[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                          32   129
  AMP PEAK 5(7Q31.2) WILD-TYPE                        29    75
D5V11, multiclass
                                  clus
vv                                 AMP PEAK 5(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          2
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                32
  WHITE                                                   129
                                  clus
vv                                 AMP PEAK 5(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  29
  WHITE                                                      75
[1] 4 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     6 153
  AMP PEAK 5(7Q31.2) WILD-TYPE   6  86
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(7Q31.2) MUTATED      6  153
  AMP PEAK 5(7Q31.2) WILD-TYPE    6   86
                        clus
vv                       AMP PEAK 5(7Q31.2) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                        153
                        clus
vv                       AMP PEAK 5(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           86
[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   165  31
  AMP PEAK 6(17Q25.2) WILD-TYPE  73  13
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                          196                            86 
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                           31                            13 
$`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-5P-A9JY 
       25.58         5.29        16.18        22.49         0.13        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K9 TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7585 
       19.36        27.09        18.21        61.05        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 
       19.13         0.89         0.23        16.64        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.31         0.76        19.63        19.73        14.33 
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-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-A5DJ 
       12.46         9.63        76.64        49.32        66.71        49.25 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
        2.20        37.51        21.67        24.56        16.87        20.25 
TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       16.77        21.07        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-A5W9 
       15.12        43.99        22.06         2.10        19.23         0.16 
TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5886 
       17.49        86.76         8.88        43.20        47.80        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       25.35        13.25         7.66         0.95        11.97         7.92 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7058 TCGA-BQ-7060 
       48.26        96.92        50.40        49.84        11.28         7.04 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        48.85        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-EV-5901 TCGA-EV-5903 
       79.86        80.88        51.19        61.02        34.19        24.89 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6793 
       13.08         2.40         1.18         4.01        51.78        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       39.25        71.44        25.84         6.38        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R 
       16.90        80.65       194.79         3.68         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
       17.95        12.89        11.21        84.89        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83T TCGA-IA-A83V 
       56.75        25.22        16.80         2.04        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       22.26        21.34        16.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        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        87.09         6.61        99.12 
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        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       44.61        28.80        27.06        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        53.10        43.76        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
      125.29        62.83        98.96        86.37        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-V9-A7HT TCGA-WN-AB4C 
       47.47        65.13        21.60       110.73        31.73        39.06 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       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 
       91.73        75.42        54.64        39.88        38.99        33.07 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JU TCGA-5P-A9JV 
       24.33        31.20        12.82        11.57        12.26        67.17 
TCGA-5P-A9JW TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KH TCGA-A4-7287 
      106.55        43.04        12.99        12.39        67.43        19.63 
TCGA-A4-7583 TCGA-A4-7828 TCGA-A4-7997 TCGA-A4-8312 TCGA-A4-A48D TCGA-AL-3467 
        0.10         7.82        30.48        23.28        12.46        70.19 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A656 TCGA-B3-3926 TCGA-B9-4116 
       62.66        67.73        19.56        20.32        10.09        20.61 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 
       17.23        14.86        12.30        19.27        63.72        22.92 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5894 
       21.63        40.83        26.04        30.28        10.82         2.76 
TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7055 TCGA-BQ-7056 
      123.62        93.34        44.84        61.28        26.27        20.12 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G 
        7.63         7.17        74.60        19.00        10.68         0.43 
TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DE 
       90.90        25.15        20.52        12.92        27.65        16.31 
TCGA-HE-A5NK TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83W TCGA-MH-A854 TCGA-MH-A855 
       73.25        19.99        85.78        67.17        17.62        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-AAVK TCGA-P4-AAVM 
       31.13        29.26        99.78        42.94        52.27        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A7SM TCGA-SX-A7SO TCGA-UN-AAZ9 TCGA-UZ-A9PN 
       78.90        19.73        11.93        41.33        18.02        37.35 
TCGA-UZ-A9PQ TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       86.27        51.35        26.01        18.64        18.64        18.05 
TCGA-Y8-A8RZ TCGA-Y8-A8S1 
        3.68        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 
                        24.51                         24.74 
[1] "0.1 - 194.8 (24.5)" "0.1 - 123.6 (24.7)"
[1] "hr=" "1.1"
D6V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 6(17Q25.2) MUTATED       125       17        30       10
  AMP PEAK 6(17Q25.2) WILD-TYPE      46        5        22        5
D6V3, multiclass
           clus
vv          AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  STAGE I                           125                            46
  STAGE II                           17                             5
  STAGE III                          30                            22
  STAGE IV                           10                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  AMP PEAK 6(17Q25.2) MUTATED   135  26    38
  AMP PEAK 6(17Q25.2) WILD-TYPE  55   7    24
D6V4, multiclass
       clus
vv      AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  T1                            135                            55
  T2                             26                             7
  T3+T4                          38                            24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  AMP PEAK 6(17Q25.2) MUTATED   31 13  4
  AMP PEAK 6(17Q25.2) WILD-TYPE 17 11  1
D6V5, multiclass
    clus
vv   AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  N0                          31                            17
  N1                          13                            11
  N2                           4                             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   55  6
  AMP PEAK 6(17Q25.2) WILD-TYPE 38  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(17Q25.2) MUTATED     55    6
  AMP PEAK 6(17Q25.2) WILD-TYPE   38    3
   clus
vv  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  0                          55                            38
  1                           6                             3
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK 6(17Q25.2) MUTATED    45 155
  AMP PEAK 6(17Q25.2) WILD-TYPE  31  56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(17Q25.2) MUTATED     45  155
  AMP PEAK 6(17Q25.2) WILD-TYPE   31   56
        clus
vv       AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  FEMALE                          45                            31
  MALE                           155                            56
[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                          35   149
  AMP PEAK 6(17Q25.2) WILD-TYPE                        26    55
D6V11, multiclass
                                  clus
vv                                 AMP PEAK 6(17Q25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 35
  WHITE                                                    149
                                  clus
vv                                 AMP PEAK 6(17Q25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                       55
[1] 4 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     7 171
  AMP PEAK 6(17Q25.2) WILD-TYPE   5  68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(17Q25.2) MUTATED      7  171
  AMP PEAK 6(17Q25.2) WILD-TYPE    5   68
                        clus
vv                       AMP PEAK 6(17Q25.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         171
                        clus
vv                       AMP PEAK 6(17Q25.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            68
[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    25   4
  AMP PEAK 7(19P13.2) WILD-TYPE 213  40
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                           29                           253 
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                            4                            40 
$`AMP PEAK 7(19P13.2) MUTATED`
TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JR TCGA-5P-A9KC TCGA-A4-7732 
       58.22         4.57        56.81         5.29        12.39        19.13 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3472 TCGA-B9-4113 TCGA-B9-4116 TCGA-B9-4617 
       16.31        15.75        66.71        50.50        20.61         1.15 
TCGA-BQ-5885 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-DW-5561 TCGA-DW-7840 TCGA-EV-5901 
       30.28         0.95        11.97        13.61         3.75        34.19 
TCGA-F9-A7Q0 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-A5NJ 
       13.08        39.25         6.38        23.08         3.68        56.75 
TCGA-IZ-8196 TCGA-P4-A5E7 TCGA-P4-AAVL TCGA-SX-A7SU TCGA-UZ-A9PX 
       21.34        87.09        16.01        43.76        65.13 

$`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        91.73 
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        39.88        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       33.07        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-5P-A9JU 
       16.18        22.49         0.13        12.82        11.57        12.26 
TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       67.17       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       15.48        71.80        62.93        43.04        19.36        12.99 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       27.09        67.43        18.21        19.63        61.05         0.10 
TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
       21.37        35.18         0.89         7.82         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-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
        8.48         8.28        12.99        12.46         9.63        70.19 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       76.64        49.32        62.66        67.73        49.25         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56        37.51        21.67        24.56        16.87        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77        20.32        21.07        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       34.49        12.46        10.16        28.18        26.40         0.46 
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        17.23 
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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        26.04        25.35        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        7.66         7.92         2.76       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-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       48.85       129.86        35.93        37.55        24.46        13.78 
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-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
       61.02        74.60        19.00        24.89        10.68         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        90.90        11.05 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LB TCGA-G7-A8LD 
       71.44        25.15        20.52        25.84        17.98        16.90 
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        12.89        11.21        16.31        84.89        26.01 
TCGA-HE-A5NI TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       11.84        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-A6M8 
       85.78        88.24        96.69        67.17        22.26        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.36        12.76        10.55        18.41        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        17.62 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E8 
       12.13        31.13        29.26        15.48        99.78        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO 
        6.61        99.12        92.58        52.27        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       19.73        17.75        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        41.33        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       41.62        26.47        53.10        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      103.63       125.29        37.35        62.83        98.96        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PZ TCGA-UZ-A9Q0 
       86.37        71.24        30.67        47.47        21.60       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       51.35        31.73        26.01        39.06        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         3.68         6.02 
TCGA-Y8-A8S1 
       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 
                        87.09                        194.79 
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                        19.13                         25.22 
[1] "0.9 - 87.1 (19.1)"  "0.1 - 194.8 (25.2)"
[1] "hr=" "1.1"
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 7(19P13.2) MUTATED        17        2         5        1
  AMP PEAK 7(19P13.2) WILD-TYPE     154       20        47       14
D7V3, multiclass
           clus
vv          AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  STAGE I                            17                           154
  STAGE II                            2                            20
  STAGE III                           5                            47
  STAGE IV                            1                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  AMP PEAK 7(19P13.2) MUTATED    19   7     5
  AMP PEAK 7(19P13.2) WILD-TYPE 171  26    57
D7V4, multiclass
       clus
vv      AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  T1                             19                           171
  T2                              7                            26
  T3+T4                           5                            57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  AMP PEAK 7(19P13.2) MUTATED    7  2  0
  AMP PEAK 7(19P13.2) WILD-TYPE 41 22  5
D7V5, multiclass
    clus
vv   AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  N0                           7                            41
  N1                           2                            22
  N2                           0                             5
[1] 3 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 82  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(19P13.2) MUTATED     11    1
  AMP PEAK 7(19P13.2) WILD-TYPE   82    8
   clus
vv  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  0                          11                            82
  1                           1                             8
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK 7(19P13.2) MUTATED     9  22
  AMP PEAK 7(19P13.2) WILD-TYPE  67 189
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(19P13.2) MUTATED      9   22
  AMP PEAK 7(19P13.2) WILD-TYPE   67  189
        clus
vv       AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  FEMALE                           9                            67
  MALE                            22                           189
[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    19
  AMP PEAK 7(19P13.2) WILD-TYPE                        53   185
D7V11, multiclass
                                  clus
vv                                 AMP PEAK 7(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     19
                                  clus
vv                                 AMP PEAK 7(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   53
  WHITE                                                      185
[1] 4 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  26
  AMP PEAK 7(19P13.2) WILD-TYPE  10 213
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(19P13.2) MUTATED      2   26
  AMP PEAK 7(19P13.2) WILD-TYPE   10  213
                        clus
vv                       AMP PEAK 7(19P13.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          26
                        clus
vv                       AMP PEAK 7(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           213
[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    38  17
  DEL PEAK  1(1P36.31) WILD-TYPE 200  27
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            55                            227 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            17                             27 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9JY TCGA-5P-A9K3 
       91.73        54.64        51.52        12.82        49.58        15.48 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-8098 
       43.04        19.36        67.43        18.21         0.10        29.46 
TCGA-A4-A5XZ TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-3926 
       15.75        12.99         9.63        49.25        37.51        10.09 
TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5877 
       20.61         2.10        17.23        14.86        86.76         8.88 
TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5894 
       22.92        21.63        30.28        13.25         7.66         2.76 
TCGA-BQ-7044 TCGA-BQ-7055 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 
      123.62        26.27        19.00        10.68        13.08         4.01 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 
       25.15        20.52        25.84        23.08        16.90         3.68 
TCGA-GL-8500 TCGA-HE-A5NK TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EA TCGA-P4-AAVO 
       27.65        73.25         2.04        10.55         6.61        78.90 
TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-A9G9 
       19.73        14.07        18.02        37.35        86.27        26.01 
TCGA-Y8-A8RZ 
        3.68 

$`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        39.88        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       33.07        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-5P-A9JU 
        5.29        16.18        22.49         0.13        11.57        12.26 
TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 
       67.17       106.55        90.21        22.26        78.64        71.80 
TCGA-5P-A9K6 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7287 TCGA-A4-7288 
       62.93        12.99        12.39        27.09        19.63        61.05 
TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 
       21.37        35.18        19.13         0.89         7.82         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-A4-8517 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-A57E TCGA-A4-A5DU TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
        8.48        16.31         8.28        12.46        70.19        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87        20.25        16.77        20.32 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       21.07        33.83        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       50.50        28.18        26.40         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI 
       43.99        22.06        19.23         0.16        17.49        12.30 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       19.27        63.72        43.20        47.80        40.83        26.04 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       26.04        25.35        10.82         0.95        11.97         7.92 
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-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        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        48.85        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        74.60        34.19 
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        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE 
       11.05        39.25        71.44         6.38        17.98        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
      194.79        12.92         1.05        12.43        17.95        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21        16.31        84.89        26.01        11.84        56.75 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
       67.17        22.26        21.34        16.34        12.36        12.76 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        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        17.62        12.13        31.13        29.26 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.09        42.94        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
       52.27        16.01        50.60        17.75        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       44.61        28.80        27.06        11.93        19.00        41.33 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ 
       16.31        41.62        26.47        53.10        43.76        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PR 
      117.40       103.63       125.29        62.83        98.96        86.37 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 
       71.24        30.67        47.47        65.13        21.60       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       51.35        31.73        39.06        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  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 
                         19.36                          25.64 
[1] "0.1 - 123.6 (19.4)" "0.1 - 194.8 (25.6)"
[1] "hr=" "3.4"
D8V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  1(1P36.31) MUTATED        17        3        22        5
  DEL PEAK  1(1P36.31) WILD-TYPE     154       19        30       10
D8V3, multiclass
           clus
vv          DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  STAGE I                             17                            154
  STAGE II                             3                             19
  STAGE III                           22                             30
  STAGE IV                             5                             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    21   7    27
  DEL PEAK  1(1P36.31) WILD-TYPE 169  26    35
D8V4, multiclass
       clus
vv      DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T1                              21                            169
  T2                               7                             26
  T3+T4                           27                             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  1(1P36.31) MUTATED    7 13  2
  DEL PEAK  1(1P36.31) WILD-TYPE 41 11  3
D8V5, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  N0                            7                             41
  N1                           13                             11
  N2                            2                              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 77  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     16    3
  DEL PEAK  1(1P36.31) WILD-TYPE   77    6
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                           16                             77
  1                            3                              6
[1] 2 2
[1] FALSE
D8V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    21  34
  DEL PEAK  1(1P36.31) WILD-TYPE  55 177
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     21   34
  DEL PEAK  1(1P36.31) WILD-TYPE   55  177
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                           21                             55
  MALE                             34                            177
[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    38
  DEL PEAK  1(1P36.31) WILD-TYPE                        49   166
D8V11, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      38
                                  clus
vv                                 DEL PEAK  1(1P36.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    49
  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"
D8V12, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED     1  44
  DEL PEAK  1(1P36.31) WILD-TYPE  11 195
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      1   44
  DEL PEAK  1(1P36.31) WILD-TYPE   11  195
                        clus
vv                       DEL PEAK  1(1P36.31) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           44
                        clus
vv                       DEL PEAK  1(1P36.31) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            195
[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     5   3
  DEL PEAK  2(2P12) WILD-TYPE 233  41
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          8                         274 
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          3                          41 
$`DEL PEAK  2(2P12) MUTATED`
TCGA-4A-A93X TCGA-5P-A9K3 TCGA-5P-A9KH TCGA-A4-A57E TCGA-BQ-5875 TCGA-BQ-5885 
       12.82        15.48        67.43         8.48        86.76        30.28 
TCGA-G7-6792 TCGA-UZ-A9PQ 
       90.90        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        91.73        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        39.88        38.99        33.07        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-5P-A9JU TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY 
        0.13        11.57        12.26        67.17       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7287 
       19.36        12.99        12.39        27.09        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       61.05         0.10        21.37        35.18        19.13         0.89 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       12.99        12.46         9.63        70.19        76.64        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       66.71        62.66        67.73        49.25         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
       37.51        21.67        24.56        16.87        20.25        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       20.32        21.07        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        17.23         0.16        14.86        17.49        12.30 
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-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.82         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        48.85        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 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6793 
        2.40         1.18         0.43         4.01        51.78        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        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        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21        16.31        84.89        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       88.24        96.69        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.36        12.76        10.55        18.41        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        17.62 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        31.13        29.26        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        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        19.73        17.75        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        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 
       41.33        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       62.83        98.96        86.37        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       65.13        21.60       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       39.06        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         3.68         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 
                      90.90                      194.79 
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                     48.855                      24.395 
[1] "8.5 - 90.9 (48.9)"  "0.1 - 194.8 (24.4)"
[1] "hr=" "1.6"
D9V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  2(2P12) MUTATED         1        0         3        2
  DEL PEAK  2(2P12) WILD-TYPE     170       22        49       13
D9V3, multiclass
           clus
vv          DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  STAGE I                           1                         170
  STAGE II                          0                          22
  STAGE III                         3                          49
  STAGE IV                          2                          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     2   3     3
  DEL PEAK  2(2P12) WILD-TYPE 188  30    59
D9V4, multiclass
       clus
vv      DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  T1                            2                         188
  T2                            3                          30
  T3+T4                         3                          59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2
  DEL PEAK  2(2P12) MUTATED    2  2  0
  DEL PEAK  2(2P12) WILD-TYPE 46 22  5
D9V5, multiclass
    clus
vv   DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  N0                         2                          46
  N1                         2                          22
  N2                         0                           5
[1] 3 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 91  8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(2P12) MUTATED      2    1
  DEL PEAK  2(2P12) WILD-TYPE   91    8
   clus
vv  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  0                         2                          91
  1                         1                           8
[1] 2 2
[1] FALSE
D9V7, binary
                             cls
clus                            0   1
  DEL PEAK  2(2P12) MUTATED     1   7
  DEL PEAK  2(2P12) WILD-TYPE  75 204
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(2P12) MUTATED      1    7
  DEL PEAK  2(2P12) WILD-TYPE   75  204
        clus
vv       DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  FEMALE                         1                          75
  MALE                           7                         204
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
D9V10, continuous
[1] "Remove cluster labels:"    "DEL PEAK  2(2P12) MUTATED"
clus
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          1                          53 
                 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-B9-4114                  TCGA-B9-4117 
"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-7963                  TCGA-F9-A97G 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-6793                  TCGA-G7-6795 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-7501                  TCGA-G7-A8LB 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-A8LD                  TCGA-G7-A8LE 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-GL-7773                  TCGA-GL-A9DD 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-HE-A5NI                  TCGA-IA-A40U 
"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-A5E6                  TCGA-P4-AAVK 
"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-WN-AB4C                  TCGA-Y8-A894 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-Y8-A896                  TCGA-Y8-A8RY 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-Y8-A8RZ 
"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     6
  DEL PEAK  2(2P12) WILD-TYPE                        59   198
D9V11, multiclass
                                  clus
vv                                 DEL PEAK  2(2P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                    6
                                  clus
vv                                 DEL PEAK  2(2P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 59
  WHITE                                                    198
[1] 4 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   7
  DEL PEAK  2(2P12) WILD-TYPE  12 232
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(2P12) MUTATED      0    7
  DEL PEAK  2(2P12) WILD-TYPE   12  232
                        clus
vv                       DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  HISPANIC OR LATINO                             0                          12
  NOT HISPANIC OR LATINO                         7                         232
[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     7   2
  DEL PEAK  3(2Q22.1) WILD-TYPE 231  42
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            9                           273 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            2                            42 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9KH TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B9-A69E 
       51.52        12.82        67.43        12.99         9.63        14.86 
TCGA-BQ-5878 TCGA-BQ-5888 TCGA-Q2-A5QZ 
       63.72        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        91.73        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 
       39.88        38.99        33.07        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-5P-A9JU TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
       11.57        12.26        67.17       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7287 
       19.36        12.99        12.39        27.09        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       61.05         0.10        21.37        35.18        19.13         0.89 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         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-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
        8.28        12.46        70.19        76.64        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       62.66        67.73        49.25         2.20        19.56        37.51 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87        20.25        16.77        20.32 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       21.07        33.83        10.09        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-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
       17.23         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-5889 TCGA-BQ-5890 
       26.04        30.28        26.04        25.35        10.82         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        48.85        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        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        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        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        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        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        84.89        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       96.69        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.76        10.55        18.41        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        17.62        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       31.13        29.26        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       78.90        19.73        17.75        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        41.33        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9PP 
      117.40       103.63       125.29        37.35        62.83        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        86.37        71.24        30.67        47.47        65.13 
TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       21.60       110.73        51.35        31.73        26.01        39.06 
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 
        3.68         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 
                        67.43                        194.79 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                        14.07                         24.89 
[1] "9.6 - 67.4 (14.1)"  "0.1 - 194.8 (24.9)"
[1] "hr=" "1.7"
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  3(2Q22.1) MUTATED         1        0         6        2
  DEL PEAK  3(2Q22.1) WILD-TYPE     170       22        46       13
D10V3, multiclass
           clus
vv          DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE I                             1                           170
  STAGE II                            0                            22
  STAGE III                           6                            46
  STAGE IV                            2                            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     3   0     7
  DEL PEAK  3(2Q22.1) WILD-TYPE 187  33    55
D10V4, multiclass
       clus
vv      DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1                              3                           187
  T2                              0                            33
  T3+T4                           7                            55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  3(2Q22.1) MUTATED    1  4  0
  DEL PEAK  3(2Q22.1) WILD-TYPE 47 20  5
D10V5, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  N0                           1                            47
  N1                           4                            20
  N2                           0                             5
[1] 3 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 90  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      3    1
  DEL PEAK  3(2Q22.1) WILD-TYPE   90    8
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                           3                            90
  1                           1                             8
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     4   6
  DEL PEAK  3(2Q22.1) WILD-TYPE  72 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      4    6
  DEL PEAK  3(2Q22.1) WILD-TYPE   72  205
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                           4                            72
  MALE                             6                           205
[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     8
  DEL PEAK  3(2Q22.1) WILD-TYPE                        60   196
D10V11, multiclass
                                  clus
vv                                 DEL PEAK  3(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                      8
                                  clus
vv                                 DEL PEAK  3(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   60
  WHITE                                                      196
[1] 4 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   7
  DEL PEAK  3(2Q22.1) WILD-TYPE  12 232
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      0    7
  DEL PEAK  3(2Q22.1) WILD-TYPE   12  232
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           7
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           232
[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    10   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 228  43
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           11                           271 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            1                            43 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-4A-A93X TCGA-5P-A9KH TCGA-A4-7585 TCGA-A4-A5Y0 TCGA-B3-4104 TCGA-B9-4117 
       12.82        67.43        35.18         8.28        34.49         0.46 
TCGA-B9-A69E TCGA-BQ-5878 TCGA-MH-A855 TCGA-Q2-A5QZ TCGA-Y8-A8RZ 
       14.86        63.72        12.13        14.07         3.68 

$`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        91.73        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        39.88        38.99        33.07        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-5P-A9JU TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY 
        0.13        11.57        12.26        67.17       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 
       43.04        19.36        12.99        12.39        27.09        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        21.37        19.13         0.89 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         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-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       12.99        12.46         9.63        70.19        76.64        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       66.71        62.66        67.73        49.25         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
       37.51        21.67        24.56        16.87        20.25        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 
       20.32        21.07        33.83        10.09        30.58        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
       10.16        50.50        28.18        26.40        20.61         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        17.23 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        0.16        17.49        12.30        86.76        19.27         8.88 
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-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         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        48.85        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        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        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        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        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        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        84.89        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       96.69        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.76        10.55        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       29.26        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        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 
       19.73        17.75        47.90        49.45        44.61        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        41.33        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      103.63       125.29        37.35        62.83        98.96        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ 
       86.37        71.24        30.67        47.47        65.13        21.60 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       15.91        18.64        18.05        15.62        25.28         6.02 
TCGA-Y8-A8S1 
       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 
                        67.43                        194.79 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                        14.07                         24.89 
[1] "0.5 - 67.4 (14.1)"  "0.1 - 194.8 (24.9)"
[1] "hr=" "1.1"
D11V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  4(2Q37.3) MUTATED         2        2         5        1
  DEL PEAK  4(2Q37.3) WILD-TYPE     169       20        47       14
D11V3, multiclass
           clus
vv          DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  STAGE I                             2                           169
  STAGE II                            2                            20
  STAGE III                           5                            47
  STAGE IV                            1                            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     3   3     6
  DEL PEAK  4(2Q37.3) WILD-TYPE 187  30    56
D11V4, multiclass
       clus
vv      DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  T1                              3                           187
  T2                              3                            30
  T3+T4                           6                            56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  4(2Q37.3) MUTATED    2  2  0
  DEL PEAK  4(2Q37.3) WILD-TYPE 46 22  5
D11V5, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  N0                           2                            46
  N1                           2                            22
  N2                           0                             5
[1] 3 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 89  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      4    0
  DEL PEAK  4(2Q37.3) WILD-TYPE   89    9
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                           4                            89
  1                           0                             9
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     6   6
  DEL PEAK  4(2Q37.3) WILD-TYPE  70 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      6    6
  DEL PEAK  4(2Q37.3) WILD-TYPE   70  205
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                           6                            70
  MALE                             6                           205
[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                            74 
                   TCGA-2Z-A9JE                    TCGA-2Z-A9JK 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-2Z-A9JL                    TCGA-2Z-A9JN 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-2Z-A9JT                    TCGA-4A-A93W 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-4A-A93Y                    TCGA-5P-A9JU 
"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-A4-8098                    TCGA-A4-8310 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-8311                    TCGA-A4-8312 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-8517                    TCGA-A4-8518 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-8630                    TCGA-A4-A48D 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-A4ZT                    TCGA-A4-A57E 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-A5DU                    TCGA-A4-A5XZ 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-A6HP                    TCGA-AL-3466 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DW-5560                    TCGA-DW-5561 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7834                    TCGA-DW-7836 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7837                    TCGA-DW-7838 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7839                    TCGA-DW-7840 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7841                    TCGA-DW-7842 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7963                    TCGA-EV-5901 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-EV-5902                    TCGA-EV-5903 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-F9-A7Q0                    TCGA-G7-6789 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-6790                    TCGA-G7-6792 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-6793                    TCGA-G7-6795 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-6796                    TCGA-G7-6797 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-7501                    TCGA-G7-7502 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-A4TM                    TCGA-G7-A8LB 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-A8LC                    TCGA-G7-A8LD 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-A8LE                    TCGA-IA-A40U 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-IA-A40X                    TCGA-IA-A40Y 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-J7-8537                    TCGA-P4-AAVK 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A71R                    TCGA-SX-A71S 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A71U                    TCGA-SX-A71V 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SL                    TCGA-SX-A7SM 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SN                    TCGA-SX-A7SO 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SP                    TCGA-SX-A7SQ 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SR                    TCGA-SX-A7SS 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SU                    TCGA-UZ-A9PL 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-UZ-A9PZ                    TCGA-V9-A7HT 
"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     8
  DEL PEAK  4(2Q37.3) WILD-TYPE                        58   196
D11V11, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                      8
                                  clus
vv                                 DEL PEAK  4(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   58
  WHITE                                                      196
[1] 4 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  10
  DEL PEAK  4(2Q37.3) WILD-TYPE  12 229
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      0   10
  DEL PEAK  4(2Q37.3) WILD-TYPE   12  229
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          10
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           229
[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    14  11
  DEL PEAK  5(3P22.1) WILD-TYPE 224  33
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                           25                           257 
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                           11                            33 
$`DEL PEAK  5(3P22.1) MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-5P-A9K3 TCGA-5P-A9K9 TCGA-A4-A57E 
       54.64        51.52        38.99        15.48        19.36         8.48 
TCGA-A4-A5Y1 TCGA-AL-3473 TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5882 
       12.99        62.66         2.10        14.86         8.88        21.63 
TCGA-BQ-5892 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD 
       11.97        79.86         4.01        20.52        23.08        16.90 
TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UZ-A9PQ TCGA-WN-A9G9 
        3.68         2.04        10.55        14.07        86.27        26.01 
TCGA-Y8-A8RZ 
        3.68 

$`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        91.73        75.42        34.85        56.81        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       33.07        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-5P-A9JU TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.26        67.17       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       78.64        71.80        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       27.09        67.43        18.21        19.63        61.05         0.10 
TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 
       21.37        35.18        19.13         0.89         7.82         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-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
       16.96        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ 
       70.19        76.64        49.32        66.71        67.73        49.25 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
        2.20        19.56        37.51        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        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-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        19.23        17.23         0.16        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76        19.27        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-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         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        48.85        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        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        0.43        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 
       25.15        25.84         6.38        17.98        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        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21        16.31        84.89        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25        25.22        16.80        19.99        85.78        88.24 
TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       96.69        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        18.41        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        17.62        12.13        31.13 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       29.26        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        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 
       19.73        17.75        47.90        49.45        44.61        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        41.33        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PR 
      103.63       125.29        37.35        62.83        98.96        86.37 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 
       71.24        30.67        47.47        65.13        21.60       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       51.35        31.73        39.06        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 
                         2.04                          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 
                        15.48                         25.35 
[1] "2.0 - 86.3 (15.5)"  "0.1 - 194.8 (25.4)"
[1] "hr=" "5.1"
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     166       21        38       12
D12V3, multiclass
           clus
vv          DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  STAGE I                             5                           166
  STAGE II                            1                            21
  STAGE III                          14                            38
  STAGE IV                            3                            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  5(3P22.1) MUTATED     6   4    15
  DEL PEAK  5(3P22.1) WILD-TYPE 184  29    47
D12V4, multiclass
       clus
vv      DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  T1                              6                           184
  T2                              4                            29
  T3+T4                          15                            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  5(3P22.1) MUTATED    6  8  2
  DEL PEAK  5(3P22.1) WILD-TYPE 42 16  3
D12V5, multiclass
    clus
vv   DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  N0                           6                            42
  N1                           8                            16
  N2                           2                             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 89  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED      4    2
  DEL PEAK  5(3P22.1) WILD-TYPE   89    7
   clus
vv  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  0                           4                            89
  1                           2                             7
[1] 2 2
[1] FALSE
D12V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P22.1) MUTATED     7  18
  DEL PEAK  5(3P22.1) WILD-TYPE  69 193
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED      7   18
  DEL PEAK  5(3P22.1) WILD-TYPE   69  193
        clus
vv       DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  FEMALE                           7                            69
  MALE                            18                           193
[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    18
  DEL PEAK  5(3P22.1) WILD-TYPE                        56   186
D12V11, multiclass
                                  clus
vv                                 DEL PEAK  5(3P22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     18
                                  clus
vv                                 DEL PEAK  5(3P22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   56
  WHITE                                                      186
[1] 4 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  22
  DEL PEAK  5(3P22.1) WILD-TYPE  12 217
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED      0   22
  DEL PEAK  5(3P22.1) WILD-TYPE   12  217
                        clus
vv                       DEL PEAK  5(3P22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          22
                        clus
vv                       DEL PEAK  5(3P22.1) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           217
[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    19  12
  DEL PEAK  6(4Q34.3) WILD-TYPE 219  32
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           31                           251 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           12                            32 
$`DEL PEAK  6(4Q34.3) MUTATED`
TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K3 TCGA-5P-A9K9 TCGA-A4-7287 TCGA-A4-8098 
       51.52        12.82        15.48        19.36        19.63        29.46 
TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-3926 TCGA-B3-4104 
        8.48        12.99        49.25        37.51        10.09        34.49 
TCGA-BQ-5876 TCGA-BQ-5882 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-DZ-6131 TCGA-F9-A4JJ 
       19.27        21.63         7.66         2.76        79.86        10.68 
TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-7501 TCGA-GL-7966 TCGA-HE-A5NK TCGA-IA-A40Y 
       13.08         0.43        20.52         3.68        73.25         2.04 
TCGA-J7-8537 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-AAVK TCGA-Q2-A5QZ TCGA-SX-A7SS 
       10.55        42.94         6.61        52.27        14.07        53.10 
TCGA-UN-AAZ9 
       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        91.73        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 
       39.88        38.99        33.07        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-5P-A9JU TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
       11.57        12.26        67.17       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        71.80        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        61.05         0.10 
TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 
       21.37        35.18        19.13         0.89         7.82         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-A4-8517 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-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       76.64        49.32        66.71        62.66        67.73         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        20.25        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 
       20.32        21.07        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-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23        17.23 
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-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        10.82         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
       11.97         7.92       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        48.85 
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-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        40.77        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF 
       61.02        74.60        34.19        19.00        24.89         2.40 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        1.18         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       71.44        25.15        25.84         6.38        17.98        23.08 
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        12.89        11.21        16.31        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       26.01        11.84        56.75        25.22        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       85.78        88.24        96.69        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       16.34        12.36        12.76        18.41        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        17.62 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        31.13        29.26        15.48        99.78        87.09 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       99.12        92.58        16.01        50.60        78.90        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        49.45        44.61        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        41.33        16.31        41.62        26.47 
TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       43.76        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       62.83        98.96        86.27        86.37        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       47.47        65.13        21.60       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        39.06        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         3.68         6.02        13.28 

  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                         0.43                          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 
                        18.02                         25.35 
[1] "0.4 - 79.9 (18.0)"  "0.1 - 194.8 (25.4)"
[1] "hr=" "4.9"
D13V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  6(4Q34.3) MUTATED         7        2        17        3
  DEL PEAK  6(4Q34.3) WILD-TYPE     164       20        35       12
D13V3, multiclass
           clus
vv          DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  STAGE I                             7                           164
  STAGE II                            2                            20
  STAGE III                          17                            35
  STAGE IV                            3                            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   5    18
  DEL PEAK  6(4Q34.3) WILD-TYPE 181  28    44
D13V4, multiclass
       clus
vv      DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  T1                              9                           181
  T2                              5                            28
  T3+T4                          18                            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  6(4Q34.3) MUTATED    7 10  1
  DEL PEAK  6(4Q34.3) WILD-TYPE 41 14  4
D13V5, multiclass
    clus
vv   DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  N0                           7                            41
  N1                          10                            14
  N2                           1                             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 81  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     12    2
  DEL PEAK  6(4Q34.3) WILD-TYPE   81    7
   clus
vv  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  0                          12                            81
  1                           2                             7
[1] 2 2
[1] FALSE
D13V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(4Q34.3) MUTATED    15  17
  DEL PEAK  6(4Q34.3) WILD-TYPE  61 194
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     15   17
  DEL PEAK  6(4Q34.3) WILD-TYPE   61  194
        clus
vv       DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  FEMALE                          15                            61
  MALE                            17                           194
[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    19
  DEL PEAK  6(4Q34.3) WILD-TYPE                        55   185
D13V11, multiclass
                                  clus
vv                                 DEL PEAK  6(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     19
                                  clus
vv                                 DEL PEAK  6(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   55
  WHITE                                                      185
[1] 4 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  24
  DEL PEAK  6(4Q34.3) WILD-TYPE  10 215
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED      2   24
  DEL PEAK  6(4Q34.3) WILD-TYPE   10  215
                        clus
vv                       DEL PEAK  6(4Q34.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          24
                        clus
vv                       DEL PEAK  6(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           215
[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 230  40
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                            12                            270 
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                             4                             40 
$`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        91.73        39.88        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 
       33.07        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-5P-A9JU TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.26        67.17       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7288 
       12.99        12.39        27.09        67.43        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
        0.10        21.37        35.18        19.13         0.89         7.82 
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        70.19        76.64        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       66.71        62.66        67.73        49.25         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
       37.51        21.67        24.56        16.87        20.25        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       20.32        21.07        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        17.23         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 
       10.82         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        48.85        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        74.60 
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        90.90        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84         6.38        17.98        23.08 
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        12.89        11.21        16.31        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W 
       19.99         2.04        85.78        88.24        96.69        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       22.26        21.34        16.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        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        17.62        12.13        31.13        29.26 
TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       15.48        87.09        42.94        99.12        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        19.73        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        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        41.33        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       37.35        62.83        98.96        86.27        86.37        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       30.67        47.47        65.13        21.60       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       31.73        26.01        39.06        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         3.68         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                         24.725 
[1] "2.8 - 99.8 (20.6)"  "0.1 - 194.8 (24.7)"
[1] "hr=" "2"  
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     166       22        47       13
D14V3, multiclass
           clus
vv          DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE
  STAGE I                              5                            166
  STAGE II                             0                             22
  STAGE III                            5                             47
  STAGE IV                             2                             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  7(5P15.33) MUTATED     5   1     7
  DEL PEAK  7(5P15.33) WILD-TYPE 185  32    55
D14V4, multiclass
       clus
vv      DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE
  T1                               5                            185
  T2                               1                             32
  T3+T4                            7                             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK  7(5P15.33) MUTATED    0  5  1
  DEL PEAK  7(5P15.33) WILD-TYPE 48 19  4
D14V5, multiclass
    clus
vv   DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE
  N0                            0                             48
  N1                            5                             19
  N2                            1                              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"
D14V6, binary
                                cls
clus                              0  1
  DEL PEAK  7(5P15.33) MUTATED    4  1
  DEL PEAK  7(5P15.33) WILD-TYPE 89  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(5P15.33) MUTATED      4    1
  DEL PEAK  7(5P15.33) WILD-TYPE   89    8
   clus
vv  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE
  0                            4                             89
  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  69 205
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(5P15.33) MUTATED      7    6
  DEL PEAK  7(5P15.33) WILD-TYPE   69  205
        clus
vv       DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE
  FEMALE                            7                             69
  MALE                              6                            205
[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                             74 
                    TCGA-2Z-A9JE                     TCGA-2Z-A9JK 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-2Z-A9JL                     TCGA-2Z-A9JN 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-2Z-A9JT                     TCGA-4A-A93W 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-4A-A93X                     TCGA-4A-A93Y 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-5P-A9JU                     TCGA-A4-7828 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-8098                     TCGA-A4-8310 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-8311                     TCGA-A4-8312 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-8517                     TCGA-A4-8518 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-8630                     TCGA-A4-A48D 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-A4ZT                     TCGA-A4-A57E 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-A5DU                     TCGA-A4-A5XZ 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-A6HP                     TCGA-AL-3466 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-5560                     TCGA-DW-5561 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-7834                     TCGA-DW-7836 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-7837                     TCGA-DW-7838 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-7839                     TCGA-DW-7840 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-7841                     TCGA-DW-7842 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-7963                     TCGA-EV-5901 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-EV-5902                     TCGA-EV-5903 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-F9-A7Q0                     TCGA-G7-6789 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-6790                     TCGA-G7-6792 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-6795                     TCGA-G7-6796 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-6797                     TCGA-G7-7501 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-7502                     TCGA-G7-A4TM 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-A8LB                     TCGA-G7-A8LC 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-A8LD                     TCGA-G7-A8LE 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-IA-A40U                     TCGA-IA-A40X 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-IA-A40Y                     TCGA-J7-8537 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-P4-AAVK                     TCGA-Q2-A5QZ 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A71R                     TCGA-SX-A71S 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A71U                     TCGA-SX-A71V 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A7SL                     TCGA-SX-A7SM 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A7SN                     TCGA-SX-A7SO 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A7SP                     TCGA-SX-A7SQ 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A7SR                     TCGA-SX-A7SS 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A7SU                     TCGA-UZ-A9PL 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-UZ-A9PZ                     TCGA-V9-A7HT 
"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                        59   195
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                                    59
  WHITE                                                       195
[1] 4 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  11 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(5P15.33) MUTATED      1    8
  DEL PEAK  7(5P15.33) WILD-TYPE   11  231
                        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                            231
[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 233  39
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                           10                           272 
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                            5                            39 
$`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        91.73        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        39.88        38.99        33.07        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-5P-A9JU TCGA-5P-A9JV TCGA-5P-A9JW 
        0.13        12.82        11.57        12.26        67.17       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
       49.58        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       62.93        43.04        19.36        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 
       67.43        61.05         0.10        21.37        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
        0.89         7.82         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        70.19 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       76.64        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56        37.51        21.67        24.56        16.87        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77        20.32        21.07        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        17.23         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        10.82         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        48.85        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        74.60 
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        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       23.08        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        12.89        11.21        16.31 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       84.89        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
       67.17        22.26        21.34        16.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.55        18.41        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        17.62        12.13        31.13 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB 
       29.26        15.48        99.78        87.09        42.94        99.12 
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        19.73 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        49.45        44.61        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        41.33        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      103.63       125.29        37.35        62.83        98.96        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ 
       86.37        71.24        30.67        47.47        65.13        21.60 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        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         3.68 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        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 
                        18.92                         25.02 
[1] "2.8 - 79.9 (18.9)"  "0.1 - 194.8 (25.0)"
[1] "hr=" "5.4"
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     170       21        45       14
D15V3, multiclass
           clus
vv          DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  STAGE I                             1                           170
  STAGE II                            1                            21
  STAGE III                           7                            45
  STAGE IV                            1                            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  8(5Q35.2) MUTATED     1   1     9
  DEL PEAK  8(5Q35.2) WILD-TYPE 189  32    53
D15V4, multiclass
       clus
vv      DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  T1                              1                           189
  T2                              1                            32
  T3+T4                           9                            53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  8(5Q35.2) MUTATED    1  4  0
  DEL PEAK  8(5Q35.2) WILD-TYPE 47 20  5
D15V5, multiclass
    clus
vv   DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  N0                           1                            47
  N1                           4                            20
  N2                           0                             5
[1] 3 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 90  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5Q35.2) MUTATED      3    1
  DEL PEAK  8(5Q35.2) WILD-TYPE   90    8
   clus
vv  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  0                           3                            90
  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  69 207
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5Q35.2) MUTATED      7    4
  DEL PEAK  8(5Q35.2) WILD-TYPE   69  207
        clus
vv       DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  FEMALE                           7                            69
  MALE                             4                           207
[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                            75 
                   TCGA-2Z-A9JE                    TCGA-2Z-A9JK 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-2Z-A9JL                    TCGA-2Z-A9JN 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-2Z-A9JT                    TCGA-4A-A93W 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-4A-A93X                    TCGA-4A-A93Y 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-5P-A9JU                    TCGA-A4-7828 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-8098                    TCGA-A4-8310 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-8311                    TCGA-A4-8312 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-8517                    TCGA-A4-8518 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-8630                    TCGA-A4-A48D 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-A4ZT                    TCGA-A4-A57E 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-A5DU                    TCGA-A4-A5XZ 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-A6HP                    TCGA-AL-3466 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-5560                    TCGA-DW-5561 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7834                    TCGA-DW-7836 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7837                    TCGA-DW-7838 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7839                    TCGA-DW-7840 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7841                    TCGA-DW-7842 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7963                    TCGA-EV-5901 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-EV-5902                    TCGA-EV-5903 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-F9-A7Q0                    TCGA-G7-6789 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-6790                    TCGA-G7-6792 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-6793                    TCGA-G7-6795 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-6796                    TCGA-G7-6797 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-7501                    TCGA-G7-7502 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-A4TM                    TCGA-G7-A8LB 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-A8LC                    TCGA-G7-A8LD 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-A8LE                    TCGA-IA-A40U 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-IA-A40X                    TCGA-IA-A40Y 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-J7-8537                    TCGA-P4-AAVK 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-Q2-A5QZ                    TCGA-SX-A71R 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A71S                    TCGA-SX-A71U 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A71V                    TCGA-SX-A7SL 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SM                    TCGA-SX-A7SN 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SO                    TCGA-SX-A7SP 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SQ                    TCGA-SX-A7SR 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SS                    TCGA-SX-A7SU 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-UZ-A9PL                    TCGA-UZ-A9PZ 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-V9-A7HT 
"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                        60   196
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                                   60
  WHITE                                                      196
[1] 4 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  11 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5Q35.2) MUTATED      1    6
  DEL PEAK  8(5Q35.2) WILD-TYPE   11  233
                        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                           233
[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    19   6
  DEL PEAK  9(6P12.3) WILD-TYPE 219  38
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                           25                           257 
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                            6                            38 
$`DEL PEAK  9(6P12.3) MUTATED`
TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-5P-A9JU TCGA-5P-A9K9 TCGA-5P-A9KH 
       91.73        54.64        51.52        12.26        19.36        67.43 
TCGA-A4-7286 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B9-A44B TCGA-BQ-5882 TCGA-BQ-5890 
       18.21        49.25        10.09         2.10        21.63         7.66 
TCGA-BQ-7048 TCGA-BQ-7056 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 
       93.34        20.12        19.00        13.08         4.01        11.05 
TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A8LC TCGA-P4-A5E8 TCGA-SX-A7SL TCGA-UN-AAZ9 
       25.15        25.84        23.08        42.94        27.06        18.02 
TCGA-Y8-A896 
       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        39.88        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       33.07        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-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       67.17       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       15.48        71.80        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       27.09        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         7.82         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       70.19        76.64        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
        2.20        19.56        37.51        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 
       20.25        16.77        20.32        21.07        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-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23        17.23         0.16        14.86        17.49        12.30 
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-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       13.25        10.82         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        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        48.85        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        74.60        34.19 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       24.89        10.68         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
       90.90        39.25        71.44        20.52         6.38        17.98 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        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        12.89        11.21        16.31 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       84.89        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
       67.17        22.26        21.34        16.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.55        18.41        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        17.62        12.13        31.13 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB 
       29.26        15.48        99.78        87.09         6.61        99.12 
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        19.73 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        41.33        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       53.10        43.76        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       37.35        62.83        98.96        86.27        86.37        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       30.67        47.47        65.13        21.60       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        15.91        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         3.68         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 
                        20.12                         25.22 
[1] "2.1 - 93.3 (20.1)"  "0.1 - 194.8 (25.2)"
[1] "hr=" "1.8"
D16V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  9(6P12.3) MUTATED         9        0        12        2
  DEL PEAK  9(6P12.3) WILD-TYPE     162       22        40       13
D16V3, multiclass
           clus
vv          DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  STAGE I                             9                           162
  STAGE II                            0                            22
  STAGE III                          12                            40
  STAGE IV                            2                            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  9(6P12.3) MUTATED    11   1    14
  DEL PEAK  9(6P12.3) WILD-TYPE 179  32    48
D16V4, multiclass
       clus
vv      DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  T1                             11                           179
  T2                              1                            32
  T3+T4                          14                            48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  9(6P12.3) MUTATED    6  1  3
  DEL PEAK  9(6P12.3) WILD-TYPE 42 23  2
D16V5, multiclass
    clus
vv   DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  N0                           6                            42
  N1                           1                            23
  N2                           3                             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   11  0
  DEL PEAK  9(6P12.3) WILD-TYPE 82  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6P12.3) MUTATED     11    0
  DEL PEAK  9(6P12.3) WILD-TYPE   82    9
   clus
vv  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  0                          11                            82
  1                           0                             9
[1] 2 2
[1] FALSE
D16V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(6P12.3) MUTATED     9  17
  DEL PEAK  9(6P12.3) WILD-TYPE  67 194
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6P12.3) MUTATED      9   17
  DEL PEAK  9(6P12.3) WILD-TYPE   67  194
        clus
vv       DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  FEMALE                           9                            67
  MALE                            17                           194
[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    20
  DEL PEAK  9(6P12.3) WILD-TYPE                        59   184
D16V11, multiclass
                                  clus
vv                                 DEL PEAK  9(6P12.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     20
                                  clus
vv                                 DEL PEAK  9(6P12.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   59
  WHITE                                                      184
[1] 4 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  22
  DEL PEAK  9(6P12.3) WILD-TYPE  12 217
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6P12.3) MUTATED      0   22
  DEL PEAK  9(6P12.3) WILD-TYPE   12  217
                        clus
vv                       DEL PEAK  9(6P12.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          22
                        clus
vv                       DEL PEAK  9(6P12.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           217
[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    22   6
  DEL PEAK 10(6Q22.31) WILD-TYPE 216  38
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                            28                            254 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                             6                             38 
$`DEL PEAK 10(6Q22.31) MUTATED`
TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-5P-A9JU TCGA-5P-A9KH 
       91.73        54.64        51.52        39.88        12.26        67.43 
TCGA-A4-7286 TCGA-B3-3926 TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5882 TCGA-BQ-5888 
       18.21        10.09         2.10        86.76        21.63        13.25 
TCGA-BQ-5889 TCGA-BQ-7056 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 
       10.82        20.12        19.00        13.08         4.01        11.05 
TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-J7-8537 TCGA-P4-A5EB TCGA-Q2-A5QZ 
       25.84        23.08         3.68        10.55        99.12        14.07 
TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-UZ-A9PQ TCGA-Y8-A896 
       27.06        18.02        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        33.07 
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-5P-A9JV 
       16.18        22.49         0.13        12.82        11.57        67.17 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC 
       71.80        62.93        43.04        19.36        12.99        12.39 
TCGA-5P-A9KE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       27.09        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         7.82         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       70.19        76.64        49.32        66.71        62.66        67.73 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56        37.51        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87        20.25        16.77        20.32        21.07        33.83 
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-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       22.06        19.23        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       12.30        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-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-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        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        48.85        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        74.60        34.19 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       24.89        10.68         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
       90.90        39.25        71.44        25.15        20.52         6.38 
TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       17.98        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        12.89        11.21        16.31 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       84.89        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
       67.17        22.26        21.34        16.34        12.36        12.76 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        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        17.62        12.13        31.13        29.26 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       15.48        99.78        87.09        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        19.73        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        49.45        44.61        28.80        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       41.33        16.31        41.62        26.47        53.10        43.76 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PO 
       26.20       117.40       103.63       125.29        37.35        62.83 
TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.37        71.24        30.67        47.47        65.13 
TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       21.60       110.73        51.35        31.73        26.01        39.06 
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         3.68 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                           2.1                            0.1 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                         99.12                         194.79 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                         18.82                          25.25 
[1] "2.1 - 99.1 (18.8)"  "0.1 - 194.8 (25.2)"
[1] "hr=" "1.5"
D17V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 10(6Q22.31) MUTATED        12        0        12        3
  DEL PEAK 10(6Q22.31) WILD-TYPE     159       22        40       12
D17V3, multiclass
           clus
vv          DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  STAGE I                             12                            159
  STAGE II                             0                             22
  STAGE III                           12                             40
  STAGE IV                             3                             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 10(6Q22.31) MUTATED    13   1    15
  DEL PEAK 10(6Q22.31) WILD-TYPE 177  32    47
D17V4, multiclass
       clus
vv      DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  T1                              13                            177
  T2                               1                             32
  T3+T4                           15                             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 10(6Q22.31) MUTATED    5  4  2
  DEL PEAK 10(6Q22.31) WILD-TYPE 43 20  3
D17V5, multiclass
    clus
vv   DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  N0                            5                             43
  N1                            4                             20
  N2                            2                              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"
D17V6, binary
                                cls
clus                              0  1
  DEL PEAK 10(6Q22.31) MUTATED   12  1
  DEL PEAK 10(6Q22.31) WILD-TYPE 81  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.31) MUTATED     12    1
  DEL PEAK 10(6Q22.31) WILD-TYPE   81    8
   clus
vv  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  0                           12                             81
  1                            1                              8
[1] 2 2
[1] FALSE
D17V7, binary
                                cls
clus                               0   1
  DEL PEAK 10(6Q22.31) MUTATED    13  16
  DEL PEAK 10(6Q22.31) WILD-TYPE  63 195
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.31) MUTATED     13   16
  DEL PEAK 10(6Q22.31) WILD-TYPE   63  195
        clus
vv       DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  FEMALE                           13                             63
  MALE                             16                            195
[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    20
  DEL PEAK 10(6Q22.31) WILD-TYPE                        57   184
D17V11, multiclass
                                  clus
vv                                 DEL PEAK 10(6Q22.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      20
                                  clus
vv                                 DEL PEAK 10(6Q22.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    57
  WHITE                                                       184
[1] 4 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  23
  DEL PEAK 10(6Q22.31) WILD-TYPE  12 216
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.31) MUTATED      0   23
  DEL PEAK 10(6Q22.31) WILD-TYPE   12  216
                        clus
vv                       DEL PEAK 10(6Q22.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           23
                        clus
vv                       DEL PEAK 10(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            216
[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    24   7
  DEL PEAK 11(6Q25.3) WILD-TYPE 214  37
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                           31                           251 
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                            7                            37 
$`DEL PEAK 11(6Q25.3) MUTATED`
TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-5P-A9JU TCGA-5P-A9K9 
       91.73        54.64        51.52        39.88        12.26        19.36 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B9-A44B TCGA-BQ-5875 
       67.43        18.21        49.25        10.09         2.10        86.76 
TCGA-BQ-5882 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-7056 TCGA-EV-5902 TCGA-F9-A7Q0 
       21.63        13.25         7.66        20.12        19.00        13.08 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y 
        4.01        11.05        25.84        23.08         3.68         2.04 
TCGA-J7-8537 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       10.55        99.12        14.07        27.06        18.02        86.27 
TCGA-Y8-A896 
       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        33.07 
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-5P-A9JV 
       16.18        22.49         0.13        12.82        11.57        67.17 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        43.04        12.99        12.39        27.09 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 
       19.63        61.05         0.10        21.37        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
        0.89         7.82         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        70.19 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       76.64        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56        37.51        21.67        24.56        16.87        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        21.07        33.83        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-A5W7 
        0.46         1.15        15.12        43.99        22.06        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 
       17.23         0.16        14.86        17.49        12.30        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
        8.88        63.72        22.92        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 
       26.04        30.28        26.04        25.35        10.82         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-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-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        48.85 
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-5903 TCGA-F9-A4JJ 
       51.19        61.02        74.60        34.19        24.89        10.68 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
        2.40         1.18         0.43        51.78        90.90        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
       71.44        25.15        20.52         6.38        17.98        16.90 
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        12.89        11.21        16.31        84.89        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       85.78        88.24        96.69        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       16.34        12.36        12.76        18.41        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        17.62 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        31.13        29.26        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94         6.61        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       78.90        19.73        17.75        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        11.93        19.00        41.33        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        53.10        43.76        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS 
      125.29        37.35        62.83        98.96        86.37        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       30.67        47.47        65.13        21.60       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        15.91        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         3.68         6.02        13.28 

  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                         2.04                          0.10 
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                        99.12                        194.79 
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                        19.00                         25.28 
[1] "2.0 - 99.1 (19.0)"  "0.1 - 194.8 (25.3)"
[1] "hr=" "1.7"
D18V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 11(6Q25.3) MUTATED        12        0        15        2
  DEL PEAK 11(6Q25.3) WILD-TYPE     159       22        37       13
D18V3, multiclass
           clus
vv          DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE
  STAGE I                            12                           159
  STAGE II                            0                            22
  STAGE III                          15                            37
  STAGE IV                            2                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  DEL PEAK 11(6Q25.3) MUTATED    13   1    18
  DEL PEAK 11(6Q25.3) WILD-TYPE 177  32    44
D18V4, multiclass
       clus
vv      DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE
  T1                             13                           177
  T2                              1                            32
  T3+T4                          18                            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 11(6Q25.3) MUTATED    6  4  3
  DEL PEAK 11(6Q25.3) WILD-TYPE 42 20  2
D18V5, multiclass
    clus
vv   DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE
  N0                           6                            42
  N1                           4                            20
  N2                           3                             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   13  0
  DEL PEAK 11(6Q25.3) WILD-TYPE 80  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q25.3) MUTATED     13    0
  DEL PEAK 11(6Q25.3) WILD-TYPE   80    9
   clus
vv  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE
  0                          13                            80
  1                           0                             9
[1] 2 2
[1] FALSE
D18V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(6Q25.3) MUTATED    16  16
  DEL PEAK 11(6Q25.3) WILD-TYPE  60 195
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q25.3) MUTATED     16   16
  DEL PEAK 11(6Q25.3) WILD-TYPE   60  195
        clus
vv       DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE
  FEMALE                          16                            60
  MALE                            16                           195
[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    23
  DEL PEAK 11(6Q25.3) WILD-TYPE                        57   181
D18V11, multiclass
                                  clus
vv                                 DEL PEAK 11(6Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     23
                                  clus
vv                                 DEL PEAK 11(6Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   57
  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"
D18V12, binary
                               cls
clus                              0   1
  DEL PEAK 11(6Q25.3) MUTATED     0  26
  DEL PEAK 11(6Q25.3) WILD-TYPE  12 213
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q25.3) MUTATED      0   26
  DEL PEAK 11(6Q25.3) WILD-TYPE   12  213
                        clus
vv                       DEL PEAK 11(6Q25.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          26
                        clus
vv                       DEL PEAK 11(6Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           213
[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    20  17
  DEL PEAK 12(9P21.3) WILD-TYPE 218  27
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           37                           245 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           17                            27 
$`DEL PEAK 12(9P21.3) MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-4A-A93X TCGA-5P-A9K9 TCGA-A4-7286 
       54.64        51.52        39.88        12.82        19.36        18.21 
TCGA-A4-7287 TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B3-3926 
       19.63         8.48        12.99         9.63        49.25        10.09 
TCGA-B9-4116 TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5888 TCGA-BQ-5889 
       20.61        14.86         8.88        22.92        13.25        10.82 
TCGA-BQ-7048 TCGA-BQ-7056 TCGA-DZ-6131 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 
       93.34        20.12        79.86        13.08         4.01        11.05 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y 
       71.44        20.52        23.08        16.90         3.68         2.04 
TCGA-J7-8537 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-SX-A71V TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       10.55         6.61        16.01        28.80        18.02        86.27 
TCGA-Y8-A896 
       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        91.73        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 
       33.07        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-5P-A9JU 
        5.29        16.18        22.49         0.13        11.57        12.26 
TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       67.17       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       15.48        71.80        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       27.09        67.43        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         7.82         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-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       15.75         8.28        12.46        70.19        76.64        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        19.56        37.51 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87        20.25        16.77        20.32 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       21.07        33.83        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       50.50        28.18        26.40         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23        17.23         0.16 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 
       17.49        12.30        86.76        19.27        63.72        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-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        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        48.85        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        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       24.89        10.68         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       90.90        39.25        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        12.89        11.21        16.31        84.89        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       85.78        88.24        96.69        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       16.34        12.36        12.76        18.41        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        17.62 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        31.13        29.26        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO 
       42.94        99.12        92.58        52.27        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       19.73        17.75        14.07        47.90        49.45        44.61 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        41.33        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        53.10        43.76        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS 
      125.29        37.35        62.83        98.96        86.37        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       30.67        47.47        65.13        21.60       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        15.91        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         3.68         6.02        13.28 

  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                         2.04                          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 
                        18.02                         26.01 
[1] "2.0 - 93.3 (18.0)"  "0.1 - 194.8 (26.0)"
[1] "hr=" "6.1"
D19V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 12(9P21.3) MUTATED        10        0        19        7
  DEL PEAK 12(9P21.3) WILD-TYPE     161       22        33        8
D19V3, multiclass
           clus
vv          DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  STAGE I                            10                           161
  STAGE II                            0                            22
  STAGE III                          19                            33
  STAGE IV                            7                             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    25
  DEL PEAK 12(9P21.3) WILD-TYPE 179  30    37
D19V4, multiclass
       clus
vv      DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  T1                             11                           179
  T2                              3                            30
  T3+T4                          25                            37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK 12(9P21.3) MUTATED    7 14  3
  DEL PEAK 12(9P21.3) WILD-TYPE 41 10  2
D19V5, multiclass
    clus
vv   DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  N0                           7                            41
  N1                          14                            10
  N2                           3                             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 83  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED     10    4
  DEL PEAK 12(9P21.3) WILD-TYPE   83    5
   clus
vv  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  0                          10                            83
  1                           4                             5
[1] 2 2
[1] FALSE
D19V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(9P21.3) MUTATED    19  20
  DEL PEAK 12(9P21.3) WILD-TYPE  57 191
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED     19   20
  DEL PEAK 12(9P21.3) WILD-TYPE   57  191
        clus
vv       DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  FEMALE                          19                            57
  MALE                            20                           191
[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    31
  DEL PEAK 12(9P21.3) WILD-TYPE                        56   173
D19V11, multiclass
                                  clus
vv                                 DEL PEAK 12(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     31
                                  clus
vv                                 DEL PEAK 12(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        3
  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"
D19V12, binary
                               cls
clus                              0   1
  DEL PEAK 12(9P21.3) MUTATED     1  33
  DEL PEAK 12(9P21.3) WILD-TYPE  11 206
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED      1   33
  DEL PEAK 12(9P21.3) WILD-TYPE   11  206
                        clus
vv                       DEL PEAK 12(9P21.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          33
                        clus
vv                       DEL PEAK 12(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           206
[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   6
  DEL PEAK 13(10Q21.1) WILD-TYPE 226  38
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                            18                            264 
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                             6                             38 
$`DEL PEAK 13(10Q21.1) MUTATED`
TCGA-2Z-A9J8 TCGA-5P-A9JU TCGA-5P-A9KH TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-A44B 
       91.73        12.26        67.43        12.99        49.25         2.10 
TCGA-BQ-5876 TCGA-BQ-5882 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-7502 
       19.27        21.63        79.86         4.01        20.52        25.84 
TCGA-G7-A8LC TCGA-GL-7966 TCGA-J7-8537 TCGA-P4-A5E6 TCGA-P4-AAVO TCGA-Q2-A5QZ 
       23.08         3.68        10.55        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 
       39.88        38.99        33.07        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-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
       12.82        11.57        67.17       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7287 
       19.36        12.99        12.39        27.09        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       61.05         0.10        21.37        35.18        19.13         0.89 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         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-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        8.28        12.46         9.63        70.19        76.64        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        19.56        37.51 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87        20.25        16.77        20.32 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       21.07        33.83        10.09        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-A5W7 TCGA-B9-A5W8 
        1.15        15.12        43.99        22.06        19.23        17.23 
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-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-5890 
       30.28        26.04        25.35        13.25        10.82         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        48.85        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        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
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        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        84.89        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       96.69        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        18.41        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        17.62        12.13        31.13 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       29.26        15.48        87.09        42.94         6.61        99.12 
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        19.73        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        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        41.33        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       37.35        62.83        98.96        86.27        86.37        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       30.67        47.47        65.13        21.60       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       31.73        26.01        39.06        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         3.68         6.02        13.28 

  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                           2.1                            0.1 
  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 
                        21.075                         25.020 
[1] "2.1 - 99.8 (21.1)"  "0.1 - 194.8 (25.0)"
[1] "hr=" "2.2"
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 13(10Q21.1) MUTATED         5        0        12        1
  DEL PEAK 13(10Q21.1) WILD-TYPE     166       22        40       14
D20V3, multiclass
           clus
vv          DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE
  STAGE I                              5                            166
  STAGE II                             0                             22
  STAGE III                           12                             40
  STAGE IV                             1                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK 13(10Q21.1) MUTATED     8   0    11
  DEL PEAK 13(10Q21.1) WILD-TYPE 182  33    51
D20V4, multiclass
       clus
vv      DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE
  T1                               8                            182
  T2                               0                             33
  T3+T4                           11                             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 13(10Q21.1) MUTATED    3  5  1
  DEL PEAK 13(10Q21.1) WILD-TYPE 45 19  4
D20V5, multiclass
    clus
vv   DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE
  N0                            3                             45
  N1                            5                             19
  N2                            1                              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"
D20V6, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q21.1) MUTATED    5  0
  DEL PEAK 13(10Q21.1) WILD-TYPE 88  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q21.1) MUTATED      5    0
  DEL PEAK 13(10Q21.1) WILD-TYPE   88    9
   clus
vv  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE
  0                            5                             88
  1                            0                              9
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                               0   1
  DEL PEAK 13(10Q21.1) MUTATED     7  12
  DEL PEAK 13(10Q21.1) WILD-TYPE  69 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q21.1) MUTATED      7   12
  DEL PEAK 13(10Q21.1) WILD-TYPE   69  199
        clus
vv       DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE
  FEMALE                            7                             69
  MALE                             12                            199
[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    12
  DEL PEAK 13(10Q21.1) WILD-TYPE                        57   192
D20V11, multiclass
                                  clus
vv                                 DEL PEAK 13(10Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      12
                                  clus
vv                                 DEL PEAK 13(10Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    57
  WHITE                                                       192
[1] 4 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  15
  DEL PEAK 13(10Q21.1) WILD-TYPE  12 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q21.1) MUTATED      0   15
  DEL PEAK 13(10Q21.1) WILD-TYPE   12  224
                        clus
vv                       DEL PEAK 13(10Q21.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           15
                        clus
vv                       DEL PEAK 13(10Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            224
[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    18  11
  DEL PEAK 14(11Q22.3) WILD-TYPE 220  33
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                            29                            253 
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                            11                             33 
$`DEL PEAK 14(11Q22.3) MUTATED`
TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K9 
        4.57        56.81        54.64        51.52        12.82        19.36 
TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B3-4104 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 
       12.99        37.51        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        10.82         7.66       123.62         0.43         4.01 
TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-J7-8537 TCGA-PJ-A5Z8 
       11.05        25.84        16.90         2.04        10.55        19.73 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8S1 
       86.27        71.24        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 
       91.73        75.42        34.85        39.88        38.99        33.07 
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-5P-A9JU TCGA-5P-A9JV 
       16.18        22.49         0.13        11.57        12.26        67.17 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 
       67.43        18.21        19.63        61.05         0.10        21.37 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
       35.18        19.13         0.89         7.82         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-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 
       70.19        76.64        49.32        66.71        62.66        67.73 
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 
       20.25        16.77        20.32        21.07        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        17.23         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        48.85 
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        74.60        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        90.90 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
       39.25        71.44        25.15        20.52         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       23.08        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        12.89        11.21        16.31 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       84.89        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W 
       16.80        19.99        85.78        88.24        96.69        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36        12.76        18.41 
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        17.62        12.13        31.13        29.26        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        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        49.45        44.61        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        41.33        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        62.83        98.96        86.37        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       65.13        21.60       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       39.06        15.91        18.05        15.62        25.28         3.68 
TCGA-Y8-A8S0 
        6.02 

  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                          0.43                           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 
                         18.64                          25.35 
[1] "0.4 - 123.6 (18.6)" "0.1 - 194.8 (25.4)"
[1] "hr=" "3.9"
D21V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 14(11Q22.3) MUTATED         7        3        14        6
  DEL PEAK 14(11Q22.3) WILD-TYPE     164       19        38        9
D21V3, multiclass
           clus
vv          DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  STAGE I                              7                            164
  STAGE II                             3                             19
  STAGE III                           14                             38
  STAGE IV                             6                              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    18
  DEL PEAK 14(11Q22.3) WILD-TYPE 182  28    44
D21V4, multiclass
       clus
vv      DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  T1                               8                            182
  T2                               5                             28
  T3+T4                           18                             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 14(11Q22.3) MUTATED    3  9  3
  DEL PEAK 14(11Q22.3) WILD-TYPE 45 15  2
D21V5, multiclass
    clus
vv   DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  N0                            3                             45
  N1                            9                             15
  N2                            3                              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 84  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q22.3) MUTATED      9    3
  DEL PEAK 14(11Q22.3) WILD-TYPE   84    6
   clus
vv  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  0                            9                             84
  1                            3                              6
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                               0   1
  DEL PEAK 14(11Q22.3) MUTATED    10  21
  DEL PEAK 14(11Q22.3) WILD-TYPE  66 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q22.3) MUTATED     10   21
  DEL PEAK 14(11Q22.3) WILD-TYPE   66  190
        clus
vv       DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  FEMALE                           10                             66
  MALE                             21                            190
[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    22
  DEL PEAK 14(11Q22.3) WILD-TYPE                        56   182
D21V11, multiclass
                                  clus
vv                                 DEL PEAK 14(11Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      22
                                  clus
vv                                 DEL PEAK 14(11Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    56
  WHITE                                                       182
[1] 4 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  26
  DEL PEAK 14(11Q22.3) WILD-TYPE  12 213
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q22.3) MUTATED      0   26
  DEL PEAK 14(11Q22.3) WILD-TYPE   12  213
                        clus
vv                       DEL PEAK 14(11Q22.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           26
                        clus
vv                       DEL PEAK 14(11Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            213
[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    15  12
  DEL PEAK 15(11Q23.3) WILD-TYPE 223  32
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                            27                            255 
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                            12                             32 
$`DEL PEAK 15(11Q23.3) MUTATED`
TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K9 
        4.57        56.81        54.64        51.52        12.82        19.36 
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-4104 TCGA-B9-A44B TCGA-BQ-5876 
       12.99        49.25        37.51        34.49         2.10        19.27 
TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-F9-A97G 
        8.88        21.63        10.82         7.66       123.62         0.43 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-J7-8537 
        4.01        11.05        25.84        16.90         2.04        10.55 
TCGA-UZ-A9PQ TCGA-Y8-A896 TCGA-Y8-A8S1 
       86.27        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 
       91.73        75.42        34.85        39.88        38.99        33.07 
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-5P-A9JU TCGA-5P-A9JV 
       16.18        22.49         0.13        11.57        12.26        67.17 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 
       67.43        18.21        19.63        61.05         0.10        21.37 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
       35.18        19.13         0.89         7.82         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-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 
       70.19        76.64        49.32        66.71        62.66        67.73 
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        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77        20.32        21.07        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-A5W7 
        0.46         1.15        15.12        43.99        22.06        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
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-5891 TCGA-BQ-5892 
       30.28        26.04        25.35        13.25         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        7.92         2.76        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        48.85        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-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
       13.08         2.40         1.18        51.78        90.90        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       71.44        25.15        20.52         6.38        17.98        23.08 
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        12.89        11.21        16.31        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 
       19.99        85.78        88.24        96.69        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36        12.76        18.41        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 
       17.62        12.13        31.13        29.26        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.09        42.94         6.61        99.12        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        19.73        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        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        41.33        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       37.35        62.83        98.96        86.37        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       47.47        65.13        21.60       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 
       26.01        39.06        18.64        15.91        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       25.28         3.68         6.02 

  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                          0.43                           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 
                         16.90                          25.28 
[1] "0.4 - 123.6 (16.9)" "0.1 - 194.8 (25.3)"
[1] "hr=" "4.8"
D22V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 15(11Q23.3) MUTATED         5        2        15        6
  DEL PEAK 15(11Q23.3) WILD-TYPE     166       20        37        9
D22V3, multiclass
           clus
vv          DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  STAGE I                              5                            166
  STAGE II                             2                             20
  STAGE III                           15                             37
  STAGE IV                             6                              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    19
  DEL PEAK 15(11Q23.3) WILD-TYPE 184  29    43
D22V4, multiclass
       clus
vv      DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  T1                               6                            184
  T2                               4                             29
  T3+T4                           19                             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 15(11Q23.3) MUTATED    3  9  3
  DEL PEAK 15(11Q23.3) WILD-TYPE 45 15  2
D22V5, multiclass
    clus
vv   DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  N0                            3                             45
  N1                            9                             15
  N2                            3                              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 85  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q23.3) MUTATED      8    3
  DEL PEAK 15(11Q23.3) WILD-TYPE   85    6
   clus
vv  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  0                            8                             85
  1                            3                              6
[1] 2 2
[1] FALSE
D22V7, binary
                                cls
clus                               0   1
  DEL PEAK 15(11Q23.3) MUTATED     8  21
  DEL PEAK 15(11Q23.3) WILD-TYPE  68 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q23.3) MUTATED      8   21
  DEL PEAK 15(11Q23.3) WILD-TYPE   68  190
        clus
vv       DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  FEMALE                            8                             68
  MALE                             21                            190
[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    21
  DEL PEAK 15(11Q23.3) WILD-TYPE                        57   183
D22V11, multiclass
                                  clus
vv                                 DEL PEAK 15(11Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      21
                                  clus
vv                                 DEL PEAK 15(11Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    57
  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"
D22V12, binary
                                cls
clus                               0   1
  DEL PEAK 15(11Q23.3) MUTATED     0  24
  DEL PEAK 15(11Q23.3) WILD-TYPE  12 215
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q23.3) MUTATED      0   24
  DEL PEAK 15(11Q23.3) WILD-TYPE   12  215
                        clus
vv                       DEL PEAK 15(11Q23.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           24
                        clus
vv                       DEL PEAK 15(11Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            215
[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    36  14
  DEL PEAK 16(14Q11.2) WILD-TYPE 202  30
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                            50                            232 
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                            14                             30 
$`DEL PEAK 16(14Q11.2) MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JK TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-A4-7286 
       54.64        38.99        15.48        43.04        19.36        18.21 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-AL-3466 
        0.10        35.18        30.48        29.46        12.99         9.63 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 
       62.66        67.73        49.25        37.51        16.77        10.09 
TCGA-B3-4103 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-BQ-5876 TCGA-BQ-5885 TCGA-BQ-5888 
       30.58        20.61        17.23        19.27        30.28        13.25 
TCGA-BQ-5889 TCGA-BQ-5894 TCGA-DW-5560 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-F9-A4JJ 
       10.82         2.76        48.85        79.86        80.88        10.68 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 
       13.08         4.01        11.05        71.44        20.52        25.84 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40U 
       23.08        16.90        27.65        16.31        73.25        16.80 
TCGA-IA-A40Y TCGA-MH-A854 TCGA-P4-A5EA TCGA-PJ-A5Z8 TCGA-SX-A71V TCGA-UN-AAZ9 
        2.04        17.62         6.61        19.73        28.80        18.02 
TCGA-UZ-A9PN TCGA-WN-A9G9 
       37.35        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        91.73        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 
       39.88        33.07        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-5P-A9JU TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
       11.57        12.26        67.17       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9KA TCGA-5P-A9KC 
       22.26        78.64        71.80        62.93        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7732 
       27.09        67.43        19.63        61.05        21.37        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 
        0.89         7.82         0.23        16.64        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-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU 
       12.46        70.19        76.64        49.32        66.71         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A656 
       19.56        21.67        24.56        16.87        20.25        20.32 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       21.07        33.83        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-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       22.06         2.10        19.23         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-5886 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        26.04        25.35 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         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-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
        3.81        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-6133 
       13.78         3.75        14.63         3.02        40.77        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF 
       61.02        74.60        34.19        19.00        24.89         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 
        1.18         0.43        51.78        90.90        39.25        25.15 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
        6.38        17.98        80.65       194.79        12.92         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        12.89        11.21        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S 
       26.01        11.84        56.75        25.22        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       88.24        96.69        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.36        12.76        10.55        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A855 
       34.29        27.78        30.38        27.65        20.25        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       31.13        29.26        15.48        99.78        87.09        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL 
       17.75        14.07        47.90        49.45        44.61        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        41.33        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       53.10        43.76        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       62.83        98.96        86.27        86.37        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       47.47        65.13        21.60       110.73        51.35        31.73 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       39.06        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         3.68         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 
                        20.125                         25.185 
[1] "0.1 - 80.9 (20.1)"  "0.1 - 194.8 (25.2)"
[1] "hr=" "3.1"
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     149       19        38        9
D23V3, multiclass
           clus
vv          DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  STAGE I                             22                            149
  STAGE II                             3                             19
  STAGE III                           14                             38
  STAGE IV                             6                              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 16(14Q11.2) MUTATED    24   5    22
  DEL PEAK 16(14Q11.2) WILD-TYPE 166  28    40
D23V4, multiclass
       clus
vv      DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  T1                              24                            166
  T2                               5                             28
  T3+T4                           22                             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 16(14Q11.2) MUTATED    9  8  4
  DEL PEAK 16(14Q11.2) WILD-TYPE 39 16  1
D23V5, multiclass
    clus
vv   DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  N0                            9                             39
  N1                            8                             16
  N2                            4                              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 75  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(14Q11.2) MUTATED     18    3
  DEL PEAK 16(14Q11.2) WILD-TYPE   75    6
   clus
vv  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  0                           18                             75
  1                            3                              6
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                               0   1
  DEL PEAK 16(14Q11.2) MUTATED    21  30
  DEL PEAK 16(14Q11.2) WILD-TYPE  55 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(14Q11.2) MUTATED     21   30
  DEL PEAK 16(14Q11.2) WILD-TYPE   55  181
        clus
vv       DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  FEMALE                           21                             55
  MALE                             30                            181
[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    36
  DEL PEAK 16(14Q11.2) WILD-TYPE                        51   168
D23V11, multiclass
                                  clus
vv                                 DEL PEAK 16(14Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      36
                                  clus
vv                                 DEL PEAK 16(14Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    51
  WHITE                                                       168
[1] 4 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  43
  DEL PEAK 16(14Q11.2) WILD-TYPE  11 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(14Q11.2) MUTATED      1   43
  DEL PEAK 16(14Q11.2) WILD-TYPE   11  196
                        clus
vv                       DEL PEAK 16(14Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           43
                        clus
vv                       DEL PEAK 16(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            196
[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    35  15
  DEL PEAK 17(14Q24.2) WILD-TYPE 203  29
  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                            50                            232 
  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                            15                             29 
$`DEL PEAK 17(14Q24.2) MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9K9 
       54.64        51.52        38.99        15.48        43.04        19.36 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-A5Y1 
       18.21        19.63         0.10        30.48        29.46        12.99 
TCGA-AL-3466 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A655 
        9.63        62.66        67.73        49.25        37.51        16.77 
TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-BQ-5876 TCGA-BQ-5880 TCGA-BQ-5885 
       10.09        20.61        17.23        19.27        43.20        30.28 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-F9-A4JJ 
       13.25        10.82         2.76        79.86        80.88        10.68 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 
       13.08         4.01        11.05        71.44        20.52        25.84 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40U 
       23.08        16.90        27.65        16.31        73.25        16.80 
TCGA-IA-A40Y TCGA-MH-A854 TCGA-P4-A5EA TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-UN-AAZ9 
        2.04        17.62         6.61        19.73        14.07        18.02 
TCGA-UZ-A9PN TCGA-WN-A9G9 
       37.35        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        91.73        75.42        34.85        56.81        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       33.07        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-5P-A9JU TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.26        67.17       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       78.64        71.80        62.93        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       67.43        61.05        21.37        35.18        19.13         0.89 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
        7.82         0.23        16.64        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-AT-A5NU TCGA-B1-5398 
       70.19        76.64        49.32        66.71         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56        16.87        20.25        20.32        21.07 
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-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       22.06         2.10        19.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 
       12.30        86.76         8.88        63.72        22.92        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 
       21.63        40.83        26.04        26.04        25.35         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 
       48.85        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-6133 
       13.78         3.75        14.63         3.02        40.77        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF 
       61.02        74.60        34.19        19.00        24.89         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 
        1.18         0.43        51.78        90.90        39.25        25.15 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
        6.38        17.98        80.65       194.79        12.92         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        12.89        11.21        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S 
       26.01        11.84        56.75        25.22        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       88.24        96.69        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.36        12.76        10.55        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A855 
       34.29        27.78        30.38        27.65        20.25        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       31.13        29.26        15.48        99.78        87.09        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        49.45        44.61        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        41.33        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       53.10        43.76        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       62.83        98.96        86.27        86.37        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       47.47        65.13        21.60       110.73        51.35        31.73 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       39.06        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         3.68         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 
                        19.495                         25.315 
[1] "0.1 - 80.9 (19.5)"  "0.1 - 194.8 (25.3)"
[1] "hr=" "3.4"
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     151       19        37        9
D24V3, multiclass
           clus
vv          DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE
  STAGE I                             20                            151
  STAGE II                             3                             19
  STAGE III                           15                             37
  STAGE IV                             6                              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 17(14Q24.2) MUTATED    22   5    23
  DEL PEAK 17(14Q24.2) WILD-TYPE 168  28    39
D24V4, multiclass
       clus
vv      DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE
  T1                              22                            168
  T2                               5                             28
  T3+T4                           23                             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 17(14Q24.2) MUTATED    8  9  4
  DEL PEAK 17(14Q24.2) WILD-TYPE 40 15  1
D24V5, multiclass
    clus
vv   DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE
  N0                            8                             40
  N1                            9                             15
  N2                            4                              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 79  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(14Q24.2) MUTATED     14    3
  DEL PEAK 17(14Q24.2) WILD-TYPE   79    6
   clus
vv  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE
  0                           14                             79
  1                            3                              6
[1] 2 2
[1] FALSE
D24V7, binary
                                cls
clus                               0   1
  DEL PEAK 17(14Q24.2) MUTATED    21  29
  DEL PEAK 17(14Q24.2) WILD-TYPE  55 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(14Q24.2) MUTATED     21   29
  DEL PEAK 17(14Q24.2) WILD-TYPE   55  182
        clus
vv       DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE
  FEMALE                           21                             55
  MALE                             29                            182
[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    35
  DEL PEAK 17(14Q24.2) WILD-TYPE                        50   169
D24V11, multiclass
                                  clus
vv                                 DEL PEAK 17(14Q24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      35
                                  clus
vv                                 DEL PEAK 17(14Q24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    50
  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"
D24V12, binary
                                cls
clus                               0   1
  DEL PEAK 17(14Q24.2) MUTATED     1  42
  DEL PEAK 17(14Q24.2) WILD-TYPE  11 197
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(14Q24.2) MUTATED      1   42
  DEL PEAK 17(14Q24.2) WILD-TYPE   11  197
                        clus
vv                       DEL PEAK 17(14Q24.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           42
                        clus
vv                       DEL PEAK 17(14Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            197
[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  11
  DEL PEAK 18(15Q13.3) WILD-TYPE 215  33
  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                            34                            248 
  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                            11                             33 
$`DEL PEAK 18(15Q13.3) MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9JY TCGA-5P-A9K9 TCGA-A4-7286 
       54.64        51.52        12.82        49.58        19.36        18.21 
TCGA-A4-7583 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B1-5398 TCGA-B3-3926 TCGA-B9-A5W8 
        0.10        12.99         9.63        19.56        10.09        17.23 
TCGA-B9-A8YI TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-F9-A4JJ 
       12.30        22.92        21.63        10.82         2.76        10.68 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD 
       13.08         4.01        71.44        25.84        23.08        16.90 
TCGA-GL-6846 TCGA-GL-7966 TCGA-HE-A5NK TCGA-IA-A40Y TCGA-P4-A5EA TCGA-PJ-A5Z8 
      194.79         3.68        73.25         2.04         6.61        19.73 
TCGA-UN-AAZ9 TCGA-UZ-A9PP TCGA-Y8-A896 TCGA-Y8-A8S1 
       18.02        98.96        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        91.73        75.42        34.85        56.81        39.88 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        33.07        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-5P-A9JU TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       12.26        67.17       106.55        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       15.48        71.80        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7585 
       27.09        67.43        19.63        61.05        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         7.82         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        70.19        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       49.32        66.71        62.66        67.73        49.25         2.20 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
       37.51        21.67        24.56        16.87        20.25        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        21.07        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-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        0.16        14.86        17.49        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       63.72        43.20        47.80        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        25.35        13.25         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-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        48.85        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-5902 TCGA-EV-5903 TCGA-F9-A7VF 
       61.02        74.60        34.19        19.00        24.89         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        90.90        11.05        39.25 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-7773 
       25.15        20.52         6.38        17.98        80.65        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        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
       16.31        84.89        26.01        11.84        56.75        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W 
       16.80        19.99        85.78        88.24        96.69        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       22.26        21.34        16.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        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        17.62        12.13        31.13        29.26 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.09        42.94        99.12        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        49.45        44.61        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        41.33        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       43.76        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PO TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       62.83        86.27        86.37        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       65.13        21.60       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       39.06        18.64        15.91        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 
        3.68         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 
                        17.625                         26.010 
[1] "0.1 - 194.8 (17.6)" "0.1 - 129.9 (26.0)"
[1] "hr=" "3.3"
D25V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 18(15Q13.3) MUTATED        12        1        12        6
  DEL PEAK 18(15Q13.3) WILD-TYPE     159       21        40        9
D25V3, multiclass
           clus
vv          DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE
  STAGE I                             12                            159
  STAGE II                             1                             21
  STAGE III                           12                             40
  STAGE IV                             6                              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   2    19
  DEL PEAK 18(15Q13.3) WILD-TYPE 176  31    43
D25V4, multiclass
       clus
vv      DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE
  T1                              14                            176
  T2                               2                             31
  T3+T4                           19                             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 18(15Q13.3) MUTATED    4 11  2
  DEL PEAK 18(15Q13.3) WILD-TYPE 44 13  3
D25V5, multiclass
    clus
vv   DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE
  N0                            4                             44
  N1                           11                             13
  N2                            2                              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 83  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(15Q13.3) MUTATED     10    3
  DEL PEAK 18(15Q13.3) WILD-TYPE   83    6
   clus
vv  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE
  0                           10                             83
  1                            3                              6
[1] 2 2
[1] FALSE
D25V7, binary
                                cls
clus                               0   1
  DEL PEAK 18(15Q13.3) MUTATED    12  23
  DEL PEAK 18(15Q13.3) WILD-TYPE  64 188
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(15Q13.3) MUTATED     12   23
  DEL PEAK 18(15Q13.3) WILD-TYPE   64  188
        clus
vv       DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE
  FEMALE                           12                             64
  MALE                             23                            188
[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    25
  DEL PEAK 18(15Q13.3) WILD-TYPE                        56   179
D25V11, multiclass
                                  clus
vv                                 DEL PEAK 18(15Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      25
                                  clus
vv                                 DEL PEAK 18(15Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    56
  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"
D25V12, binary
                                cls
clus                               0   1
  DEL PEAK 18(15Q13.3) MUTATED     1  29
  DEL PEAK 18(15Q13.3) WILD-TYPE  11 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(15Q13.3) MUTATED      1   29
  DEL PEAK 18(15Q13.3) WILD-TYPE   11  210
                        clus
vv                       DEL PEAK 18(15Q13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           29
                        clus
vv                       DEL PEAK 18(15Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            210
[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     5   6
  DEL PEAK 19(16Q24.1) WILD-TYPE 233  38
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                            11                            271 
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                             6                             38 
$`DEL PEAK 19(16Q24.1) MUTATED`
TCGA-2Z-A9JI TCGA-5P-A9JU TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-B9-A8YI TCGA-BQ-5882 
       51.52        12.26        19.63        12.99        12.30        21.63 
TCGA-BQ-5893 TCGA-F9-A97G TCGA-G7-6793 TCGA-G7-A8LD TCGA-IA-A40X 
        7.92         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        91.73        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 
       39.88        38.99        33.07        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-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
       12.82        11.57        67.17       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       19.36        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       61.05         0.10        21.37        35.18        19.13         0.89 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         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-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        8.28        12.46         9.63        70.19        76.64        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       66.71        62.66        67.73        49.25         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
       37.51        21.67        24.56        16.87        20.25        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       20.32        21.07        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-BQ-5875 
       19.23        17.23         0.16        14.86        17.49        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-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-5894 TCGA-BQ-7044 
       10.82         7.66         0.95        11.97         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        48.85        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        74.60 
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-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        1.18         4.01        51.78        90.90        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84         6.38        17.98        23.08 
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        12.89        11.21        16.31        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 
        2.04        85.78        88.24        96.69        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD 
       21.34        16.34        12.36        12.76        10.55        18.41 
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        17.62        12.13        31.13        29.26        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        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        19.73        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        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        41.33        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
      125.29        37.35        62.83        98.96        86.27        86.37 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 
       71.24        30.67        47.47        65.13        21.60       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       51.35        31.73        26.01        39.06        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         3.68         6.02 
TCGA-Y8-A8S1 
       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 
                         12.99                          25.28 
[1] "0.4 - 51.5 (13.0)"  "0.1 - 194.8 (25.3)"
[1] "hr=" "8.2"
D26V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 19(16Q24.1) MUTATED         3        0         7        2
  DEL PEAK 19(16Q24.1) WILD-TYPE     168       22        45       13
D26V3, multiclass
           clus
vv          DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE
  STAGE I                              3                            168
  STAGE II                             0                             22
  STAGE III                            7                             45
  STAGE IV                             2                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK 19(16Q24.1) MUTATED     4   0     8
  DEL PEAK 19(16Q24.1) WILD-TYPE 186  33    54
D26V4, multiclass
       clus
vv      DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE
  T1                               4                            186
  T2                               0                             33
  T3+T4                            8                             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 19(16Q24.1) MUTATED    3  3  1
  DEL PEAK 19(16Q24.1) WILD-TYPE 45 21  4
D26V5, multiclass
    clus
vv   DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE
  N0                            3                             45
  N1                            3                             21
  N2                            1                              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"
D26V6, binary
                                cls
clus                              0  1
  DEL PEAK 19(16Q24.1) MUTATED    4  1
  DEL PEAK 19(16Q24.1) WILD-TYPE 89  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16Q24.1) MUTATED      4    1
  DEL PEAK 19(16Q24.1) WILD-TYPE   89    8
   clus
vv  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE
  0                            4                             89
  1                            1                              8
[1] 2 2
[1] FALSE
D26V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(16Q24.1) MUTATED     4   8
  DEL PEAK 19(16Q24.1) WILD-TYPE  72 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16Q24.1) MUTATED      4    8
  DEL PEAK 19(16Q24.1) WILD-TYPE   72  203
        clus
vv       DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE
  FEMALE                            4                             72
  MALE                              8                            203
[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     7
  DEL PEAK 19(16Q24.1) WILD-TYPE                        59   197
D26V11, multiclass
                                  clus
vv                                 DEL PEAK 19(16Q24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                       7
                                  clus
vv                                 DEL PEAK 19(16Q24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    59
  WHITE                                                       197
[1] 4 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  10
  DEL PEAK 19(16Q24.1) WILD-TYPE  12 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16Q24.1) MUTATED      0   10
  DEL PEAK 19(16Q24.1) WILD-TYPE   12  229
                        clus
vv                       DEL PEAK 19(16Q24.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           10
                        clus
vv                       DEL PEAK 19(16Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            229
[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   7
  DEL PEAK 20(19P13.3) WILD-TYPE 222  37
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                            23                            259 
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                             7                             37 
$`DEL PEAK 20(19P13.3) MUTATED`
TCGA-2Z-A9JG TCGA-5P-A9JU TCGA-5P-A9K9 TCGA-5P-A9KC TCGA-A4-7286 TCGA-A4-8310 
       54.64        12.26        19.36        12.39        18.21        25.64 
TCGA-A4-8517 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B1-7332 TCGA-B9-A44B TCGA-B9-A5W7 
       19.63        12.99         9.63        37.51         2.10        19.23 
TCGA-BQ-5876 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD 
       19.27         7.66         0.95         4.01        25.84        16.90 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UZ-A9PN TCGA-UZ-A9PP 
        2.04        10.55        14.07        37.35        98.96 

$`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        91.73        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 
       39.88        38.99        33.07        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-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
       12.82        11.57        67.17       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.99        27.09        67.43        19.63        61.05         0.10 
TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 
       21.37        35.18        19.13         0.89         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       16.64        30.48        29.46        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-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
       16.31        15.75         8.28        12.46        70.19        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       49.32        66.71        62.66        67.73        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        20.25        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       20.32        21.07        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-A5W8 
        0.46         1.15        15.12        43.99        22.06        17.23 
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-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.82 
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-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 
       48.85        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        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 
       20.52         6.38        17.98        23.08        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 
       12.89        11.21        16.31        84.89        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       56.75        73.25        25.22        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       88.24        96.69        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36        12.76        18.41        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        17.62        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       31.13        29.26        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       78.90        19.73        17.75        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        41.33        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PO TCGA-UZ-A9PQ TCGA-UZ-A9PR 
      117.40       103.63       125.29        62.83        86.27        86.37 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 
       71.24        30.67        47.47        65.13        21.60       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       51.35        31.73        26.01        39.06        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         3.68         6.02 
TCGA-Y8-A8S1 
       13.28 

  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                          0.95                           0.10 
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                         98.96                         194.79 
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                         16.90                          25.35 
[1] "0.9 - 99.0 (16.9)"  "0.1 - 194.8 (25.4)"
[1] "hr=" "3.7"
D27V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 20(19P13.3) MUTATED         6        1        11        2
  DEL PEAK 20(19P13.3) WILD-TYPE     165       21        41       13
D27V3, multiclass
           clus
vv          DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  STAGE I                              6                            165
  STAGE II                             1                             21
  STAGE III                           11                             41
  STAGE IV                             2                             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 20(19P13.3) MUTATED     8   1    14
  DEL PEAK 20(19P13.3) WILD-TYPE 182  32    48
D27V4, multiclass
       clus
vv      DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  T1                               8                            182
  T2                               1                             32
  T3+T4                           14                             48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 20(19P13.3) MUTATED    3  5  2
  DEL PEAK 20(19P13.3) WILD-TYPE 45 19  3
D27V5, multiclass
    clus
vv   DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  N0                            3                             45
  N1                            5                             19
  N2                            2                              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    5  1
  DEL PEAK 20(19P13.3) WILD-TYPE 88  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(19P13.3) MUTATED      5    1
  DEL PEAK 20(19P13.3) WILD-TYPE   88    8
   clus
vv  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  0                            5                             88
  1                            1                              8
[1] 2 2
[1] FALSE
D27V7, binary
                                cls
clus                               0   1
  DEL PEAK 20(19P13.3) MUTATED     8  15
  DEL PEAK 20(19P13.3) WILD-TYPE  68 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(19P13.3) MUTATED      8   15
  DEL PEAK 20(19P13.3) WILD-TYPE   68  196
        clus
vv       DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  FEMALE                            8                             68
  MALE                             15                            196
[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                             52 
                    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-B9-4114 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-B9-4117                     TCGA-B9-A69E 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-DW-5561                     TCGA-DW-7963 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-F9-A97G                     TCGA-G7-6793 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-G7-6795                     TCGA-G7-7501 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-G7-A8LB                     TCGA-G7-A8LE 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-GL-7773                     TCGA-GL-A9DD 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-HE-A5NI                     TCGA-IA-A40U 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-MH-A854                     TCGA-MH-A856 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-P4-A5E6                     TCGA-P4-AAVK 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-PJ-A5Z9                     TCGA-SX-A71S 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-SX-A71U                     TCGA-SX-A7SL 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-SX-A7SM                     TCGA-SX-A7SR 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-SX-A7SS                     TCGA-UZ-A9PM 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-UZ-A9PO                     TCGA-UZ-A9PR 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-UZ-A9PS                     TCGA-UZ-A9PX 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-WN-A9G9                     TCGA-WN-AB4C 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-Y8-A894                     TCGA-Y8-A896 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-Y8-A8RY                     TCGA-Y8-A8RZ 
"DEL PEAK 20(19P13.3) WILD-TYPE" "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    18
  DEL PEAK 20(19P13.3) WILD-TYPE                        57   186
D27V11, multiclass
                                  clus
vv                                 DEL PEAK 20(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      18
                                  clus
vv                                 DEL PEAK 20(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    57
  WHITE                                                       186
[1] 4 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  22
  DEL PEAK 20(19P13.3) WILD-TYPE  12 217
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(19P13.3) MUTATED      0   22
  DEL PEAK 20(19P13.3) WILD-TYPE   12  217
                        clus
vv                       DEL PEAK 20(19P13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           22
                        clus
vv                       DEL PEAK 20(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            217
[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    14   5
  DEL PEAK 21(19Q13.42) WILD-TYPE 224  39
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                             19                             263 
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                              5                              39 
$`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        37.51        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 
       37.35 

$`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        91.73        75.42        34.85        56.81        39.88 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        33.07        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-5P-A9JU TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
       11.57        12.26        67.17       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 
       19.36        12.99        12.39        27.09        67.43        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       61.05         0.10        21.37        35.18        19.13         0.89 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8312 
        7.82         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 
       70.19        76.64        49.32        66.71        62.66        67.73 
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 
       20.25        16.77        20.32        21.07        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        17.23         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        10.82         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        48.85        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 
       74.60        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        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       71.44        25.15        20.52         6.38        17.98        23.08 
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        12.89        11.21        16.31        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 
       19.99        85.78        88.24        96.69        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD 
       21.34        16.34        12.36        12.76        10.55        18.41 
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        17.62        12.13        31.13        29.26        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        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        19.73        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        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        41.33        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       62.83        98.96        86.27        86.37        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       47.47        65.13        21.60       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        39.06        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         3.68         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 
                          19.63                           24.56 
[1] "0.9 - 93.3 (19.6)"  "0.1 - 194.8 (24.6)"
[1] "hr=" "2.4"
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     166       21        41       14
D28V3, multiclass
           clus
vv          DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE
  STAGE I                               5                             166
  STAGE II                              1                              21
  STAGE III                            11                              41
  STAGE IV                              1                              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2 T3+T4
  DEL PEAK 21(19Q13.42) MUTATED     6   1    12
  DEL PEAK 21(19Q13.42) WILD-TYPE 184  32    50
D28V4, multiclass
       clus
vv      DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE
  T1                                6                             184
  T2                                1                              32
  T3+T4                            12                              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 21(19Q13.42) MUTATED    3  3  1
  DEL PEAK 21(19Q13.42) WILD-TYPE 45 21  4
D28V5, multiclass
    clus
vv   DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE
  N0                             3                              45
  N1                             3                              21
  N2                             1                               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"
D28V6, binary
                                 cls
clus                               0  1
  DEL PEAK 21(19Q13.42) MUTATED    4  0
  DEL PEAK 21(19Q13.42) WILD-TYPE 89  9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(19Q13.42) MUTATED      4    0
  DEL PEAK 21(19Q13.42) WILD-TYPE   89    9
   clus
vv  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE
  0                             4                              89
  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  70 198
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(19Q13.42) MUTATED      6   13
  DEL PEAK 21(19Q13.42) WILD-TYPE   70  198
        clus
vv       DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE
  FEMALE                             6                              70
  MALE                              13                             198
[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                        57   190
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                                     57
  WHITE                                                        190
[1] 4 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  12 221
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(19Q13.42) MUTATED      0   18
  DEL PEAK 21(19Q13.42) WILD-TYPE   12  221
                        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                             221
[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    46  16
  DEL PEAK 22(22Q12.2) WILD-TYPE 192  28
  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                            62                            220 
  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                            16                             28 
$`DEL PEAK 22(22Q12.2) MUTATED`
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9JU TCGA-5P-A9JY TCGA-5P-A9KC 
       54.64        51.52        12.82        12.26        49.58        12.39 
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-8098 TCGA-A4-8517 TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       18.21        61.05        29.46        19.63         8.28        12.99 
TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A47O TCGA-B3-3925 TCGA-B3-3926 
        9.63        49.25        37.51        16.87        33.83        10.09 
TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5884 
        2.10        17.23        86.76         8.88        22.92        26.04 
TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7050 
       30.28         7.66         0.95         2.76       123.62        61.28 
TCGA-BQ-7051 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-EV-5902 
       50.40        26.27        20.12         7.17        79.86        19.00 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6797 
       10.68        13.08         1.18         4.01        11.05        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 
       20.52        25.84        23.08         3.68         2.04        10.55 
TCGA-MH-A856 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-AAVO TCGA-Q2-A5QZ 
       31.13        42.94         6.61        99.12        78.90        14.07 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-AB4C 
       27.06        11.93        18.02        37.35        86.27        39.06 
TCGA-Y8-A896 TCGA-Y8-A8RZ 
       18.64         3.68 

$`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        91.73        75.42        34.85        56.81        39.88 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        33.07        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-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
       67.17       106.55        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KE 
       71.80        62.93        43.04        19.36        12.99        27.09 
TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 
       67.43        19.63         0.10        21.37        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
        0.89         7.82         0.23        16.64        30.48        25.64 
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-A6HP 
       12.46        16.96         8.48        16.31        15.75        12.46 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       70.19        76.64        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56        20.25        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       20.32        21.07        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-A5W9 TCGA-B9-A69E 
       15.12        43.99        22.06        19.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 
       17.49        12.30        19.27        63.72        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       21.63        40.83        26.04        25.35        13.25        10.82 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
       11.97         7.92        48.26        96.92        93.34        44.84 
TCGA-BQ-7053 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 
       49.84        11.28         7.63         7.04         3.81        48.85 
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-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        40.77        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A97G 
       61.02        74.60        34.19        24.89         2.40         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-A4TM TCGA-G7-A8LB 
       51.78        90.90        39.25        71.44         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-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95        12.89        11.21        16.31        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 
       19.99        85.78        88.24        96.69        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36        12.76        18.41        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-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       17.62        12.13        29.26        15.48        99.78        87.09 
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        19.73        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SO 
       47.90        49.45        44.61        28.80        19.00        41.33 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ 
       16.31        41.62        26.47        53.10        43.76        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PO TCGA-UZ-A9PP TCGA-UZ-A9PR 
      117.40       103.63       125.29        62.83        98.96        86.37 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9PZ TCGA-UZ-A9Q0 
       71.24        30.67        47.47        65.13        21.60       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 
       51.35        31.73        26.01        18.64        15.91        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.02        13.28 

  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                          0.95                           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 
                        19.315                         25.465 
[1] "0.9 - 123.6 (19.3)" "0.1 - 194.8 (25.5)"
[1] "hr=" "2.6"
D29V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 22(22Q12.2) MUTATED        22        3        26        8
  DEL PEAK 22(22Q12.2) WILD-TYPE     149       19        26        7
D29V3, multiclass
           clus
vv          DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE
  STAGE I                             22                            149
  STAGE II                             3                             19
  STAGE III                           26                             26
  STAGE IV                             8                              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    25   7    31
  DEL PEAK 22(22Q12.2) WILD-TYPE 165  26    31
D29V4, multiclass
       clus
vv      DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE
  T1                              25                            165
  T2                               7                             26
  T3+T4                           31                             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 22(22Q12.2) MUTATED   11 15  2
  DEL PEAK 22(22Q12.2) WILD-TYPE 37  9  3
D29V5, multiclass
    clus
vv   DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE
  N0                           11                             37
  N1                           15                              9
  N2                            2                              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"
D29V6, binary
                                cls
clus                              0  1
  DEL PEAK 22(22Q12.2) MUTATED   23  5
  DEL PEAK 22(22Q12.2) WILD-TYPE 70  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(22Q12.2) MUTATED     23    5
  DEL PEAK 22(22Q12.2) WILD-TYPE   70    4
   clus
vv  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE
  0                           23                             70
  1                            5                              4
[1] 2 2
[1] FALSE
D29V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(22Q12.2) MUTATED    27  36
  DEL PEAK 22(22Q12.2) WILD-TYPE  49 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(22Q12.2) MUTATED     27   36
  DEL PEAK 22(22Q12.2) WILD-TYPE   49  175
        clus
vv       DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE
  FEMALE                           27                             49
  MALE                             36                            175
[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    45
  DEL PEAK 22(22Q12.2) WILD-TYPE                        49   159
D29V11, multiclass
                                  clus
vv                                 DEL PEAK 22(22Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      45
                                  clus
vv                                 DEL PEAK 22(22Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    49
  WHITE                                                       159
[1] 4 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  48
  DEL PEAK 22(22Q12.2) WILD-TYPE   9 191
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(22Q12.2) MUTATED      3   48
  DEL PEAK 22(22Q12.2) WILD-TYPE    9  191
                        clus
vv                       DEL PEAK 22(22Q12.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           48
                        clus
vv                       DEL PEAK 22(22Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            191
[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    21  12
  DEL PEAK 23(XP11.4) WILD-TYPE 217  32
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                           33                           249 
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                           12                            32 
$`DEL PEAK 23(XP11.4) MUTATED`
TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K3 
       59.01        91.73        54.64        51.52        12.82        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K8 TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-A5Y1 
       71.80        43.04        67.43        18.21        19.63        12.99 
TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 
       37.51        10.09        20.61         2.10        19.27         8.88 
TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       22.92        21.63        25.35        79.86        10.68        13.08 
TCGA-F9-A97G TCGA-G7-6793 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD TCGA-J7-8537 
        0.43        11.05        25.15        20.52        16.90        10.55 
TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       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        39.88        38.99        33.07 
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-5P-A9JU TCGA-5P-A9JV 
       16.18        22.49         0.13        11.57        12.26        67.17 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K6 
      106.55        49.58        90.21        22.26        78.64        62.93 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7288 TCGA-A4-7583 
       19.36        12.99        12.39        27.09        61.05         0.10 
TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 
       21.37        35.18        19.13         0.89         7.82         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        70.19        76.64        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       67.73        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        20.25        16.77        20.32        21.07        33.83 
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-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       26.40         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        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       86.76        63.72        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       30.28        26.04        13.25        10.82         7.66         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-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 
       48.85        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-6132 
       13.78         3.75        14.63         3.02        40.77        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        74.60        34.19        19.00        24.89 
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        90.90        39.25 
TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       71.44        25.84         6.38        17.98        23.08        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        12.89        11.21        16.31        84.89        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 
        2.04        85.78        88.24        96.69        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36        12.76        18.41        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 
       17.62        12.13        31.13        29.26        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.09        42.94         6.61        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
       16.01        50.60        78.90        19.73        17.75        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        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 
       41.33        16.31        41.62        26.47        53.10        43.76 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PO 
       26.20       117.40       103.63       125.29        37.35        62.83 
TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.37        71.24        30.67        47.47        65.13 
TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       21.60       110.73        51.35        31.73        26.01        39.06 
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 
        3.68         6.02        13.28 

  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                         0.43                          0.10 
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                        91.73                        194.79 
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                        19.63                         25.58 
[1] "0.4 - 91.7 (19.6)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "3.3"
D30V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 23(XP11.4) MUTATED         8        1        16        3
  DEL PEAK 23(XP11.4) WILD-TYPE     163       21        36       12
D30V3, multiclass
           clus
vv          DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE
  STAGE I                             8                           163
  STAGE II                            1                            21
  STAGE III                          16                            36
  STAGE IV                            3                            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    12   4    18
  DEL PEAK 23(XP11.4) WILD-TYPE 178  29    44
D30V4, multiclass
       clus
vv      DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE
  T1                             12                           178
  T2                              4                            29
  T3+T4                          18                            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 23(XP11.4) MUTATED    5  8  1
  DEL PEAK 23(XP11.4) WILD-TYPE 43 16  4
D30V5, multiclass
    clus
vv   DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE
  N0                           5                            43
  N1                           8                            16
  N2                           1                             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"
D30V6, binary
                               cls
clus                             0  1
  DEL PEAK 23(XP11.4) MUTATED    9  1
  DEL PEAK 23(XP11.4) WILD-TYPE 84  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(XP11.4) MUTATED      9    1
  DEL PEAK 23(XP11.4) WILD-TYPE   84    8
   clus
vv  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE
  0                           9                            84
  1                           1                             8
[1] 2 2
[1] FALSE
D30V7, binary
                               cls
clus                              0   1
  DEL PEAK 23(XP11.4) MUTATED    15  19
  DEL PEAK 23(XP11.4) WILD-TYPE  61 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(XP11.4) MUTATED     15   19
  DEL PEAK 23(XP11.4) WILD-TYPE   61  192
        clus
vv       DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE
  FEMALE                          15                            61
  MALE                            19                           192
[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    20
  DEL PEAK 23(XP11.4) WILD-TYPE                        52   184
D30V11, multiclass
                                  clus
vv                                 DEL PEAK 23(XP11.4) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     20
                                  clus
vv                                 DEL PEAK 23(XP11.4) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   52
  WHITE                                                      184
[1] 4 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  26
  DEL PEAK 23(XP11.4) WILD-TYPE  12 213
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(XP11.4) MUTATED      0   26
  DEL PEAK 23(XP11.4) WILD-TYPE   12  213
                        clus
vv                       DEL PEAK 23(XP11.4) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          26
                        clus
vv                       DEL PEAK 23(XP11.4) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           213
[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  12
  DEL PEAK 24(XQ28) WILD-TYPE 223  32
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                         27                         255 
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                         12                          32 
$`DEL PEAK 24(XQ28) MUTATED`
TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K3 TCGA-5P-A9K8 
       91.73        54.64        51.52        12.82        15.48        43.04 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-A5Y1 TCGA-AL-3466 
       67.43        18.21        19.63         0.10        12.99         9.63 
TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5876 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-F9-A4JJ 
       37.51        10.09        19.27        22.92        21.63        10.68 
TCGA-F9-A7Q0 TCGA-G7-6793 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD TCGA-J7-8537 
       13.08        11.05        25.15        20.52        16.90        10.55 
TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       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        39.88        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       33.07        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-5P-A9JU 
        5.29        16.18        22.49         0.13        11.57        12.26 
TCGA-5P-A9JV TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       67.17       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        19.36        12.99        12.39        27.09 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
       61.05        21.37        35.18        19.13         0.89         7.82 
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-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46        70.19        76.64        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       67.73        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        20.25        16.77        20.32        21.07        33.83 
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        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 
       17.49        12.30        86.76         8.88        63.72        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-5893 
       13.25        10.82         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        48.85        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-5902 TCGA-EV-5903 TCGA-F9-A7VF 
       61.02        74.60        34.19        19.00        24.89         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
        1.18         0.43         4.01        51.78        90.90        39.25 
TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       71.44        25.84         6.38        17.98        23.08        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        12.89        11.21        16.31        84.89        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IA-A83W TCGA-IZ-8195 
        2.04        85.78        88.24        96.69        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36        12.76        18.41        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 
       17.62        12.13        31.13        29.26        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.09        42.94         6.61        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
       16.01        50.60        78.90        19.73        17.75        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        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 
       41.33        16.31        41.62        26.47        53.10        43.76 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PO 
       26.20       117.40       103.63       125.29        37.35        62.83 
TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.37        71.24        30.67        47.47        65.13 
TCGA-UZ-A9PZ TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       21.60       110.73        51.35        31.73        26.01        39.06 
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 
        3.68         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 
                      91.73                      194.79 
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                      18.21                       25.58 
[1] "0.1 - 91.7 (18.2)"  "0.1 - 194.8 (25.6)"
[1] "hr=" "4.5"
D31V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 24(XQ28) MUTATED         8        1        12        3
  DEL PEAK 24(XQ28) WILD-TYPE     163       21        40       12
D31V3, multiclass
           clus
vv          DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  STAGE I                           8                         163
  STAGE II                          1                          21
  STAGE III                        12                          40
  STAGE IV                          3                          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    11   3    14
  DEL PEAK 24(XQ28) WILD-TYPE 179  30    48
D31V4, multiclass
       clus
vv      DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  T1                           11                         179
  T2                            3                          30
  T3+T4                        14                          48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2
  DEL PEAK 24(XQ28) MUTATED    3  8  1
  DEL PEAK 24(XQ28) WILD-TYPE 45 16  4
D31V5, multiclass
    clus
vv   DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  N0                         3                          45
  N1                         8                          16
  N2                         1                           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"
D31V6, binary
                             cls
clus                           0  1
  DEL PEAK 24(XQ28) MUTATED    8  1
  DEL PEAK 24(XQ28) WILD-TYPE 85  8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 24(XQ28) MUTATED      8    1
  DEL PEAK 24(XQ28) WILD-TYPE   85    8
   clus
vv  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  0                         8                          85
  1                         1                           8
[1] 2 2
[1] FALSE
D31V7, binary
                             cls
clus                            0   1
  DEL PEAK 24(XQ28) MUTATED    13  15
  DEL PEAK 24(XQ28) WILD-TYPE  63 196
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 24(XQ28) MUTATED     13   15
  DEL PEAK 24(XQ28) WILD-TYPE   63  196
        clus
vv       DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  FEMALE                        13                          63
  MALE                          15                         196
[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    17
  DEL PEAK 24(XQ28) WILD-TYPE                        54   187
D31V11, multiclass
                                  clus
vv                                 DEL PEAK 24(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                                7
  WHITE                                                   17
                                  clus
vv                                 DEL PEAK 24(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 54
  WHITE                                                    187
[1] 4 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  23
  DEL PEAK 24(XQ28) WILD-TYPE  12 216
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 24(XQ28) MUTATED      0   23
  DEL PEAK 24(XQ28) WILD-TYPE   12  216
                        clus
vv                       DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             0                          12
  NOT HISPANIC OR LATINO                        23                         216
[1] 2 2
[1] FALSE
