[1] "ofn"         "-oTKIPAN-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/KIPAN-TP/15081103/KIPAN-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIPAN-TP/15087107/transformed.cor.cli.txt"

nPatients in clinical file=914, in cluster file=882, common to both=859
[1]  39 859
[1] "AMP PEAK  1(1Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q32.1) MUTATED AMP PEAK  1(1Q32.1) WILD-TYPE 
                           81                           778 
  AMP PEAK  1(1Q32.1) MUTATED AMP PEAK  1(1Q32.1) WILD-TYPE 
                           81                           778 
[1] "AMP PEAK  2(2Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2Q32.1) MUTATED AMP PEAK  2(2Q32.1) WILD-TYPE 
                          133                           726 
  AMP PEAK  2(2Q32.1) MUTATED AMP PEAK  2(2Q32.1) WILD-TYPE 
                          133                           726 
[1] "AMP PEAK  3(3Q26.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                           185                            674 
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                           185                            674 
[1] "AMP PEAK  4(5Q35.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(5Q35.1) MUTATED AMP PEAK  4(5Q35.1) WILD-TYPE 
                          372                           487 
  AMP PEAK  4(5Q35.1) MUTATED AMP PEAK  4(5Q35.1) WILD-TYPE 
                          372                           487 
[1] "AMP PEAK  5(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(7Q31.2) MUTATED AMP PEAK  5(7Q31.2) WILD-TYPE 
                          364                           495 
  AMP PEAK  5(7Q31.2) MUTATED AMP PEAK  5(7Q31.2) WILD-TYPE 
                          364                           495 
[1] "AMP PEAK  6(8Q24.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(8Q24.22) MUTATED AMP PEAK  6(8Q24.22) WILD-TYPE 
                           121                            738 
  AMP PEAK  6(8Q24.22) MUTATED AMP PEAK  6(8Q24.22) WILD-TYPE 
                           121                            738 
[1] "AMP PEAK  7(10P14) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(10P14) MUTATED AMP PEAK  7(10P14) WILD-TYPE 
                          33                          826 
  AMP PEAK  7(10P14) MUTATED AMP PEAK  7(10P14) WILD-TYPE 
                          33                          826 
[1] "AMP PEAK  8(17Q25.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(17Q25.2) MUTATED AMP PEAK  8(17Q25.2) WILD-TYPE 
                           232                            627 
  AMP PEAK  8(17Q25.2) MUTATED AMP PEAK  8(17Q25.2) WILD-TYPE 
                           232                            627 
[1] "AMP PEAK  9(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(19P13.2) MUTATED AMP PEAK  9(19P13.2) WILD-TYPE 
                            97                            762 
  AMP PEAK  9(19P13.2) MUTATED AMP PEAK  9(19P13.2) WILD-TYPE 
                            97                            762 
[1] "AMP PEAK 10(XP22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(XP22.2) MUTATED AMP PEAK 10(XP22.2) WILD-TYPE 
                          121                           738 
  AMP PEAK 10(XP22.2) MUTATED AMP PEAK 10(XP22.2) WILD-TYPE 
                          121                           738 
[1] "AMP PEAK 11(XP11.4) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(XP11.4) MUTATED AMP PEAK 11(XP11.4) WILD-TYPE 
                          129                           730 
  AMP PEAK 11(XP11.4) MUTATED AMP PEAK 11(XP11.4) WILD-TYPE 
                          129                           730 
[1] "AMP PEAK 12(XQ11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(XQ11.2) MUTATED AMP PEAK 12(XQ11.2) WILD-TYPE 
                          128                           731 
  AMP PEAK 12(XQ11.2) MUTATED AMP PEAK 12(XQ11.2) WILD-TYPE 
                          128                           731 
[1] "AMP PEAK 13(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(XQ28) MUTATED AMP PEAK 13(XQ28) WILD-TYPE 
                        132                         727 
  AMP PEAK 13(XQ28) MUTATED AMP PEAK 13(XQ28) WILD-TYPE 
                        132                         727 
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           203                            656 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           203                            656 
[1] "DEL PEAK  2(1P31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                          161                           698 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                          161                           698 
[1] "DEL PEAK  3(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                        112                         747 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                        112                         747 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                          110                           749 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                          110                           749 
[1] "DEL PEAK  5(3P26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                          486                           373 
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                          486                           373 
[1] "DEL PEAK  6(3P21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P21.2) MUTATED DEL PEAK  6(3P21.2) WILD-TYPE 
                          499                           360 
  DEL PEAK  6(3P21.2) MUTATED DEL PEAK  6(3P21.2) WILD-TYPE 
                          499                           360 
[1] "DEL PEAK  7(3P14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE 
                          405                           454 
  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE 
                          405                           454 
[1] "DEL PEAK  8(3P12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE 
                          334                           525 
  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE 
                          334                           525 
[1] "DEL PEAK  9(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          111                           748 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          111                           748 
[1] "DEL PEAK 10(5P15.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                            31                            828 
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                            31                            828 
[1] "DEL PEAK 11(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                           225                            634 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                           225                            634 
[1] "DEL PEAK 12(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        230                         629 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        230                         629 
[1] "DEL PEAK 13(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                        231                         628 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                        231                         628 
[1] "DEL PEAK 14(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                          181                           678 
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                          181                           678 
[1] "DEL PEAK 15(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                        196                         663 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                        196                         663 
[1] "DEL PEAK 16(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          207                           652 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          207                           652 
[1] "DEL PEAK 17(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE 
                            162                             697 
  DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE 
                            162                             697 
[1] "DEL PEAK 18(11Q21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(11Q21) MUTATED DEL PEAK 18(11Q21) WILD-TYPE 
                          60                          799 
  DEL PEAK 18(11Q21) MUTATED DEL PEAK 18(11Q21) WILD-TYPE 
                          60                          799 
[1] "DEL PEAK 19(11Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(11Q23.1) MUTATED DEL PEAK 19(11Q23.1) WILD-TYPE 
                            70                            789 
  DEL PEAK 19(11Q23.1) MUTATED DEL PEAK 19(11Q23.1) WILD-TYPE 
                            70                            789 
[1] "DEL PEAK 20(13Q12.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(13Q12.13) MUTATED DEL PEAK 20(13Q12.13) WILD-TYPE 
                            148                             711 
  DEL PEAK 20(13Q12.13) MUTATED DEL PEAK 20(13Q12.13) WILD-TYPE 
                            148                             711 
[1] "DEL PEAK 21(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           148                            711 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           148                            711 
[1] "DEL PEAK 22(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE 
                           274                            585 
  DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE 
                           274                            585 
[1] "DEL PEAK 23(16Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(16Q23.3) MUTATED DEL PEAK 23(16Q23.3) WILD-TYPE 
                            36                            823 
  DEL PEAK 23(16Q23.3) MUTATED DEL PEAK 23(16Q23.3) WILD-TYPE 
                            36                            823 
[1] "DEL PEAK 24(18Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(18Q22.2) MUTATED DEL PEAK 24(18Q22.2) WILD-TYPE 
                           152                            707 
  DEL PEAK 24(18Q22.2) MUTATED DEL PEAK 24(18Q22.2) WILD-TYPE 
                           152                            707 
[1] "DEL PEAK 25(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(19P13.3) MUTATED DEL PEAK 25(19P13.3) WILD-TYPE 
                            40                            819 
  DEL PEAK 25(19P13.3) MUTATED DEL PEAK 25(19P13.3) WILD-TYPE 
                            40                            819 
[1] "DEL PEAK 26(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(XP22.2) MUTATED DEL PEAK 26(XP22.2) WILD-TYPE 
                          123                           736 
  DEL PEAK 26(XP22.2) MUTATED DEL PEAK 26(XP22.2) WILD-TYPE 
                          123                           736 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 859 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=198,	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=589,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "1"     "858"  
freq.contrast "858"   "1"    
both >= 3     "FALSE" "FALSE"
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=42,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=44,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 859 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "NEOPLASM_DISEASESTAGE"        
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "KARNOFSKY_PERFORMANCE_SCORE"   "HISTOLOGICAL_TYPE"            
 [9] "NUMBER_PACK_YEARS_SMOKED"      "YEAR_OF_TOBACCO_SMOKING_ONSET"
[11] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=63, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
462 123 251  15 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
462 123 251  15 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
462 123 251  15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
462 123 251  15 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
317  43   6 
[1] "table(vv)"
vv
 N0  N1  N2 
317  43   6 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
317  43   6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
317  43   6 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=42, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=39, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q32.1) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1Q32.1) MUTATED    46  34
  AMP PEAK  1(1Q32.1) WILD-TYPE 586 177
  AMP PEAK  1(1Q32.1) MUTATED AMP PEAK  1(1Q32.1) WILD-TYPE 
                           80                           763 
  AMP PEAK  1(1Q32.1) MUTATED AMP PEAK  1(1Q32.1) WILD-TYPE 
                           34                           177 
$`AMP PEAK  1(1Q32.1) MUTATED`
TCGA-KN-8427 TCGA-A3-3316 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3372 TCGA-A3-3382 
        0.99        49.08        34.29        31.07        24.16        18.87 
TCGA-AK-3430 TCGA-AK-3450 TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4815 
       15.78        58.49        22.45        43.96         6.64        52.21 
TCGA-B0-4819 TCGA-B0-4838 TCGA-B0-4848 TCGA-B0-5092 TCGA-B0-5096 TCGA-B0-5109 
        6.02        27.42        29.03        15.09         2.24        19.30 
TCGA-B0-5115 TCGA-B0-5701 TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-5551 TCGA-BP-4160 
       26.20        56.94         0.36        23.31         0.53        94.72 
TCGA-BP-4161 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4329 TCGA-BP-4331 TCGA-BP-4342 
       90.28        61.78        64.27        27.78        80.68        74.17 
TCGA-BP-4352 TCGA-BP-4756 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4781 TCGA-BP-4963 
       11.31        12.30        13.15         5.33        68.38        60.30 
TCGA-BP-4971 TCGA-BP-4974 TCGA-BP-4986 TCGA-BP-5173 TCGA-BP-5175 TCGA-CJ-4635 
       48.89         7.23        25.81         1.78        30.64        46.55 
TCGA-CJ-4640 TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4895 TCGA-CJ-4916 
       65.69        74.27        64.27        66.21        39.45        45.14 
TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-6027 TCGA-CJ-6032 
       18.81        79.89        18.87        22.32        60.99        83.77 
TCGA-CW-5587 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4859 
       73.18        83.90        18.77        46.16        69.21        58.75 
TCGA-CZ-5452 TCGA-G6-A5PC TCGA-MM-A564 TCGA-2Z-A9J2 TCGA-A4-7287 TCGA-A4-A5Y1 
       58.82         7.96        19.96        59.01        19.63        12.99 
TCGA-AL-3466 TCGA-AL-A5DJ TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
        9.63        49.25        30.28        25.35         7.66         0.95 
TCGA-BQ-5893 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y 
        7.92        79.86         4.01        16.90         3.68         2.04 
TCGA-Q2-A5QZ TCGA-WN-A9G9 
       14.07        26.01 

$`AMP PEAK  1(1Q32.1) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       25.48        25.91        65.19       104.52         3.55        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       36.82        47.21         0.53        39.16        24.16        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       37.15        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       37.38        48.82        21.86         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       29.92        18.44        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       55.76        20.71        18.64        28.31        65.52        20.28 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 
      109.91        29.10        84.36        73.08        66.31        60.92 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       72.07        68.61        67.20        57.37        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 
       42.08        40.01        48.69        45.93        28.73        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        3.32         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        19.73         3.16         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       40.44        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4839 TCGA-B0-4841 
       78.44        68.71        40.70        45.30        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5094 TCGA-B0-5095 
       11.90         7.30        25.32        18.51        10.95         8.05 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5116 
       52.54        30.48        29.95        35.90        11.80        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 
       46.68        56.78        60.33        84.92        90.12        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
        0.53         4.64         5.46         0.23        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 
       24.23        17.16        16.60         6.38        14.27        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       85.51       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 
       89.36        23.05        77.03        62.24        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       53.42         3.58        62.07        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 
        0.07        93.99        18.48        52.24        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       31.33        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4774 
       41.75        71.80        48.07        61.68        10.82        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       60.59        13.51        56.91        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
       58.98        14.24        49.38        45.50        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        6.35        79.30        74.20        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
       31.27         0.95        59.84        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        54.61        53.52        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 
       83.97        49.25        79.66        47.18        75.06        77.36 
TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       71.87        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       27.65        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 
       38.56         3.06         4.57        63.88        72.00        84.66 
TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       25.71        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 
       67.00        53.26        53.42        75.58        62.66         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5588 
       64.57        92.02        81.83         5.39        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35       105.93       103.43        25.45 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
        0.59        47.08         6.77        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04         5.46        61.41        63.42         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        57.21        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       56.84        23.90        66.02        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        4.18        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       15.25        10.85         7.04        75.55        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       56.91         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       54.64        51.52        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       24.33        31.20        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 
       22.49         0.13        12.82        11.57        18.21        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 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-3467 
        8.48        16.31        15.75         8.28        12.46        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       76.64        13.55        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        2.10        19.23         6.81         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 
       43.20        47.80        21.63        40.83        26.04        26.04 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       13.25        10.88        11.97         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-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        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       13.68        25.84         6.38        17.98        17.33        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       56.75        73.25         5.49        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       25.68        27.39        12.99        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  AMP PEAK  1(1Q32.1) MUTATED AMP PEAK  1(1Q32.1) WILD-TYPE 
                         0.36                          0.07 
  AMP PEAK  1(1Q32.1) MUTATED AMP PEAK  1(1Q32.1) WILD-TYPE 
                        94.72                        194.79 
  AMP PEAK  1(1Q32.1) MUTATED AMP PEAK  1(1Q32.1) WILD-TYPE 
                        26.81                         30.67 
[1] "0.4 - 94.7 (26.8)"  "0.1 - 194.8 (30.7)"
[1] "hr=" "2"  
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  1(1Q32.1) MUTATED        24       10        32       15
  AMP PEAK  1(1Q32.1) WILD-TYPE     424       93       158       85
D1V3, multiclass
           clus
vv          AMP PEAK  1(1Q32.1) MUTATED AMP PEAK  1(1Q32.1) WILD-TYPE
  STAGE I                            24                           424
  STAGE II                           10                            93
  STAGE III                          32                           158
  STAGE IV                           15                            85
[1] 4 2
[1] 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(1Q32.1) MUTATED    27  12  41   1
  AMP PEAK  1(1Q32.1) WILD-TYPE 435 111 210  14
D1V4, multiclass
    clus
vv   AMP PEAK  1(1Q32.1) MUTATED AMP PEAK  1(1Q32.1) WILD-TYPE
  T1                          27                           435
  T2                          12                           111
  T3                          41                           210
  T4                           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                             N0  N1  N2
  AMP PEAK  1(1Q32.1) MUTATED    35  10   1
  AMP PEAK  1(1Q32.1) WILD-TYPE 282  33   5
D1V5, multiclass
    clus
vv   AMP PEAK  1(1Q32.1) MUTATED AMP PEAK  1(1Q32.1) WILD-TYPE
  N0                          35                           282
  N1                          10                            33
  N2                           1                             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"
D1V6, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q32.1) MUTATED    54  14
  AMP PEAK  1(1Q32.1) WILD-TYPE 488  75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q32.1) MUTATED     54   14
  AMP PEAK  1(1Q32.1) WILD-TYPE  488   75
   clus
vv  AMP PEAK  1(1Q32.1) MUTATED AMP PEAK  1(1Q32.1) WILD-TYPE
  0                          54                           488
  1                          14                            75
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q32.1) MUTATED    29  52
  AMP PEAK  1(1Q32.1) WILD-TYPE 258 520
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q32.1) MUTATED     29   52
  AMP PEAK  1(1Q32.1) WILD-TYPE  258  520
        clus
vv       AMP PEAK  1(1Q32.1) MUTATED AMP PEAK  1(1Q32.1) WILD-TYPE
  FEMALE                          29                           258
  MALE                            52                           520
[1] 2 2
[1] FALSE
D1V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  AMP PEAK  1(1Q32.1) MUTATED                    1
  AMP PEAK  1(1Q32.1) WILD-TYPE                 65
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  AMP PEAK  1(1Q32.1) MUTATED                                  62
  AMP PEAK  1(1Q32.1) WILD-TYPE                               462
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK  1(1Q32.1) MUTATED                                      18
  AMP PEAK  1(1Q32.1) WILD-TYPE                                   251
D1V9, multiclass
                                       clus
vv                                      AMP PEAK  1(1Q32.1) MUTATED
  KIDNEY CHROMOPHOBE                                              1
  KIDNEY CLEAR CELL RENAL CARCINOMA                              62
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          18
                                       clus
vv                                      AMP PEAK  1(1Q32.1) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               65
  KIDNEY CLEAR CELL RENAL CARCINOMA                               462
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           251
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
D1V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(1Q32.1) MUTATED                                  0     1
  AMP PEAK  1(1Q32.1) WILD-TYPE                                2    14
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q32.1) MUTATED                           5    74
  AMP PEAK  1(1Q32.1) WILD-TYPE                       111   628
D1V12, multiclass
                                  clus
vv                                 AMP PEAK  1(1Q32.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     74
                                  clus
vv                                 AMP PEAK  1(1Q32.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       14
  BLACK OR AFRICAN AMERICAN                                  111
  WHITE                                                      628
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q32.1) MUTATED     6  52
  AMP PEAK  1(1Q32.1) WILD-TYPE  36 545
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q32.1) MUTATED      6   52
  AMP PEAK  1(1Q32.1) WILD-TYPE   36  545
                        clus
vv                       AMP PEAK  1(1Q32.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          52
                        clus
vv                       AMP PEAK  1(1Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                36
  NOT HISPANIC OR LATINO                           545
[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   103  30
  AMP PEAK  2(2Q32.1) WILD-TYPE 529 181
  AMP PEAK  2(2Q32.1) MUTATED AMP PEAK  2(2Q32.1) WILD-TYPE 
                          133                           710 
  AMP PEAK  2(2Q32.1) MUTATED AMP PEAK  2(2Q32.1) WILD-TYPE 
                           30                           181 
$`AMP PEAK  2(2Q32.1) MUTATED`
TCGA-KN-8427 TCGA-KO-8410 TCGA-3Z-A93Z TCGA-A3-3372 TCGA-A3-3382 TCGA-A3-A8CQ 
        0.99        87.78        12.66        24.16        18.87         0.10 
TCGA-AK-3429 TCGA-AK-3444 TCGA-AK-3450 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       66.31        48.36        58.49         2.14        19.73         3.16 
TCGA-B0-4811 TCGA-B0-4821 TCGA-B0-5099 TCGA-B0-5104 TCGA-B0-5113 TCGA-B0-5702 
       46.59        40.44        15.95        90.48        11.80        52.77 
TCGA-B4-5832 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4620 TCGA-B8-5159 TCGA-B8-5550 
        0.23         5.46         0.36        25.55        23.74        14.27 
TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4170 
        0.53         4.93        90.28       101.06         0.43        77.03 
TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4342 TCGA-BP-4347 
       61.78         0.07        93.99        18.48        74.17        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4768 
       12.23        31.89        12.30        41.75        48.07        13.15 
TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4969 TCGA-BP-4985 
       60.59        68.38        37.25        47.97        58.98        31.30 
TCGA-BP-4989 TCGA-BP-5001 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5178 
        3.88        38.70         1.78        74.20         9.63        62.86 
TCGA-BP-5185 TCGA-BP-5196 TCGA-BP-5200 TCGA-CJ-4644 TCGA-CJ-4876 TCGA-CJ-4893 
       37.22        33.47        34.95        11.05        64.27        24.66 
TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5672 
       59.44        47.67        51.29        49.28        63.88        72.00 
TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5587 TCGA-CW-5591 
       84.66        61.91        53.42        83.77        73.18        74.66 
TCGA-CZ-4854 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 
       46.16        58.75         6.77        56.28        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5469 TCGA-DV-A4W0 TCGA-EU-5905 TCGA-2Z-A9J5 TCGA-2Z-A9JR 
       10.85        31.10        66.02         3.91       100.27         5.29 
TCGA-A4-7585 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       35.18        16.96         8.48        16.31        15.75         8.28 
TCGA-AL-3466 TCGA-AL-3471 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A657 
        9.63        13.55        44.61         2.20         7.33         6.58 
TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5878 TCGA-BQ-5885 
       10.16         0.46         2.10        14.86        63.72        30.28 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7046 TCGA-DW-5561 TCGA-DZ-6131 
       11.97         7.92         2.76        96.92        13.61        79.86 
TCGA-DZ-6133 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 
       51.19         1.18         4.01        51.78        39.25        25.84 
TCGA-G7-A8LC TCGA-GL-7966 TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40U 
       17.33         3.68        17.95        68.12        11.84        16.80 
TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5E8 
        2.04        11.97        29.10        11.41        34.29        42.94 
TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SQ TCGA-UZ-A9PK 
       84.95        17.75        14.07        28.80        41.62        60.03 
TCGA-UZ-A9PQ 
       86.27 

$`AMP PEAK  2(2Q32.1) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       25.48        25.91        65.19       104.52         3.55        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       92.71        16.67        80.38       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       57.17        61.58        63.95        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        0.53        39.16        24.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
       43.20        55.76        20.71        18.64        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV TCGA-A3-A8OW 
       20.28        15.39        22.65         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 
      109.91        29.10        84.36        73.08        15.78        60.92 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       72.07        68.61        67.20        57.37        46.78        42.08 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       40.01        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        3.32         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 
       43.96         6.64         3.25        20.25        15.72         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 
       10.95         8.05         2.24        21.86        52.08        62.89 
TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.87        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       21.44        37.22        14.76        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       90.12        56.94        39.55       120.59        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        12.30        21.30        31.30        11.77 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       10.36        32.98        21.57        16.67         9.57         5.75 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        1.25         0.53         4.64         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 
       27.16        27.55        25.05        24.66        17.19        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       23.01        20.91         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       17.16        16.60         6.38        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K 
       29.88        17.06         1.74         8.42        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4163 
       16.27        14.17       111.02        85.51        94.72        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4176 
       32.61        99.85        89.36        23.05        62.24        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4341 TCGA-BP-4343 
       80.68        37.25        21.21        15.16        52.24        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       54.77        49.08        11.31        12.33        33.99        31.33 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4765 
       72.59        77.98        77.62         5.98        44.15        71.80 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       61.68        10.82         5.33        61.97        13.51        56.91 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 
       36.39        10.98        36.95         6.71         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 
       46.45        25.81        36.95        27.22        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5180 
       48.10         6.35        79.30        30.64        52.27        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 
       49.15        38.30        42.44        37.25        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       19.82        44.55        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       53.52        58.95        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4881 
       47.18        74.27        75.06        77.36        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4895 
       63.98        68.55        26.93        50.01        27.65        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
       50.24        56.35        49.97        58.92        49.18        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       79.89        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
       62.10        73.35        67.00        53.26        60.99        75.58 
TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       62.66         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       85.78        66.31        78.18         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
      103.43        18.77        25.45         0.59        47.08        69.21 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 
       63.42        58.82         0.82        23.74        18.44        56.94 
TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       55.33        10.22        21.76        57.21        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40         1.94        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       23.90        18.12         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        15.25 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J6 
       10.85         7.04        75.55        59.01        58.22        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       31.20        29.36        25.58        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
       19.73        14.33        12.46        12.99        12.46        58.45 
TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M 
       76.64        30.35        25.08        49.25        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       24.56        16.87         3.55        16.77         0.46        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        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-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       19.23         6.81         0.16        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
       19.27         8.88        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 
        7.66         0.95       123.62        48.26        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-7834 
        7.63         7.04         7.17         3.81        11.61       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-6134 TCGA-DZ-6135 TCGA-EV-5901 
        3.02        40.77        80.88        61.02        54.90        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-A4TM 
       48.62        11.05        34.82        25.15        13.68         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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH 
        1.05        12.43         0.89        11.21         4.60        13.41 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       56.75        73.25         5.49        19.99        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA 
       25.97        21.44        15.48        99.78        87.22         6.61 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        47.44        33.04        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       38.63        16.31        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       14.83        21.93         0.53        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  AMP PEAK  2(2Q32.1) MUTATED AMP PEAK  2(2Q32.1) WILD-TYPE 
                         0.07                          0.10 
  AMP PEAK  2(2Q32.1) MUTATED AMP PEAK  2(2Q32.1) WILD-TYPE 
                       101.06                        194.79 
  AMP PEAK  2(2Q32.1) MUTATED AMP PEAK  2(2Q32.1) WILD-TYPE 
                        30.28                         30.53 
[1] "0.1 - 101.1 (30.3)" "0.1 - 194.8 (30.5)"
[1] "hr=" "1"  
D2V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  2(2Q32.1) MUTATED        68       11        37       16
  AMP PEAK  2(2Q32.1) WILD-TYPE     380       92       153       84
D2V3, multiclass
           clus
vv          AMP PEAK  2(2Q32.1) MUTATED AMP PEAK  2(2Q32.1) WILD-TYPE
  STAGE I                            68                           380
  STAGE II                           11                            92
  STAGE III                          37                           153
  STAGE IV                           16                            84
[1] 4 2
[1] 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    69  15  46   3
  AMP PEAK  2(2Q32.1) WILD-TYPE 393 108 205  12
D2V4, multiclass
    clus
vv   AMP PEAK  2(2Q32.1) MUTATED AMP PEAK  2(2Q32.1) WILD-TYPE
  T1                          69                           393
  T2                          15                           108
  T3                          46                           205
  T4                           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                             N0  N1  N2
  AMP PEAK  2(2Q32.1) MUTATED    47  11   2
  AMP PEAK  2(2Q32.1) WILD-TYPE 270  32   4
D2V5, multiclass
    clus
vv   AMP PEAK  2(2Q32.1) MUTATED AMP PEAK  2(2Q32.1) WILD-TYPE
  N0                          47                           270
  N1                          11                            32
  N2                           2                             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"
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q32.1) MUTATED    85  13
  AMP PEAK  2(2Q32.1) WILD-TYPE 457  76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q32.1) MUTATED     85   13
  AMP PEAK  2(2Q32.1) WILD-TYPE  457   76
   clus
vv  AMP PEAK  2(2Q32.1) MUTATED AMP PEAK  2(2Q32.1) WILD-TYPE
  0                          85                           457
  1                          13                            76
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q32.1) MUTATED    50  83
  AMP PEAK  2(2Q32.1) WILD-TYPE 237 489
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q32.1) MUTATED     50   83
  AMP PEAK  2(2Q32.1) WILD-TYPE  237  489
        clus
vv       AMP PEAK  2(2Q32.1) MUTATED AMP PEAK  2(2Q32.1) WILD-TYPE
  FEMALE                          50                           237
  MALE                            83                           489
[1] 2 2
[1] FALSE
D2V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  AMP PEAK  2(2Q32.1) MUTATED                    2
  AMP PEAK  2(2Q32.1) WILD-TYPE                 64
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  AMP PEAK  2(2Q32.1) MUTATED                                  80
  AMP PEAK  2(2Q32.1) WILD-TYPE                               444
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK  2(2Q32.1) MUTATED                                      51
  AMP PEAK  2(2Q32.1) WILD-TYPE                                   218
D2V9, multiclass
                                       clus
vv                                      AMP PEAK  2(2Q32.1) MUTATED
  KIDNEY CHROMOPHOBE                                              2
  KIDNEY CLEAR CELL RENAL CARCINOMA                              80
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          51
                                       clus
vv                                      AMP PEAK  2(2Q32.1) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               64
  KIDNEY CLEAR CELL RENAL CARCINOMA                               444
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           218
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
D2V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(2Q32.1) MUTATED                                  0     3
  AMP PEAK  2(2Q32.1) WILD-TYPE                                2    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(2Q32.1) MUTATED                          13   114
  AMP PEAK  2(2Q32.1) WILD-TYPE                       103   588
D2V12, multiclass
                                  clus
vv                                 AMP PEAK  2(2Q32.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    114
                                  clus
vv                                 AMP PEAK  2(2Q32.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                  103
  WHITE                                                      588
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q32.1) MUTATED     7  87
  AMP PEAK  2(2Q32.1) WILD-TYPE  35 510
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q32.1) MUTATED      7   87
  AMP PEAK  2(2Q32.1) WILD-TYPE   35  510
                        clus
vv                       AMP PEAK  2(2Q32.1) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                          87
                        clus
vv                       AMP PEAK  2(2Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                35
  NOT HISPANIC OR LATINO                           510
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(3Q26.32) MUTATION ANALYSIS
D3V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  3(3Q26.32) MUTATED   131  46
  AMP PEAK  3(3Q26.32) WILD-TYPE 501 165
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                           177                            666 
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                            46                            165 
$`AMP PEAK  3(3Q26.32) MUTATED`
TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8346 TCGA-KM-8443 TCGA-KN-8427 TCGA-A3-3325 
       98.96        28.11        62.37        49.97         0.99        24.69 
TCGA-A3-3374 TCGA-A3-3387 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3453 
       43.20        20.28        68.61        67.20        57.37        45.93 
TCGA-B0-4690 TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4833 
        1.41        28.47         3.62        43.96         6.64        78.44 
TCGA-B0-4845 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5094 TCGA-B0-5097 TCGA-B0-5098 
       65.29        11.90         7.30        10.95        21.86        52.08 
TCGA-B0-5102 TCGA-B0-5109 TCGA-B0-5116 TCGA-B0-5690 TCGA-B0-5696 TCGA-B0-5710 
       90.87        19.30        21.60        79.17        56.78        47.97 
TCGA-B0-5712 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4620 TCGA-B8-4621 
       89.49         0.53         5.46        23.31        25.55        25.91 
TCGA-B8-5163 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-A54G TCGA-B8-A54I TCGA-BP-4163 
       27.02         6.38         0.53         1.74         4.93        93.34 
TCGA-BP-4167 TCGA-BP-4329 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4352 
       89.36        27.78         0.07        93.99        31.89        11.31 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4960 TCGA-BP-4964 
        5.98        44.15        13.15        68.38        71.41        61.22 
TCGA-BP-4969 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5178 
       58.98        31.30        43.00         6.35        30.64        62.86 
TCGA-BP-5198 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4871 
       19.82        14.17        65.69        11.05        21.24        79.66 
TCGA-CJ-4873 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4897 TCGA-CJ-4900 TCGA-CJ-4901 
       74.27        71.87        66.21        59.44        56.35        47.67 
TCGA-CJ-4907 TCGA-CJ-6028 TCGA-CJ-6033 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 
       49.28        53.42         7.36        66.31        74.66         1.35 
TCGA-CW-6097 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-5456 TCGA-CZ-5460 
       18.77        69.21         6.77        14.66        56.28        47.01 
TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 
       10.85        57.21        47.54         1.94        31.10        67.96 
TCGA-EU-5905 TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        3.91         7.04        59.01        58.22       100.27        56.91 
TCGA-A4-7287 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8518 
       19.63        30.48        23.97        23.31         0.76        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3468 
       14.33        12.46        16.96        16.31        15.75        76.64 
TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-4103 
       13.55         2.20         7.33        21.67         6.58        30.58 
TCGA-B3-A6W5 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.16        28.18         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5890 
       22.06         2.10        17.49        47.80        26.04         7.66 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7836 TCGA-DW-7837 
       48.26        96.92         7.04         3.81        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       24.46        40.77        80.88        51.19        54.90        34.19 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-A8LB TCGA-G7-A8LD TCGA-GL-6846 
       13.08         2.40        51.78        17.98        16.90       194.79 
TCGA-GL-A59T TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A40Y 
       17.95        11.21        68.12        11.84         5.49         2.04 
TCGA-IA-A83S TCGA-IA-A83W TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       85.78        67.17        11.97        29.10        11.41        34.29 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-P4-AAVM TCGA-PJ-A5Z9 
       99.78        87.22         6.61        16.01        50.60        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS 
       14.07        28.80        19.00        16.31        41.62        48.30 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       60.03        14.83        21.93        52.11        30.67        25.68 
TCGA-UZ-A9Q0 TCGA-Y8-A895 TCGA-Y8-A8RZ 
       12.99        15.91         6.74 

$`AMP PEAK  3(3Q26.32) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
       90.48       108.62        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       71.41        28.80        54.74       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       28.80        47.24       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19       104.52 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        3.55        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87        76.90        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
       74.93        79.04        92.71        16.67        80.38        87.78 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        86.10        77.85        57.17        61.58        63.95 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        12.16        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       36.36        38.99        37.38        48.82        21.86        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        24.16        53.29        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.64        18.87        28.31        65.52        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
       84.36        73.08        66.31        15.78        60.92        72.07 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        42.08        40.01        58.49        48.69 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         3.32         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
        3.48        19.00         1.38        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        19.73         3.16         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 
       53.88         6.71        56.68        11.64        10.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 
       43.30        11.24        25.32        18.51        15.09         8.05 
TCGA-B0-5096 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
        2.24        15.95        62.89        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
       29.95        35.90        11.80        26.20        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5697 TCGA-B0-5698 
       48.89       101.13        15.78        46.68        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5709 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      102.48        96.36        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67         9.57         5.75         0.23 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
        1.25         4.64         0.36         0.23        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 
       27.55        25.05        24.66        17.19        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74         1.18         0.85        24.23        17.16        16.60 
TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
       14.27        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        8.42        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4164 TCGA-BP-4165 
       85.51        94.72        90.28       101.06        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        0.43        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4330 TCGA-BP-4331 
       54.90        97.45        53.42         3.58        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       37.25        21.21        15.16        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 
       62.86        54.77        49.08        44.94        12.23        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
       61.97        60.59        13.51        56.91        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
       53.65        14.93        36.07        33.34        46.45        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
       79.30         1.78        74.20        52.27         9.63        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       24.62        33.47        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4641 
       59.84        46.55        63.25        73.22        75.88        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 
       53.52        58.95        83.97        49.25        47.18        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       77.36        64.27        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 
       24.66        27.65        39.45        50.24        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       58.92        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       61.91        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       75.58        62.66        83.77        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 
        5.39        85.78        73.18        78.18       105.93        83.90 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 
      103.43        25.45        46.16         0.59        47.08        58.75 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       60.59        63.39        93.04         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82         0.82        23.74        18.44        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 
       55.33        10.22        21.76        22.52         2.40        12.69 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       80.19        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       43.69        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 
       66.28        56.84        23.90        66.02        18.12         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9J1 TCGA-2Z-A9J7 
       19.43        19.96        15.25        10.85        75.55         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       12.82        11.57        18.21        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 
       19.13         0.89         0.23        16.64        29.46        25.64 
TCGA-A4-8312 TCGA-A4-8517 TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
       23.28        19.63         8.48         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
        9.63        58.45        30.35        25.08        44.61        49.25 
TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        24.56        16.87         3.55        16.77         0.46 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 
       33.83        10.09        34.49        12.46        50.50        26.40 
TCGA-B9-4116 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI 
       20.61        19.23         6.81         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-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 
       21.63        40.83        26.04        30.28        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.88         0.95        11.97         7.92         2.76       123.62 
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-7061 TCGA-DW-5560 TCGA-DW-5561 
       20.12        11.28         7.63         7.17        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 
      129.86        13.78         3.75        14.63         3.02        79.86 
TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G 
       61.02        19.00        24.89        10.68         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        4.01        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-7773 
       13.68        25.84         6.38        17.33        80.65        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DE 
        3.68        27.65         1.05        12.43         0.89         4.60 
TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83T 
       13.41        56.75        73.25        16.80        19.99        88.24 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55Z 
       22.26        21.34        16.34        12.36         0.13        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       21.44        15.48        42.94        84.95        92.58        52.27 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL 
       78.90        12.85        47.90        47.44        33.04        27.06 
TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PP 
       11.93        38.63        26.47        43.76        18.02         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PX TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       86.27        38.86        27.39        26.01        29.00        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        15.62        25.28         6.02        13.28 

  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                        194.79                         151.96 
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                        26.040                         31.315 
[1] "0.1 - 194.8 (26.0)" "0.1 - 152.0 (31.3)"
[1] "hr=" "1.1"
D3V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  3(3Q26.32) MUTATED        89       19        42       29
  AMP PEAK  3(3Q26.32) WILD-TYPE     359       84       148       71
D3V3, multiclass
           clus
vv          AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE
  STAGE I                             89                            359
  STAGE II                            19                             84
  STAGE III                           42                            148
  STAGE IV                            29                             71
[1] 4 2
[1] 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(3Q26.32) MUTATED    92  24  60   6
  AMP PEAK  3(3Q26.32) WILD-TYPE 370  99 191   9
D3V4, multiclass
    clus
vv   AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE
  T1                           92                            370
  T2                           24                             99
  T3                           60                            191
  T4                            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                              N0  N1  N2
  AMP PEAK  3(3Q26.32) MUTATED    57  15   0
  AMP PEAK  3(3Q26.32) WILD-TYPE 260  28   6
D3V5, multiclass
    clus
vv   AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE
  N0                           57                            260
  N1                           15                             28
  N2                            0                              6
[1] 3 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(3Q26.32) MUTATED    90  26
  AMP PEAK  3(3Q26.32) WILD-TYPE 452  63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.32) MUTATED     90   26
  AMP PEAK  3(3Q26.32) WILD-TYPE  452   63
   clus
vv  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE
  0                           90                            452
  1                           26                             63
[1] 2 2
[1] FALSE
D3V7, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.32) MUTATED    54 131
  AMP PEAK  3(3Q26.32) WILD-TYPE 233 441
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.32) MUTATED     54  131
  AMP PEAK  3(3Q26.32) WILD-TYPE  233  441
        clus
vv       AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE
  FEMALE                           54                            233
  MALE                            131                            441
[1] 2 2
[1] FALSE
D3V8, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  AMP PEAK  3(3Q26.32) MUTATED                    6
  AMP PEAK  3(3Q26.32) WILD-TYPE                 60
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  AMP PEAK  3(3Q26.32) MUTATED                                  86
  AMP PEAK  3(3Q26.32) WILD-TYPE                               438
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK  3(3Q26.32) MUTATED                                      93
  AMP PEAK  3(3Q26.32) WILD-TYPE                                   176
D3V9, multiclass
                                       clus
vv                                      AMP PEAK  3(3Q26.32) MUTATED
  KIDNEY CHROMOPHOBE                                               6
  KIDNEY CLEAR CELL RENAL CARCINOMA                               86
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           93
                                       clus
vv                                      AMP PEAK  3(3Q26.32) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                60
  KIDNEY CLEAR CELL RENAL CARCINOMA                                438
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, continuous
D3V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(3Q26.32) MUTATED                                  2     1
  AMP PEAK  3(3Q26.32) WILD-TYPE                                0    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(3Q26.32) MUTATED                          24   149
  AMP PEAK  3(3Q26.32) WILD-TYPE                        92   553
D3V12, multiclass
                                  clus
vv                                 AMP PEAK  3(3Q26.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  24
  WHITE                                                     149
                                  clus
vv                                 AMP PEAK  3(3Q26.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        14
  BLACK OR AFRICAN AMERICAN                                    92
  WHITE                                                       553
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.32) MUTATED     8 134
  AMP PEAK  3(3Q26.32) WILD-TYPE  34 463
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.32) MUTATED      8  134
  AMP PEAK  3(3Q26.32) WILD-TYPE   34  463
                        clus
vv                       AMP PEAK  3(3Q26.32) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          134
                        clus
vv                       AMP PEAK  3(3Q26.32) WILD-TYPE
  HISPANIC OR LATINO                                 34
  NOT HISPANIC OR LATINO                            463
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(5Q35.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(5Q35.1) MUTATED   266 105
  AMP PEAK  4(5Q35.1) WILD-TYPE 366 106
  AMP PEAK  4(5Q35.1) MUTATED AMP PEAK  4(5Q35.1) WILD-TYPE 
                          371                           472 
  AMP PEAK  4(5Q35.1) MUTATED AMP PEAK  4(5Q35.1) WILD-TYPE 
                          105                           106 
$`AMP PEAK  4(5Q35.1) MUTATED`
TCGA-KL-8327 TCGA-KL-8339 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8436 
      137.06        28.11         3.55         0.99        52.27        42.35 
TCGA-KO-8404 TCGA-KO-8414 TCGA-3Z-A93Z TCGA-A3-3307 TCGA-A3-3316 TCGA-A3-3317 
       10.68        77.85        12.66        47.21        49.08        49.02 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
       49.58        48.59        38.99        24.69        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
       21.86        34.29        52.93        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3374 
       42.97        82.32        51.25        74.76        24.16        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ 
       55.76        18.64        18.87        65.52        20.28        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OW TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3436 
       22.65         0.10        10.62        66.31        15.78        67.20 
TCGA-AK-3440 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       57.37        48.36        42.08        48.69        45.93        28.73 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4700 
       38.40        31.27        28.04         4.57         2.53        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        7.82         5.98        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 
        3.25        46.59         5.52        33.50         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4838 
       36.53        14.93        10.09        78.44        40.70        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4844 TCGA-B0-4847 TCGA-B0-4848 
       53.88         6.71        56.68        10.29        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 
        2.27        36.85        70.52        20.94        43.30        11.90 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5099 
       25.32        18.51        15.09        10.95         8.05        15.95 
TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       90.87        52.54        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5402 
       26.20         1.94        16.21        18.21        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5696 TCGA-B0-5697 
      112.80        48.89       101.13        15.78        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 
       84.92        56.94        52.77       120.59       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4099 
       96.36        89.49        61.32        97.41        35.90        12.30 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        11.77        10.36        32.98        21.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4620 
        0.23         1.25         5.46        23.31        16.80        25.55 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5550 
       20.91        23.74        27.02        24.23         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
        0.53        34.39        14.30         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 
       17.36        16.27       111.02        85.51        94.72       101.06 
TCGA-BP-4163 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       93.34         0.43        89.36        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       54.90        62.07        80.68        15.16         0.07        93.99 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 
       74.17        62.86        54.77        44.94        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4762 TCGA-BP-4763 
       12.33        31.33        72.59        77.98        44.15        41.75 
TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       13.15        60.59        13.51        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 
       48.95        36.53        36.39        37.25        36.95        47.97 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        58.98        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        31.30        25.81        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5004 
       46.45        16.47        43.00        45.07        41.62        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5170 
       27.62        37.48        35.21        36.23        48.10        79.30 
TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5183 
        1.78        30.64         9.63        62.86        49.15        42.44 
TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       37.22        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4635 TCGA-CJ-4636 
       19.82        34.95        31.27         0.95        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4644 TCGA-CJ-4869 
       73.22        14.17        75.88        54.61        11.05        83.97 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4884 
       79.66        74.27        75.06        77.36        64.27        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       69.86        64.18        30.64        68.55        50.01        24.66 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4918 
       58.92        49.28        50.33        54.48        45.14         3.06 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 
       18.81        63.88        72.00        79.89        84.66        18.87 
TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       22.32        61.91        62.10        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       53.42        62.66         7.36        92.02        81.83        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CZ-4853 TCGA-CZ-4854 
       73.18        66.31        78.18        74.66        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
        0.59        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39        93.04        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5461 
       23.74        18.44        56.28        55.33        56.94        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        57.21        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5989 
       31.10        12.69        67.96        65.65        12.26        62.63 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-A4W0 TCGA-EU-5904 
       12.16        11.67        37.15        66.28        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-GK-A6C7 
        3.91         6.77         4.18         7.96        10.29         2.01 
TCGA-MM-A564 TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9JK TCGA-2Z-A9JR TCGA-4A-A93X 
       19.96        10.85         7.04        38.99         5.29        12.82 
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        25.08 
TCGA-B1-5398 TCGA-B1-A656 TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5887 TCGA-BQ-5890 
       19.56         0.46         0.46         0.16        25.35         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-DW-7838 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-F9-A97G 
        0.95        11.97        24.46        19.00        13.08         0.43 
TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-A4EM TCGA-HE-A5NK TCGA-IA-A40X TCGA-IA-A40Y 
        4.01        17.33         1.05        73.25        19.99         2.04 
TCGA-KV-A6GD TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SQ 
       11.97        99.78        84.95        14.07        41.62 

$`AMP PEAK  4(5Q35.1) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
       65.19       104.52        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 
       59.08       115.00       100.87        76.90        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 
       57.17        61.58        63.95        12.16        36.82         0.53 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3319 TCGA-A3-3323 TCGA-A3-3343 TCGA-A3-3346 
       39.16        24.16        37.15        36.36        31.07         4.50 
TCGA-A3-3349 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3373 TCGA-A3-3378 
       45.53        10.49        28.70        74.63        53.29        20.71 
TCGA-A3-3383 TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
       28.31         0.10        11.18       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3447 
       73.08        60.92        72.07        68.61        46.78        40.01 
TCGA-AK-3450 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       58.49        22.45        37.58        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        3.32         1.41         3.48        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4815 
        3.62         2.14        20.25        15.72         0.59        52.21 
TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4834 TCGA-B0-4837 
       45.07        16.77        54.48        29.10        68.71        45.30 
TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5096 
       11.64        65.29        39.45        11.24         7.30         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5116 
       21.86        52.08        62.89        90.48        30.48        21.60 
TCGA-B0-5117 TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5695 TCGA-B0-5699 TCGA-B0-5703 
       17.59        21.44        79.17        46.68        90.12        39.55 
TCGA-B0-5706 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       79.36        32.61         1.68        16.67         9.57         5.75 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4148 TCGA-B8-4151 
        0.53         4.64         0.36         0.23        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5162 
       25.05        24.66        17.19        25.91        23.01         1.18 
TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.85        17.16        16.60        27.29        29.88        17.06 
TCGA-B8-A54K TCGA-B8-A8YJ TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4169 
       15.42        14.17        90.28        32.61        99.85        23.05 
TCGA-BP-4170 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4332 
       77.03        97.45        53.42         3.58        27.78        37.25 
TCGA-BP-4334 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4354 
       21.21        18.48        52.24        49.08        12.23        33.99 
TCGA-BP-4756 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
       12.30        77.62         5.98        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4795 
       10.82         5.33        61.97        11.64        60.95        20.38 
TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4970 TCGA-BP-4987 TCGA-BP-4993 
       10.98         6.71         6.94        14.24        36.95         5.82 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5174 
       30.64        18.51        38.70        28.87         6.35        74.20 
TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5194 
       52.27        74.40        38.30        37.25        22.78        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-CJ-4634 TCGA-CJ-4640 TCGA-CJ-4642 
       24.62        33.47        44.55        59.84        65.69        53.52 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4878 TCGA-CJ-4881 
       58.95        21.24        49.25        47.18        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4895 
       61.91        51.52        63.98        26.93        27.65        39.45 
TCGA-CJ-4905 TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 
       49.18        38.56         4.57        25.71        25.25        18.15 
TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-6087 
       53.26        75.58        83.77        64.57         5.39         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4862 TCGA-CZ-4865 
      105.93        83.90       103.43        18.77        60.59         5.46 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5987 TCGA-CZ-5988 
       55.33        47.01        47.54        80.19        14.63        22.78 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5575 TCGA-DV-5576 TCGA-G6-A8L7 
       43.69        45.96        65.88        56.84        23.90        70.13 
TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MM-A84U TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       35.87        19.43        15.25        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
      100.27        56.91         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JM 
       56.81        54.64        51.52        35.67        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       24.33        31.20        29.36        25.58        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        0.13        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       14.33        16.96        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 
       12.46        58.45        76.64        13.55        30.35        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       49.25         2.20         7.33        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
        3.55        16.77         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       20.61         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       19.23         6.81        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-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 
       10.88         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 
       11.61        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        54.90        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        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-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         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A83S 
       13.41        11.84        56.75         5.49        16.80        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
        0.13        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK 
       15.48        87.22        42.94         6.61        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        12.85        17.75        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       38.63        16.31        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  AMP PEAK  4(5Q35.1) MUTATED AMP PEAK  4(5Q35.1) WILD-TYPE 
                         0.07                          0.10 
  AMP PEAK  4(5Q35.1) MUTATED AMP PEAK  4(5Q35.1) WILD-TYPE 
                       137.06                        194.79 
  AMP PEAK  4(5Q35.1) MUTATED AMP PEAK  4(5Q35.1) WILD-TYPE 
                       36.230                        27.715 
[1] "0.1 - 137.1 (36.2)" "0.1 - 194.8 (27.7)"
[1] "hr=" "1.2"
D4V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  4(5Q35.1) MUTATED       172       42        93       62
  AMP PEAK  4(5Q35.1) WILD-TYPE     276       61        97       38
D4V3, multiclass
           clus
vv          AMP PEAK  4(5Q35.1) MUTATED AMP PEAK  4(5Q35.1) WILD-TYPE
  STAGE I                           172                           276
  STAGE II                           42                            61
  STAGE III                          93                            97
  STAGE IV                           62                            38
[1] 4 2
[1] 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(5Q35.1) MUTATED   179  55 130   7
  AMP PEAK  4(5Q35.1) WILD-TYPE 283  68 121   8
D4V4, multiclass
    clus
vv   AMP PEAK  4(5Q35.1) MUTATED AMP PEAK  4(5Q35.1) WILD-TYPE
  T1                         179                           283
  T2                          55                            68
  T3                         130                           121
  T4                           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                             N0  N1  N2
  AMP PEAK  4(5Q35.1) MUTATED   161  14   1
  AMP PEAK  4(5Q35.1) WILD-TYPE 156  29   5
D4V5, multiclass
    clus
vv   AMP PEAK  4(5Q35.1) MUTATED AMP PEAK  4(5Q35.1) WILD-TYPE
  N0                         161                           156
  N1                          14                            29
  N2                           1                             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"
D4V6, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q35.1) MUTATED   278  58
  AMP PEAK  4(5Q35.1) WILD-TYPE 264  31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q35.1) MUTATED    278   58
  AMP PEAK  4(5Q35.1) WILD-TYPE  264   31
   clus
vv  AMP PEAK  4(5Q35.1) MUTATED AMP PEAK  4(5Q35.1) WILD-TYPE
  0                         278                           264
  1                          58                            31
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q35.1) MUTATED   117 255
  AMP PEAK  4(5Q35.1) WILD-TYPE 170 317
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q35.1) MUTATED    117  255
  AMP PEAK  4(5Q35.1) WILD-TYPE  170  317
        clus
vv       AMP PEAK  4(5Q35.1) MUTATED AMP PEAK  4(5Q35.1) WILD-TYPE
  FEMALE                         117                           170
  MALE                           255                           317
[1] 2 2
[1] FALSE
D4V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  AMP PEAK  4(5Q35.1) MUTATED                    8
  AMP PEAK  4(5Q35.1) WILD-TYPE                 58
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  AMP PEAK  4(5Q35.1) MUTATED                                 330
  AMP PEAK  4(5Q35.1) WILD-TYPE                               194
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK  4(5Q35.1) MUTATED                                      34
  AMP PEAK  4(5Q35.1) WILD-TYPE                                   235
D4V9, multiclass
                                       clus
vv                                      AMP PEAK  4(5Q35.1) MUTATED
  KIDNEY CHROMOPHOBE                                              8
  KIDNEY CLEAR CELL RENAL CARCINOMA                             330
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          34
                                       clus
vv                                      AMP PEAK  4(5Q35.1) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               58
  KIDNEY CLEAR CELL RENAL CARCINOMA                               194
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           235
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, continuous
D4V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(5Q35.1) MUTATED                                  0     5
  AMP PEAK  4(5Q35.1) WILD-TYPE                                2    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(5Q35.1) MUTATED                          29   331
  AMP PEAK  4(5Q35.1) WILD-TYPE                        87   371
D4V12, multiclass
                                  clus
vv                                 AMP PEAK  4(5Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 29
  WHITE                                                    331
                                  clus
vv                                 AMP PEAK  4(5Q35.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   87
  WHITE                                                      371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q35.1) MUTATED    17 252
  AMP PEAK  4(5Q35.1) WILD-TYPE  25 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q35.1) MUTATED     17  252
  AMP PEAK  4(5Q35.1) WILD-TYPE   25  345
                        clus
vv                       AMP PEAK  4(5Q35.1) MUTATED
  HISPANIC OR LATINO                              17
  NOT HISPANIC OR LATINO                         252
                        clus
vv                       AMP PEAK  4(5Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                25
  NOT HISPANIC OR LATINO                           345
[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   268  83
  AMP PEAK  5(7Q31.2) WILD-TYPE 364 128
  AMP PEAK  5(7Q31.2) MUTATED AMP PEAK  5(7Q31.2) WILD-TYPE 
                          351                           492 
  AMP PEAK  5(7Q31.2) MUTATED AMP PEAK  5(7Q31.2) WILD-TYPE 
                           83                           128 
$`AMP PEAK  5(7Q31.2) MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8343 
      141.73       137.06        98.96        28.11        24.79        71.41 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 
       62.37       151.96        49.97        23.47        25.91       104.52 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8404 
        3.55         0.99        52.27        11.21        42.35        10.68 
TCGA-KO-8405 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       74.93        16.67        80.38        86.10        77.85        57.17 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 
       24.16        49.08        49.02        48.59        38.99        24.69 
TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3358 TCGA-A3-3363 TCGA-A3-3372 TCGA-A3-3374 
       34.29        52.93        42.97        10.49        24.16        43.20 
TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-AK-3425 
       18.87        65.52        20.28         0.10        11.18       109.91 
TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 
       84.36        66.31        15.78        72.07        67.20        57.37 
TCGA-AK-3444 TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 
       48.36        45.93         3.32         1.41         4.57         3.48 
TCGA-B0-4696 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4811 
       28.47        19.73         3.16        43.96         3.25        46.59 
TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-4828 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       52.21         6.02        10.09        27.42        53.88         6.71 
TCGA-B0-4852 TCGA-B0-5077 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5102 TCGA-B0-5109 
       36.85        43.30        10.95         2.24        90.87        19.30 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5694 TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5703 
       11.80        21.60        15.78        84.92        56.94        39.55 
TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-5639 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 
       61.32        35.90        32.98         0.23         0.53         5.46 
TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
        0.36        23.31        16.80        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5550 TCGA-B8-A54E TCGA-B8-A54I TCGA-BP-4158 TCGA-BP-4159 
       23.01        14.27        29.88         4.93       111.02        85.51 
TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
      101.06         0.43        89.36        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       64.27        97.45        37.25        15.16         0.07        93.99 
TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4759 TCGA-BP-4766 
       62.86        31.89        11.31        33.99        77.98        48.07 
TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4790 
       13.15         5.33        60.59        68.38        15.78        36.53 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4962 
       10.98        37.25         6.71        47.97        71.41        58.68 
TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 
       60.30         6.74        58.98        48.89        45.50        14.93 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4994 
       46.45        31.30        36.95         3.88        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5009 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5177 
       30.64        36.23         6.35        79.30         1.78         9.63 
TCGA-BP-5178 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4636 
       62.86        19.82        34.95        31.27        46.55        63.25 
TCGA-CJ-4638 TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4875 
       14.17        11.05        79.66        47.18        74.27        77.36 
TCGA-CJ-4885 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 
       69.86        30.64        63.98        59.44        47.67        51.29 
TCGA-CJ-4907 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5677 TCGA-CJ-5679 
       49.28         4.57        63.88        72.00        25.71        22.32 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-5591 
       61.91        62.10        73.35        53.42        66.31        74.66 
TCGA-CW-6087 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35       103.43        18.77        46.16        47.08        69.21 
TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 
        6.77        61.41        23.74        56.28        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 
       10.85        57.21        22.52         1.94        31.10        67.96 
TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5574 TCGA-G6-A8L7 TCGA-MM-A564 TCGA-MM-A84U 
       22.78        43.69        66.28        70.13        19.96        15.25 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        75.55        58.22       100.27        56.91         4.57 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       34.85        56.81        26.43        30.71        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-A4-7288 
        5.29        16.18        22.49         0.13        12.82        61.05 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
       19.13         0.89        16.64        30.48        25.64        23.97 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A57E 
       23.31         0.76        19.63        14.33        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       16.31        15.75        12.46        76.64        13.55        30.35 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       44.61        49.25         2.20        21.67        24.56         3.55 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 
        0.46         6.58        33.83        30.58        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-5881 
       15.12        43.99        22.06        19.23        17.49        47.80 
TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
       26.04        25.35        10.88         0.95        11.97         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 
      123.62        48.26        96.92        50.40         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       37.55        24.46         3.75        14.63         3.02        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 
       80.88        51.19        61.02        34.19        24.89        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 
        2.40         1.18         4.01        51.78        11.05        39.25 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 
       25.84         6.38        17.98        17.33        80.65       194.79 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DD TCGA-HE-A5NF 
        3.68        27.65        12.43        17.95        11.21        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40Y TCGA-IA-A83T 
       13.41        11.84        56.75         5.49         2.04        88.24 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       21.34        16.34        12.36        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVK 
       34.29        27.78        20.25        15.48        87.22        52.27 
TCGA-P4-AAVL TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       28.80        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PR 
       48.30        43.76        60.03        14.83        21.93        38.86 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A895 TCGA-Y8-A896 
       30.67        25.68        27.39        12.99        15.91        18.64 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       15.62        25.28         6.02 

$`AMP PEAK  5(7Q31.2) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 
       86.56        66.54        73.91        28.80        54.74        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       44.91        28.80        47.24       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8429 TCGA-KN-8431 
      129.37        87.91        25.48        65.19        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 
        2.50        59.08       115.00       100.87        76.90        79.04 
TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
       92.71        87.78       103.27        61.58        63.95        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3319 
       12.16        36.82        47.21         0.53        39.16        37.15 
TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 
       49.58        36.36        37.38        48.82        21.86        31.07 
TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3359 
        4.50        45.53        29.92        18.44        88.37        82.32 
TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 
       51.25        28.70        74.63        74.76        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       20.71        18.64        28.31        15.39        22.65         0.10 
TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 
       10.62        29.10        73.08        60.92        68.61        46.78 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 
       42.08        40.01        58.49        48.69        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        1.41         2.53        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4810 
        7.82         5.98         2.14         6.64        20.25        15.72 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 
        0.59         5.52        45.07        33.50        16.77        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 
       36.53        14.93        54.48        29.10        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       40.70        45.30        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 
       39.45        26.07        29.03         2.27        70.52        20.94 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 
        8.05        21.86        52.08        15.95        62.89        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 
       52.54        30.48        29.95        35.90        26.20        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
       79.17       112.80        48.89       101.13        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       60.33        90.12        52.77       120.59        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 
       47.97        96.36        89.49        97.41        32.61         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
       12.30        21.30        31.30        11.77        10.36        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5844 
       16.67         9.57         5.75         1.25         4.64         0.23 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5158 TCGA-B8-5159 
       27.16        27.55        25.05        24.66        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
        6.38         0.53        34.39        14.30        27.29        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        1.74         8.42        17.36        15.42        16.27        14.17 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4169 
       94.72        90.28        93.34        32.61        99.85        23.05 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       54.90        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4334 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 
       21.21        18.48        52.24        74.17        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       44.94        12.23        12.33        31.33        12.30        72.59 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4769 
       77.62         5.98        44.15        41.75        71.80        61.68 
TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
       10.82        61.97        13.51        56.91        11.64        60.95 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 
       48.95        20.38        36.39        36.95         6.94        87.45 
TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4972 
       63.62        61.22        61.51        57.40        14.24        49.38 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4986 
        7.23        47.11        53.65        36.07        33.34        25.81 
TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5000 
       27.22        46.45         5.82        45.07        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       38.70        37.02        27.62        37.48        35.21        28.87 
TCGA-BP-5168 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5181 
       48.10        74.20        30.64        52.27        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4639 
       33.47        44.55         0.95        59.84        73.22        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        54.61        53.52        58.95        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       49.25        75.06        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       57.83        64.18        51.52        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 
       24.66        27.65        39.45        50.24        56.35        49.97 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       58.92        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 
        3.06        18.81        79.89        84.66        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 
       18.15        67.00        53.26        60.99        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       83.77         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4853 
       85.78        73.18        78.18       105.93        83.90        25.45 
TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
        0.59        58.75        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5458 
        5.46        63.42        58.82         0.82        18.44        56.94 
TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5470 
       55.33        10.22        21.76        47.54         2.40        12.69 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-5566 
       80.19        65.65        12.26        14.63        62.63        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5575 TCGA-DV-5576 
       65.88        12.16        11.67        37.15        56.84        23.90 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       66.02        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MW-A4EC TCGA-2Z-A9J2 
       10.29        35.87         2.01        19.43        10.85        59.01 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK 
       67.30        75.42        54.64        51.52        35.67        38.99 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       24.33        31.20        11.57        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A48D 
       35.18         0.23        29.46        23.28        19.73        12.46 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 
        8.28        12.99         9.63        58.45        25.08        19.56 
TCGA-B1-7332 TCGA-B1-A47O TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-A44B 
        7.33        16.87        16.77        10.09        34.49         2.10 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        6.81         0.16        14.86        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        63.72        22.92        43.20        21.63        40.83 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-7048 
       30.28        26.04        13.25         7.66         7.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       44.84        61.28        49.84        26.27        20.12        11.28 
TCGA-DW-7839 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G 
       13.78        79.86        54.90        19.00        10.68         0.43 
TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7773 
       48.62        34.82        25.15        13.68        16.90        12.92 
TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X 
        1.05         0.89         4.60        73.25        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83W TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A560 TCGA-MH-A561 
       85.78        67.17        22.26         0.13        30.38        27.65 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E6 TCGA-P4-A5E8 
        0.36        12.13        25.97        21.44        99.78        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
        6.61        84.95        92.58        50.60        78.90        12.85 
TCGA-SX-A7SL TCGA-SX-A7SO TCGA-UN-AAZ9 TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
       27.06        38.63        18.02         0.53        86.27        52.11 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       26.01        29.00        18.64        18.05         6.74        13.28 

  AMP PEAK  5(7Q31.2) MUTATED AMP PEAK  5(7Q31.2) WILD-TYPE 
                         0.07                          0.10 
  AMP PEAK  5(7Q31.2) MUTATED AMP PEAK  5(7Q31.2) WILD-TYPE 
                       194.79                        129.37 
  AMP PEAK  5(7Q31.2) MUTATED AMP PEAK  5(7Q31.2) WILD-TYPE 
                        27.42                         33.29 
[1] "0.1 - 194.8 (27.4)" "0.1 - 129.4 (33.3)"
[1] "hr=" "1"  
D5V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  5(7Q31.2) MUTATED       193       37        68       54
  AMP PEAK  5(7Q31.2) WILD-TYPE     255       66       122       46
D5V3, multiclass
           clus
vv          AMP PEAK  5(7Q31.2) MUTATED AMP PEAK  5(7Q31.2) WILD-TYPE
  STAGE I                           193                           255
  STAGE II                           37                            66
  STAGE III                          68                           122
  STAGE IV                           54                            46
[1] 4 2
[1] 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   198  50 104   8
  AMP PEAK  5(7Q31.2) WILD-TYPE 264  73 147   7
D5V4, multiclass
    clus
vv   AMP PEAK  5(7Q31.2) MUTATED AMP PEAK  5(7Q31.2) WILD-TYPE
  T1                         198                           264
  T2                          50                            73
  T3                         104                           147
  T4                           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                             N0  N1  N2
  AMP PEAK  5(7Q31.2) MUTATED   118  19   4
  AMP PEAK  5(7Q31.2) WILD-TYPE 199  24   2
D5V5, multiclass
    clus
vv   AMP PEAK  5(7Q31.2) MUTATED AMP PEAK  5(7Q31.2) WILD-TYPE
  N0                         118                           199
  N1                          19                            24
  N2                           4                             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"
D5V6, binary
                               cls
clus                              0   1
  AMP PEAK  5(7Q31.2) MUTATED   189  47
  AMP PEAK  5(7Q31.2) WILD-TYPE 353  42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7Q31.2) MUTATED    189   47
  AMP PEAK  5(7Q31.2) WILD-TYPE  353   42
   clus
vv  AMP PEAK  5(7Q31.2) MUTATED AMP PEAK  5(7Q31.2) WILD-TYPE
  0                         189                           353
  1                          47                            42
[1] 2 2
[1] FALSE
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(7Q31.2) MUTATED    91 273
  AMP PEAK  5(7Q31.2) WILD-TYPE 196 299
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7Q31.2) MUTATED     91  273
  AMP PEAK  5(7Q31.2) WILD-TYPE  196  299
        clus
vv       AMP PEAK  5(7Q31.2) MUTATED AMP PEAK  5(7Q31.2) WILD-TYPE
  FEMALE                          91                           196
  MALE                           273                           299
[1] 2 2
[1] FALSE
D5V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  AMP PEAK  5(7Q31.2) MUTATED                   25
  AMP PEAK  5(7Q31.2) WILD-TYPE                 41
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  AMP PEAK  5(7Q31.2) MUTATED                                 174
  AMP PEAK  5(7Q31.2) WILD-TYPE                               350
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK  5(7Q31.2) MUTATED                                     165
  AMP PEAK  5(7Q31.2) WILD-TYPE                                   104
D5V9, multiclass
                                       clus
vv                                      AMP PEAK  5(7Q31.2) MUTATED
  KIDNEY CHROMOPHOBE                                             25
  KIDNEY CLEAR CELL RENAL CARCINOMA                             174
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                         165
                                       clus
vv                                      AMP PEAK  5(7Q31.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               41
  KIDNEY CLEAR CELL RENAL CARCINOMA                               350
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, continuous
D5V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(7Q31.2) MUTATED                                  2     8
  AMP PEAK  5(7Q31.2) WILD-TYPE                                0     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(7Q31.2) MUTATED                          43   298
  AMP PEAK  5(7Q31.2) WILD-TYPE                        73   404
D5V12, multiclass
                                  clus
vv                                 AMP PEAK  5(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 43
  WHITE                                                    298
                                  clus
vv                                 AMP PEAK  5(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   73
  WHITE                                                      404
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, binary
                               cls
clus                              0   1
  AMP PEAK  5(7Q31.2) MUTATED    14 260
  AMP PEAK  5(7Q31.2) WILD-TYPE  28 337
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7Q31.2) MUTATED     14  260
  AMP PEAK  5(7Q31.2) WILD-TYPE   28  337
                        clus
vv                       AMP PEAK  5(7Q31.2) MUTATED
  HISPANIC OR LATINO                              14
  NOT HISPANIC OR LATINO                         260
                        clus
vv                       AMP PEAK  5(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                28
  NOT HISPANIC OR LATINO                           337
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(8Q24.22) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(8Q24.22) MUTATED    80  40
  AMP PEAK  6(8Q24.22) WILD-TYPE 552 171
  AMP PEAK  6(8Q24.22) MUTATED AMP PEAK  6(8Q24.22) WILD-TYPE 
                           120                            723 
  AMP PEAK  6(8Q24.22) MUTATED AMP PEAK  6(8Q24.22) WILD-TYPE 
                            40                            171 
$`AMP PEAK  6(8Q24.22) MUTATED`
TCGA-KL-8324 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      141.73        98.96        28.11        62.37       151.96        49.97 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 
       23.47        25.91         3.55         0.99        52.27        11.21 
TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 TCGA-A3-3308 
       74.93        80.38        87.78        86.10        57.17         0.53 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3336 TCGA-AK-3425 
       24.16        49.08        37.15        24.69        34.29       109.91 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3445 TCGA-AK-3454 TCGA-B0-4688 TCGA-B0-4698 
       72.07        68.61        42.08        28.73         3.32         1.38 
TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4813 TCGA-B0-4815 
        5.98        19.73        43.96         6.64         0.59        52.21 
TCGA-B0-4821 TCGA-B0-4828 TCGA-B0-4844 TCGA-B0-5081 TCGA-B0-5097 TCGA-B0-5108 
       40.44        10.09        10.29        11.90        21.86        29.95 
TCGA-B0-5109 TCGA-B0-5701 TCGA-B0-5703 TCGA-B4-5832 TCGA-B8-5158 TCGA-B8-5163 
       19.30        56.94        39.55         0.23        20.91        27.02 
TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4174 TCGA-BP-4338 TCGA-BP-4342 TCGA-BP-4352 
        0.53         4.93        61.78        93.99        74.17        11.31 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4799 
       77.98         5.98        13.15        15.78        10.98        37.25 
TCGA-BP-4962 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5173 
       58.68        46.45        31.30        18.51         6.35         1.78 
TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5198 TCGA-CJ-4871 
       30.64         9.63        37.22        31.79        19.82        79.66 
TCGA-CJ-4881 TCGA-CJ-4890 TCGA-CJ-4901 TCGA-CJ-4912 TCGA-CJ-4923 TCGA-CJ-5677 
       66.21        68.55        47.67        54.48        18.81        25.71 
TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4858 
       62.66         7.36        66.31        74.66        46.16        69.21 
TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5462 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       61.41        56.28        10.22        57.21        47.54        22.52 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5987 TCGA-MM-A564 TCGA-2Z-A9J2 
        1.94        31.10        12.69        14.63        19.96        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9JP TCGA-4A-A93X TCGA-A4-8630 TCGA-AL-3466 TCGA-AL-3471 
       58.22        29.36        12.82        14.33         9.63        13.55 
TCGA-B9-A5W9 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-7056 TCGA-F9-A8NY TCGA-F9-A97G 
        0.16        43.20        25.35        20.12         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-A8LD TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A40Y 
        4.01        11.05        16.90         3.68         1.05         2.04 
TCGA-IZ-8195 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A71U TCGA-SX-A7SR 
       22.26         6.61        16.01        14.07        33.04        26.47 

$`AMP PEAK  6(8Q24.22) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       28.80        54.74        23.28        44.91        28.80        47.24 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      123.12        51.06        31.33       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
       65.19       104.52        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 
      115.00        42.35       100.87        76.90        10.68        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
       92.71        16.67       103.27        77.85        61.58        63.95 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3317 
       12.66        12.16        36.82        47.21        39.16        49.02 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
       49.58        48.59        36.36        38.99        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       21.86        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       10.62        29.10        84.36        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 
       60.92        67.20        57.37        46.78        48.36        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        45.93        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 
       31.27        28.04        12.13        40.70         1.41         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4699 
        4.57         2.53         3.48        28.47        19.00         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 
       65.10         7.82         2.14         3.16         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       15.72        46.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 
        6.02        36.53        14.93        54.48        29.10        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       56.68        11.64        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        2.24        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       52.54        30.48        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 
       46.68        56.78        60.33        84.92        90.12        52.77 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        11.77        10.36        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       16.67         9.57         5.75         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.01        23.74         1.18         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60         6.38        14.27        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K 
       29.88        17.06         1.74         8.42        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       23.05        77.03        62.24        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       21.21        15.16         0.07        18.48        52.24        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 
       54.77        49.08        44.94        12.23        31.89        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4760 TCGA-BP-4762 
       33.99        31.33        12.30        72.59        77.62        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
       60.95        48.95        36.53        20.38        36.39        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 
       53.65        14.93        36.07        33.34        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       45.07        30.64        41.62        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 
       37.48        35.21        36.23        28.87        48.10        79.30 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       74.20        52.27        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       42.44        37.25        22.78        13.35        27.02        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 
       11.05        21.24        83.97        49.25        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06        77.36        64.27        71.87        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4891 
       69.86        64.18        30.64        51.52        63.98        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 
       50.33        38.56        45.14         3.06         4.57        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       72.00        79.89        84.66        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15        61.91        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 
       60.99        53.42        75.58        83.77        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6087 
       81.83         5.39        85.78        73.18        78.18         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 
      105.93        83.90       103.43        18.77        25.45         0.59 
TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        58.75         6.77        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04         5.46        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       18.44        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5463 TCGA-CZ-5467 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       21.76         2.40        80.19        67.96        65.65        12.26 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        43.69        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       11.67        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC 
       70.13        35.87         2.01        19.43        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
        7.04        75.55       100.27        56.91         4.57        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       75.42        34.85        56.81        54.64        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JQ 
       38.99        26.43        30.71        24.33        31.20        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 
        5.29        16.18        22.49         0.13        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 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-A48D 
       23.28        23.31         0.76        19.63        19.73        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46        58.45        76.64        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E 
       43.99        22.06         2.10        19.23         6.81        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       44.84        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
       13.08         2.40        51.78        48.62        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        13.68        25.84         6.38        17.98        17.33 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T 
       80.65       194.79        12.92        27.65        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       56.75        73.25         5.49        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       88.24        67.17        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
       52.27        50.60        78.90        12.85        17.75        47.90 
TCGA-SX-A71S TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       47.44        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       16.31        41.62        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  AMP PEAK  6(8Q24.22) MUTATED AMP PEAK  6(8Q24.22) WILD-TYPE 
                          0.16                           0.07 
  AMP PEAK  6(8Q24.22) MUTATED AMP PEAK  6(8Q24.22) WILD-TYPE 
                        151.96                         194.79 
  AMP PEAK  6(8Q24.22) MUTATED AMP PEAK  6(8Q24.22) WILD-TYPE 
                         25.81                          31.20 
[1] "0.2 - 152.0 (25.8)" "0.1 - 194.8 (31.2)"
[1] "hr=" "1.6"
D6V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  6(8Q24.22) MUTATED        35       22        37       25
  AMP PEAK  6(8Q24.22) WILD-TYPE     413       81       153       75
D6V3, multiclass
           clus
vv          AMP PEAK  6(8Q24.22) MUTATED AMP PEAK  6(8Q24.22) WILD-TYPE
  STAGE I                             35                            413
  STAGE II                            22                             81
  STAGE III                           37                            153
  STAGE IV                            25                             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"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  6(8Q24.22) MUTATED    36  23  56   4
  AMP PEAK  6(8Q24.22) WILD-TYPE 426 100 195  11
D6V4, multiclass
    clus
vv   AMP PEAK  6(8Q24.22) MUTATED AMP PEAK  6(8Q24.22) WILD-TYPE
  T1                           36                            426
  T2                           23                            100
  T3                           56                            195
  T4                            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                              N0  N1  N2
  AMP PEAK  6(8Q24.22) MUTATED    50  12   2
  AMP PEAK  6(8Q24.22) WILD-TYPE 267  31   4
D6V5, multiclass
    clus
vv   AMP PEAK  6(8Q24.22) MUTATED AMP PEAK  6(8Q24.22) WILD-TYPE
  N0                           50                            267
  N1                           12                             31
  N2                            2                              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"
D6V6, binary
                                cls
clus                               0   1
  AMP PEAK  6(8Q24.22) MUTATED    73  22
  AMP PEAK  6(8Q24.22) WILD-TYPE 469  67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q24.22) MUTATED     73   22
  AMP PEAK  6(8Q24.22) WILD-TYPE  469   67
   clus
vv  AMP PEAK  6(8Q24.22) MUTATED AMP PEAK  6(8Q24.22) WILD-TYPE
  0                           73                            469
  1                           22                             67
[1] 2 2
[1] FALSE
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(8Q24.22) MUTATED    37  84
  AMP PEAK  6(8Q24.22) WILD-TYPE 250 488
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q24.22) MUTATED     37   84
  AMP PEAK  6(8Q24.22) WILD-TYPE  250  488
        clus
vv       AMP PEAK  6(8Q24.22) MUTATED AMP PEAK  6(8Q24.22) WILD-TYPE
  FEMALE                           37                            250
  MALE                             84                            488
[1] 2 2
[1] FALSE
D6V8, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  AMP PEAK  6(8Q24.22) MUTATED                   18
  AMP PEAK  6(8Q24.22) WILD-TYPE                 48
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  AMP PEAK  6(8Q24.22) MUTATED                                  78
  AMP PEAK  6(8Q24.22) WILD-TYPE                               446
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK  6(8Q24.22) MUTATED                                      25
  AMP PEAK  6(8Q24.22) WILD-TYPE                                   244
D6V9, multiclass
                                       clus
vv                                      AMP PEAK  6(8Q24.22) MUTATED
  KIDNEY CHROMOPHOBE                                              18
  KIDNEY CLEAR CELL RENAL CARCINOMA                               78
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           25
                                       clus
vv                                      AMP PEAK  6(8Q24.22) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                48
  KIDNEY CLEAR CELL RENAL CARCINOMA                                446
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            244
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous
D6V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(8Q24.22) MUTATED                                  0     4
  AMP PEAK  6(8Q24.22) WILD-TYPE                                2    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(8Q24.22) MUTATED                           6   108
  AMP PEAK  6(8Q24.22) WILD-TYPE                       110   594
D6V12, multiclass
                                  clus
vv                                 AMP PEAK  6(8Q24.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                     108
                                  clus
vv                                 AMP PEAK  6(8Q24.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                   110
  WHITE                                                       594
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, binary
                                cls
clus                               0   1
  AMP PEAK  6(8Q24.22) MUTATED     5  80
  AMP PEAK  6(8Q24.22) WILD-TYPE  37 517
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q24.22) MUTATED      5   80
  AMP PEAK  6(8Q24.22) WILD-TYPE   37  517
                        clus
vv                       AMP PEAK  6(8Q24.22) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           80
                        clus
vv                       AMP PEAK  6(8Q24.22) WILD-TYPE
  HISPANIC OR LATINO                                 37
  NOT HISPANIC OR LATINO                            517
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(10P14) MUTATION ANALYSIS
D7V1, survival
                              sevent
clus2                            0   1
  AMP PEAK  7(10P14) MUTATED    23   9
  AMP PEAK  7(10P14) WILD-TYPE 609 202
  AMP PEAK  7(10P14) MUTATED AMP PEAK  7(10P14) WILD-TYPE 
                          32                          811 
  AMP PEAK  7(10P14) MUTATED AMP PEAK  7(10P14) WILD-TYPE 
                           9                          202 
$`AMP PEAK  7(10P14) MUTATED`
TCGA-KL-8324 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8436 TCGA-A3-3316 TCGA-AK-3453 
      141.73         0.99        11.21        42.35        49.08        45.93 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-5109 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4143 
        3.32         1.41        19.30         0.23         5.46        23.31 
TCGA-BP-4338 TCGA-BP-4342 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4986 TCGA-BP-5175 
       93.99        74.17        13.15        68.38        25.81        30.64 
TCGA-CJ-5675 TCGA-CW-5588 TCGA-CZ-4854 TCGA-CZ-4866 TCGA-CZ-5454 TCGA-EU-5905 
       79.89        66.31        46.16        61.41        23.74         3.91 
TCGA-A4-8098 TCGA-AL-3468 TCGA-B9-4617 TCGA-BQ-5882 TCGA-F9-A7Q0 TCGA-F9-A8NY 
       29.46        76.64         1.15        21.63        13.08         1.18 
TCGA-SX-A7SS TCGA-UZ-A9PQ 
       48.30        86.27 

$`AMP PEAK  7(10P14) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 
       25.91        65.19       104.52         3.55        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 
       19.33         2.50        59.08       115.00       100.87        76.90 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68        74.93        79.04        92.71        16.67        80.38 
TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       87.78       103.27        86.10        77.85        57.17        61.58 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 
       63.95        12.66        12.16        36.82        47.21         0.53 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       39.16        24.16        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        24.69        37.38        48.82        21.86 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        60.92        72.07        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        42.08        40.01        58.49        48.69 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
       28.47        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       16.21        18.21        21.44        37.22        14.76        79.17 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        11.77        10.36        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       16.67         9.57         5.75         1.25         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.36         0.23        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       12.23        31.89        11.31        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
       61.97        60.59        13.51        56.91        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        31.30        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
        1.78        74.20        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
       75.88        65.69        54.61        53.52        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       61.91        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        73.18        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       74.66         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       25.45         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       14.66        60.59        63.39        93.04         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82         0.82        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        47.01        10.85        10.22        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE 
        2.01        19.43        19.96        15.25        10.85         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       20.61         0.46        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23         6.81         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-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        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        2.40         0.43         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        17.33        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       12.85        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       41.62        26.47        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       21.93         0.53        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  AMP PEAK  7(10P14) MUTATED AMP PEAK  7(10P14) WILD-TYPE 
                        0.23                         0.07 
  AMP PEAK  7(10P14) MUTATED AMP PEAK  7(10P14) WILD-TYPE 
                      141.73                       194.79 
  AMP PEAK  7(10P14) MUTATED AMP PEAK  7(10P14) WILD-TYPE 
                      27.635                       30.580 
[1] "0.2 - 141.7 (27.6)" "0.1 - 194.8 (30.6)"
[1] "hr=" "1.2"
D7V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  7(10P14) MUTATED        12        7         7        6
  AMP PEAK  7(10P14) WILD-TYPE     436       96       183       94
D7V3, multiclass
           clus
vv          AMP PEAK  7(10P14) MUTATED AMP PEAK  7(10P14) WILD-TYPE
  STAGE I                           12                          436
  STAGE II                           7                           96
  STAGE III                          7                          183
  STAGE IV                           6                           94
[1] 4 2
[1] 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(10P14) MUTATED    13   9   7   4
  AMP PEAK  7(10P14) WILD-TYPE 449 114 244  11
D7V4, multiclass
    clus
vv   AMP PEAK  7(10P14) MUTATED AMP PEAK  7(10P14) WILD-TYPE
  T1                         13                          449
  T2                          9                          114
  T3                          7                          244
  T4                          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                            N0  N1  N2
  AMP PEAK  7(10P14) MUTATED    12   5   0
  AMP PEAK  7(10P14) WILD-TYPE 305  38   6
D7V5, multiclass
    clus
vv   AMP PEAK  7(10P14) MUTATED AMP PEAK  7(10P14) WILD-TYPE
  N0                         12                          305
  N1                          5                           38
  N2                          0                            6
[1] 3 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(10P14) MUTATED    23   5
  AMP PEAK  7(10P14) WILD-TYPE 519  84
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK  7(10P14) MUTATED     23    5
  AMP PEAK  7(10P14) WILD-TYPE  519   84
   clus
vv  AMP PEAK  7(10P14) MUTATED AMP PEAK  7(10P14) WILD-TYPE
  0                         23                          519
  1                          5                           84
[1] 2 2
[1] FALSE
D7V7, binary
                              cls
clus                             0   1
  AMP PEAK  7(10P14) MUTATED    11  22
  AMP PEAK  7(10P14) WILD-TYPE 276 550
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK  7(10P14) MUTATED     11   22
  AMP PEAK  7(10P14) WILD-TYPE  276  550
        clus
vv       AMP PEAK  7(10P14) MUTATED AMP PEAK  7(10P14) WILD-TYPE
  FEMALE                         11                          276
  MALE                           22                          550
[1] 2 2
[1] FALSE
D7V8, continuous
                              vv
clus                           KIDNEY CHROMOPHOBE
  AMP PEAK  7(10P14) MUTATED                    4
  AMP PEAK  7(10P14) WILD-TYPE                 62
                              vv
clus                           KIDNEY CLEAR CELL RENAL CARCINOMA
  AMP PEAK  7(10P14) MUTATED                                  20
  AMP PEAK  7(10P14) WILD-TYPE                               504
                              vv
clus                           KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK  7(10P14) MUTATED                                       9
  AMP PEAK  7(10P14) WILD-TYPE                                   260
D7V9, multiclass
                                       clus
vv                                      AMP PEAK  7(10P14) MUTATED
  KIDNEY CHROMOPHOBE                                             4
  KIDNEY CLEAR CELL RENAL CARCINOMA                             20
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          9
                                       clus
vv                                      AMP PEAK  7(10P14) WILD-TYPE
  KIDNEY CHROMOPHOBE                                              62
  KIDNEY CLEAR CELL RENAL CARCINOMA                              504
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          260
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, continuous
D7V11, continuous
[1] "Remove cluster labels:"     "AMP PEAK  7(10P14) MUTATED"
clus
  AMP PEAK  7(10P14) MUTATED AMP PEAK  7(10P14) WILD-TYPE 
                           2                           65 
                  TCGA-KL-8330                   TCGA-KL-8335 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-KL-8341                   TCGA-KL-8345 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-KM-8639                   TCGA-KO-8408 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-KO-8409                   TCGA-A3-A8OV 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-A3-A8OW                   TCGA-B2-A4SR 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-B8-5158                   TCGA-DV-A4W0 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-G6-A8L7                   TCGA-MM-A563 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-MM-A84U                   TCGA-2Z-A9J3 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-2Z-A9J7                   TCGA-2Z-A9J8 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-2Z-A9JD                   TCGA-2Z-A9JI 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-2Z-A9JN                   TCGA-2Z-A9JO 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-4A-A93W                   TCGA-4A-A93Y 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-A4-A48D                   TCGA-A4-A57E 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-A4-A5Y0                   TCGA-AL-3472 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-AL-7173                   TCGA-B1-A654 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-B9-4117                   TCGA-B9-A69E 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-DW-5561                   TCGA-DW-7963 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-F9-A97G                   TCGA-G7-7501 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-G7-A8LB                   TCGA-G7-A8LD 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-G7-A8LE                   TCGA-GL-7773 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-GL-A9DD                   TCGA-HE-A5NI 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-IA-A40U                   TCGA-MH-A854 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-MH-A856                   TCGA-P4-A5E6 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-P4-AAVK                   TCGA-PJ-A5Z9 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-Q2-A5QZ                   TCGA-SX-A71S 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-SX-A71U                   TCGA-SX-A7SL 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-SX-A7SM                   TCGA-SX-A7SR 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-UZ-A9PM                   TCGA-UZ-A9PO 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-UZ-A9PR                   TCGA-UZ-A9PS 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-UZ-A9PX                   TCGA-WN-A9G9 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-WN-AB4C                   TCGA-Y8-A894 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-Y8-A896                   TCGA-Y8-A8RY 
"AMP PEAK  7(10P14) WILD-TYPE" "AMP PEAK  7(10P14) WILD-TYPE" 
                  TCGA-Y8-A8RZ 
"AMP PEAK  7(10P14) WILD-TYPE" 
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(10P14) MUTATED                                  0     2
  AMP PEAK  7(10P14) WILD-TYPE                                2    13
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(10P14) MUTATED                           3    26
  AMP PEAK  7(10P14) WILD-TYPE                       113   676
D7V12, multiclass
                                  clus
vv                                 AMP PEAK  7(10P14) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 3
  WHITE                                                    26
                                  clus
vv                                 AMP PEAK  7(10P14) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                      13
  BLACK OR AFRICAN AMERICAN                                 113
  WHITE                                                     676
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, binary
                              cls
clus                             0   1
  AMP PEAK  7(10P14) MUTATED     1  21
  AMP PEAK  7(10P14) WILD-TYPE  41 576
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK  7(10P14) MUTATED      1   21
  AMP PEAK  7(10P14) WILD-TYPE   41  576
                        clus
vv                       AMP PEAK  7(10P14) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         21
                        clus
vv                       AMP PEAK  7(10P14) WILD-TYPE
  HISPANIC OR LATINO                               41
  NOT HISPANIC OR LATINO                          576
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(17Q25.2) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  8(17Q25.2) MUTATED   183  39
  AMP PEAK  8(17Q25.2) WILD-TYPE 449 172
  AMP PEAK  8(17Q25.2) MUTATED AMP PEAK  8(17Q25.2) WILD-TYPE 
                           222                            621 
  AMP PEAK  8(17Q25.2) MUTATED AMP PEAK  8(17Q25.2) WILD-TYPE 
                            39                            172 
$`AMP PEAK  8(17Q25.2) MUTATED`
TCGA-KL-8339 TCGA-A3-3313 TCGA-A3-3325 TCGA-A3-3363 TCGA-AK-3453 TCGA-B0-4698 
       28.11        24.16        24.69        10.49        45.93         1.38 
TCGA-B0-4707 TCGA-B0-4848 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5109 TCGA-B0-5696 
       19.73        29.03        15.95        90.87        19.30        56.78 
TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4621 TCGA-B8-5551 TCGA-BP-4166 
        0.53         5.46        23.31        25.91         0.53         0.43 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4337 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4768 
       64.27        54.90         0.07        12.30        72.59        13.15 
TCGA-BP-4781 TCGA-BP-4985 TCGA-BP-5173 TCGA-BP-5176 TCGA-BP-5182 TCGA-BP-5185 
       68.38        31.30         1.78        52.27        38.30        37.22 
TCGA-BP-5200 TCGA-CJ-4873 TCGA-CJ-4882 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4912 
       34.95        74.27        61.91        47.67        49.28        54.48 
TCGA-CJ-6027 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-EU-5905 
       60.99         6.77        61.41         1.94        31.10         3.91 
TCGA-G6-A8L7 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       70.13         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JM 
       56.91         4.57        34.85        56.81        51.52        30.71 
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-A4-7286 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       18.21        61.05        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
       16.64        29.46        25.64        23.97        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.63        19.73        14.33        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3468 
       15.75         8.28        12.99        12.46         9.63        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M 
       13.55        30.35        49.25         2.20         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 
       24.56        16.87         3.55        16.77         6.58        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-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5877 
        2.10        19.23         0.16        17.49        86.76         8.88 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 
       43.20        47.80        26.04        25.35        13.25         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 
        0.95        11.97         7.92        48.26        96.92        50.40 
TCGA-BQ-7053 TCGA-BQ-7058 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
       49.84        11.28         7.04         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       61.02        34.19        24.89        13.08         2.40         1.18 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 
        4.01        51.78        11.05        39.25        34.82        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
        6.38        17.98        17.33        16.90        80.65       194.79 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68         1.05        12.43        17.95         0.89        11.21 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
       68.12        13.41        11.84        56.75         5.49        16.80 
TCGA-IA-A40Y TCGA-IA-A83T TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
        2.04        88.24        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EA 
       30.38        27.65        20.25        15.48        87.22         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
       84.95        92.58        16.01        17.75        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP 
       47.44        33.04        28.80        27.06        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM 
       41.62        26.47        48.30        43.76        60.03        14.83 
TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
        0.53        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       12.99        29.00        15.91        15.62        25.28         6.02 

$`AMP PEAK  8(17Q25.2) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 
       36.82        47.21         0.53        39.16        49.08        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
       37.15        49.58        48.59        36.36        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
       51.25        28.70        74.63        74.76        24.16        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
       43.20        55.76        20.71        18.64        18.87        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       65.52        20.28        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
       66.31        15.78        60.92        72.07        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       57.37        46.78        48.36        42.08        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       48.69        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       28.04        12.13        40.70         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4699 
        4.57         2.53         3.48        28.47        19.00         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4712 
       65.10         7.82         5.98         2.14         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       40.44        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       78.44        68.71        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       26.07         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 
       10.95         8.05         2.24        21.86        52.08        62.89 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
       90.48        52.54        30.48        29.95        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       21.44        37.22        14.76        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
      101.13        15.78        46.68        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       56.94        52.77        39.55       120.59        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        12.30        21.30        31.30        11.77 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       10.36        32.98        21.57        16.67         9.57         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
        0.23         1.25         4.64         0.36         0.23        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 
       24.23        17.16        16.60         6.38        14.27        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       99.85        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       37.25        21.21        15.16        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4759 
       31.89        11.31        12.33        33.99        31.33        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
       53.65        14.93        36.07        33.34        46.45        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 
       48.10         6.35        79.30        74.20        30.64         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
       62.86        74.40        49.15        42.44        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 
       24.62        33.47        19.82        44.55        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       65.69        54.61        53.52        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 
       83.97        49.25        79.66        47.18        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       64.27        71.87        66.21        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4913 
       49.97        51.29        58.92        49.18        50.33        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15        61.91        62.10        73.35        67.00        53.26 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
       58.75        14.66        60.59        63.39        93.04         5.46 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 
       21.76        57.21        47.54        22.52         2.40        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 
        6.77         4.18         7.96        10.29        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       19.43        19.96        15.25        10.85        67.30        75.42 
TCGA-2Z-A9JG TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        35.67        38.99        26.43        24.33        31.20 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7997 TCGA-A4-8312 
       12.82        11.57        19.63         0.10        30.48        23.28 
TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A656 
       12.46        58.45        25.08        44.61        19.56         0.46 
TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5876 
       10.09        20.61         6.81        14.86        12.30        19.27 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       63.72        22.92        21.63        40.83        26.04        30.28 
TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
       10.88         2.76       123.62        93.34        44.84        61.28 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6135 TCGA-EV-5902 
       26.27        20.12         7.63         7.17        54.90        19.00 
TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-7773 
       10.68         0.43        48.62        25.15        13.68        12.92 
TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83W 
       27.65         4.60        73.25        19.99        85.78        67.17 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E6 TCGA-P4-A5E8 
        0.36        12.13        25.97        21.44        99.78        42.94 
TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A7SM TCGA-SX-A7SO 
       52.27        50.60        78.90        12.85        11.93        38.63 
TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 
       18.02        21.93        86.27        26.01        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       18.05         6.74        13.28 

  AMP PEAK  8(17Q25.2) MUTATED AMP PEAK  8(17Q25.2) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK  8(17Q25.2) MUTATED AMP PEAK  8(17Q25.2) WILD-TYPE 
                        194.79                         151.96 
  AMP PEAK  8(17Q25.2) MUTATED AMP PEAK  8(17Q25.2) WILD-TYPE 
                         22.16                          36.82 
[1] "0.1 - 194.8 (22.2)" "0.1 - 152.0 (36.8)"
[1] "hr=" "1.1"
D8V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  8(17Q25.2) MUTATED       144       21        42       15
  AMP PEAK  8(17Q25.2) WILD-TYPE     304       82       148       85
D8V3, multiclass
           clus
vv          AMP PEAK  8(17Q25.2) MUTATED AMP PEAK  8(17Q25.2) WILD-TYPE
  STAGE I                            144                            304
  STAGE II                            21                             82
  STAGE III                           42                            148
  STAGE IV                            15                             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  8(17Q25.2) MUTATED   148  28  50   4
  AMP PEAK  8(17Q25.2) WILD-TYPE 314  95 201  11
D8V4, multiclass
    clus
vv   AMP PEAK  8(17Q25.2) MUTATED AMP PEAK  8(17Q25.2) WILD-TYPE
  T1                          148                            314
  T2                           28                             95
  T3                           50                            201
  T4                            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                              N0  N1  N2
  AMP PEAK  8(17Q25.2) MUTATED    46  16   3
  AMP PEAK  8(17Q25.2) WILD-TYPE 271  27   3
D8V5, multiclass
    clus
vv   AMP PEAK  8(17Q25.2) MUTATED AMP PEAK  8(17Q25.2) WILD-TYPE
  N0                           46                            271
  N1                           16                             27
  N2                            3                              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
  AMP PEAK  8(17Q25.2) MUTATED    92  10
  AMP PEAK  8(17Q25.2) WILD-TYPE 450  79
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(17Q25.2) MUTATED     92   10
  AMP PEAK  8(17Q25.2) WILD-TYPE  450   79
   clus
vv  AMP PEAK  8(17Q25.2) MUTATED AMP PEAK  8(17Q25.2) WILD-TYPE
  0                           92                            450
  1                           10                             79
[1] 2 2
[1] FALSE
D8V7, binary
                                cls
clus                               0   1
  AMP PEAK  8(17Q25.2) MUTATED    57 175
  AMP PEAK  8(17Q25.2) WILD-TYPE 230 397
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(17Q25.2) MUTATED     57  175
  AMP PEAK  8(17Q25.2) WILD-TYPE  230  397
        clus
vv       AMP PEAK  8(17Q25.2) MUTATED AMP PEAK  8(17Q25.2) WILD-TYPE
  FEMALE                           57                            230
  MALE                            175                            397
[1] 2 2
[1] FALSE
D8V8, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  AMP PEAK  8(17Q25.2) MUTATED                    1
  AMP PEAK  8(17Q25.2) WILD-TYPE                 65
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  AMP PEAK  8(17Q25.2) MUTATED                                  42
  AMP PEAK  8(17Q25.2) WILD-TYPE                               482
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK  8(17Q25.2) MUTATED                                     189
  AMP PEAK  8(17Q25.2) WILD-TYPE                                    80
D8V9, multiclass
                                       clus
vv                                      AMP PEAK  8(17Q25.2) MUTATED
  KIDNEY CHROMOPHOBE                                               1
  KIDNEY CLEAR CELL RENAL CARCINOMA                               42
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          189
                                       clus
vv                                      AMP PEAK  8(17Q25.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                                482
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                             80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, continuous
D8V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(17Q25.2) MUTATED                                  2     6
  AMP PEAK  8(17Q25.2) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(17Q25.2) MUTATED                          39   175
  AMP PEAK  8(17Q25.2) WILD-TYPE                        77   527
D8V12, multiclass
                                  clus
vv                                 AMP PEAK  8(17Q25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  39
  WHITE                                                     175
                                  clus
vv                                 AMP PEAK  8(17Q25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    77
  WHITE                                                       527
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, binary
                                cls
clus                               0   1
  AMP PEAK  8(17Q25.2) MUTATED     9 183
  AMP PEAK  8(17Q25.2) WILD-TYPE  33 414
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(17Q25.2) MUTATED      9  183
  AMP PEAK  8(17Q25.2) WILD-TYPE   33  414
                        clus
vv                       AMP PEAK  8(17Q25.2) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          183
                        clus
vv                       AMP PEAK  8(17Q25.2) WILD-TYPE
  HISPANIC OR LATINO                                 33
  NOT HISPANIC OR LATINO                            414
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(19P13.2) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(19P13.2) MUTATED    70  24
  AMP PEAK  9(19P13.2) WILD-TYPE 562 187
  AMP PEAK  9(19P13.2) MUTATED AMP PEAK  9(19P13.2) WILD-TYPE 
                            94                            749 
  AMP PEAK  9(19P13.2) MUTATED AMP PEAK  9(19P13.2) WILD-TYPE 
                            24                            187 
$`AMP PEAK  9(19P13.2) MUTATED`
TCGA-KL-8324 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 
      141.73        98.96        28.11        24.79        62.37       151.96 
TCGA-KM-8443 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       49.97        25.91       104.52         3.55         0.99        52.27 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-A3-3325 
       11.21        42.35        16.67        80.38        77.85        24.69 
TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4690 
       43.20        18.87        72.07        57.37        45.93         1.41 
TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4811 TCGA-B0-4822 TCGA-B0-4844 
        3.62        19.73         3.16        46.59        36.53        10.29 
TCGA-B0-5094 TCGA-B0-5102 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4143 TCGA-BP-4166 
       10.95        90.87         0.23         5.46        23.31         0.43 
TCGA-BP-4342 TCGA-BP-4351 TCGA-BP-4768 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4994 
       74.17        31.89        13.15         6.74        58.98        43.00 
TCGA-BP-5178 TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CJ-4873 
       62.86        37.22        34.95        46.55        79.66        74.27 
TCGA-CJ-4897 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6028 
       59.44        49.28        63.88        84.66        61.91        53.42 
TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 
       74.66        46.16        61.41        56.28        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-EU-5905 
       10.85        57.21         1.94        31.10        67.96         3.91 
TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JR TCGA-A4-7732 TCGA-A4-A5DU 
       58.22         4.57        56.81         5.29        19.13        16.31 
TCGA-A4-A5XZ TCGA-AL-3472 TCGA-B9-4113 TCGA-B9-4116 TCGA-B9-4617 TCGA-BQ-5885 
       15.75        30.35        50.50        20.61         1.15        30.28 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-DW-5561 TCGA-DW-7840 TCGA-EV-5901 TCGA-F9-A7Q0 
        0.95        11.97        13.61         3.75        34.19        13.08 
TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-A5NJ TCGA-IZ-8196 
       39.25         6.38        17.33         3.68        56.75        21.34 
TCGA-P4-A5E7 TCGA-P4-AAVL TCGA-SX-A7SU TCGA-UZ-A9PX 
       87.22        16.01        43.76        27.39 

$`AMP PEAK  9(19P13.2) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       44.84        86.56        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
       54.74        23.28        44.91        28.80        47.24       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       65.19        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       87.78       103.27        86.10        57.17        61.58        63.95 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        12.16        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       36.36        38.99        37.38        48.82        21.86        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        24.16        53.29        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.64        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       67.20        46.78        48.36        42.08        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       48.69        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 
       28.04        12.13        40.70         1.41         3.32         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 
        2.53         3.48        28.47        19.00         1.38        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        7.82         5.98         2.14        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       20.25        15.72         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        40.44        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 
       27.42        53.88         6.71        56.68        11.64        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       18.51        15.09         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       15.95        62.89        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       21.57        16.67         9.57         5.75         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        4.64         0.36         0.23        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       99.85        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       93.99        18.48        52.24        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        11.31        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       61.51        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 
       74.20        30.64        52.27         9.63        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       38.30        42.44        37.25        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
       19.82        44.55        31.27         0.95        59.84        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 
       58.95        11.05        21.24        83.97        49.25        47.18 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 
        4.57        18.81        72.00        79.89        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       22.32        25.25        18.15        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       53.26        60.99        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       66.31        78.18         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       18.77        25.45         0.59        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
        6.77        14.66        60.59        63.39        93.04         5.46 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 
       63.42        58.82         0.82        23.74        18.44        56.94 
TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       55.33        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       12.69        80.19        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE 
        2.01        19.43        19.96        15.25        10.85         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       75.55        59.01       100.27        56.91        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       34.85        54.64        51.52        35.67        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       30.71        24.33        31.20        29.36        25.58        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 
       22.49         0.13        12.82        11.57        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
       61.05         0.10        35.18         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-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        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       76.64        13.55        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4114 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         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        26.04        25.35        13.25        10.88 
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 
       11.61       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        54.90        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        48.62        11.05 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LB TCGA-G7-A8LD 
       34.82        25.15        13.68        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         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       11.84        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       85.78        88.24        67.17        22.26        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       21.44        15.48        99.78        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       92.58        52.27        50.60        78.90        12.85        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       48.30        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9Q0 
       86.27        38.86        52.11        30.67        25.68        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  AMP PEAK  9(19P13.2) MUTATED AMP PEAK  9(19P13.2) WILD-TYPE 
                          0.23                           0.07 
  AMP PEAK  9(19P13.2) MUTATED AMP PEAK  9(19P13.2) WILD-TYPE 
                        151.96                         194.79 
  AMP PEAK  9(19P13.2) MUTATED AMP PEAK  9(19P13.2) WILD-TYPE 
                         34.57                          30.25 
[1] "0.2 - 152.0 (34.6)" "0.1 - 194.8 (30.2)"
[1] "hr=" "1"  
D9V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  9(19P13.2) MUTATED        35       18        19       19
  AMP PEAK  9(19P13.2) WILD-TYPE     413       85       171       81
D9V3, multiclass
           clus
vv          AMP PEAK  9(19P13.2) MUTATED AMP PEAK  9(19P13.2) WILD-TYPE
  STAGE I                             35                            413
  STAGE II                            18                             85
  STAGE III                           19                            171
  STAGE IV                            19                             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  9(19P13.2) MUTATED    37  23  33   3
  AMP PEAK  9(19P13.2) WILD-TYPE 425 100 218  12
D9V4, multiclass
    clus
vv   AMP PEAK  9(19P13.2) MUTATED AMP PEAK  9(19P13.2) WILD-TYPE
  T1                           37                            425
  T2                           23                            100
  T3                           33                            218
  T4                            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                              N0  N1  N2
  AMP PEAK  9(19P13.2) MUTATED    36   6   1
  AMP PEAK  9(19P13.2) WILD-TYPE 281  37   5
D9V5, multiclass
    clus
vv   AMP PEAK  9(19P13.2) MUTATED AMP PEAK  9(19P13.2) WILD-TYPE
  N0                           36                            281
  N1                            6                             37
  N2                            1                              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
  AMP PEAK  9(19P13.2) MUTATED    52  17
  AMP PEAK  9(19P13.2) WILD-TYPE 490  72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(19P13.2) MUTATED     52   17
  AMP PEAK  9(19P13.2) WILD-TYPE  490   72
   clus
vv  AMP PEAK  9(19P13.2) MUTATED AMP PEAK  9(19P13.2) WILD-TYPE
  0                           52                            490
  1                           17                             72
[1] 2 2
[1] FALSE
D9V7, binary
                                cls
clus                               0   1
  AMP PEAK  9(19P13.2) MUTATED    26  71
  AMP PEAK  9(19P13.2) WILD-TYPE 261 501
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(19P13.2) MUTATED     26   71
  AMP PEAK  9(19P13.2) WILD-TYPE  261  501
        clus
vv       AMP PEAK  9(19P13.2) MUTATED AMP PEAK  9(19P13.2) WILD-TYPE
  FEMALE                           26                            261
  MALE                             71                            501
[1] 2 2
[1] FALSE
D9V8, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  AMP PEAK  9(19P13.2) MUTATED                   18
  AMP PEAK  9(19P13.2) WILD-TYPE                 48
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  AMP PEAK  9(19P13.2) MUTATED                                  49
  AMP PEAK  9(19P13.2) WILD-TYPE                               475
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK  9(19P13.2) MUTATED                                      30
  AMP PEAK  9(19P13.2) WILD-TYPE                                   239
D9V9, multiclass
                                       clus
vv                                      AMP PEAK  9(19P13.2) MUTATED
  KIDNEY CHROMOPHOBE                                              18
  KIDNEY CLEAR CELL RENAL CARCINOMA                               49
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           30
                                       clus
vv                                      AMP PEAK  9(19P13.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                48
  KIDNEY CLEAR CELL RENAL CARCINOMA                                475
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            239
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, continuous
D9V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(19P13.2) MUTATED                                  0     2
  AMP PEAK  9(19P13.2) WILD-TYPE                                2    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(19P13.2) MUTATED                           9    83
  AMP PEAK  9(19P13.2) WILD-TYPE                       107   619
D9V12, multiclass
                                  clus
vv                                 AMP PEAK  9(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      83
                                  clus
vv                                 AMP PEAK  9(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        13
  BLACK OR AFRICAN AMERICAN                                   107
  WHITE                                                       619
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, binary
                                cls
clus                               0   1
  AMP PEAK  9(19P13.2) MUTATED     5  67
  AMP PEAK  9(19P13.2) WILD-TYPE  37 530
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(19P13.2) MUTATED      5   67
  AMP PEAK  9(19P13.2) WILD-TYPE   37  530
                        clus
vv                       AMP PEAK  9(19P13.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           67
                        clus
vv                       AMP PEAK  9(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 37
  NOT HISPANIC OR LATINO                            530
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(XP22.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(XP22.2) MUTATED    94  20
  AMP PEAK 10(XP22.2) WILD-TYPE 538 191
  AMP PEAK 10(XP22.2) MUTATED AMP PEAK 10(XP22.2) WILD-TYPE 
                          114                           729 
  AMP PEAK 10(XP22.2) MUTATED AMP PEAK 10(XP22.2) WILD-TYPE 
                           20                           191 
$`AMP PEAK 10(XP22.2) MUTATED`
TCGA-KL-8346 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8410 
       62.37        23.47        25.91         3.55        11.21        87.78 
TCGA-KO-8413 TCGA-A3-3346 TCGA-A3-3382 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3445 
       86.10         4.50        18.87        66.31        67.20        42.08 
TCGA-AK-3453 TCGA-B0-5109 TCGA-BP-4162 TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 
       45.93        19.30       101.06        61.78         0.07        93.99 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4352 TCGA-BP-4756 TCGA-BP-4770 TCGA-BP-4799 
       62.86        49.08        11.31        12.30        10.82        37.25 
TCGA-BP-4969 TCGA-BP-4989 TCGA-CJ-4642 TCGA-CJ-4644 TCGA-CJ-4885 TCGA-CJ-4899 
       58.98         3.88        53.52        11.05        69.86        50.24 
TCGA-CJ-5681 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-5456 TCGA-CZ-5464 TCGA-CZ-5468 
       18.15        74.66        46.16        56.28        57.21         1.94 
TCGA-EU-5905 TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JQ 
        3.91        75.55        58.22       100.27        56.91        25.58 
TCGA-2Z-A9JR TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 
        5.29        23.97        23.31         0.76        19.63        14.33 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3468 
       16.96        16.31        15.75        12.46         9.63        76.64 
TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A657 TCGA-B3-4103 
       13.55         2.20        21.67        24.56         6.58        30.58 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       10.16        50.50        28.18         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5891 
       43.99        22.06         0.16        17.49        47.80         0.95 
TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DW-5561 
        7.92        48.26        96.92        50.40         3.81        13.61 
TCGA-DW-7836 TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6133 TCGA-F9-A7VF TCGA-F9-A8NY 
       35.93        14.63        40.77        51.19         2.40         1.18 
TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-GL-6846 TCGA-GL-A59T 
       51.78        39.25         6.38        17.98       194.79        17.95 
TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NL TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       68.12        11.84         5.49        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVL TCGA-PJ-A5Z9 
       34.29        87.22        84.95        52.27        16.01        17.75 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       33.04        28.80        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A895 
       48.30        60.03        25.68        27.39        12.99        15.91 

$`AMP PEAK 10(XP22.2) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 
       24.79        73.91        71.41        28.80        54.74       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       51.06        31.33       129.37        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
      104.52         0.99        52.27        87.12        19.33         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87        76.90        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 
       74.93        79.04        92.71        16.67        80.38       103.27 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       24.16        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 
       73.08        15.78        60.92        72.07        68.61        57.37 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
       46.78        48.36        40.01        58.49        48.69        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       40.70         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        3.48        28.47        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        7.82         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       40.44        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       78.44        68.71        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       29.95        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       14.27         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       77.03        62.24        64.27        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4347 
       15.16        18.48        52.24        74.17        54.77        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       12.23        31.89        12.33        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        61.68         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       48.95        36.53        20.38        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       25.81        36.95        27.22        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       54.61        58.95        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       66.21        61.91        57.83        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45        59.44        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       61.91        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       25.45         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
       63.42        58.82         0.82        23.74        18.44        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       47.54        22.52         2.40        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       43.69        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 
       66.28        56.84        23.90        66.02        18.12         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J2 
       19.43        19.96        15.25        10.85         7.04        59.01 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       31.20        29.36        16.18        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       11.57        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5Y0 
       25.64        23.28        19.73        12.46         8.48         8.28 
TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       12.99        58.45        30.35        25.08        44.61        49.25 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56         7.33        16.87         3.55        16.77         0.46 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-4116 
       33.83        10.09        34.49        12.46        26.40        20.61 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
        2.10        19.23         6.81        14.86        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 
       19.27         8.88        63.72        22.92        43.20        21.63 
TCGA-BQ-5883 TCGA-BQ-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-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 
       10.88         7.66        11.97         2.76       123.62        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       44.84        61.28        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7837 
        7.63         7.04         7.17        11.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
       24.46        13.78         3.75         3.02        79.86        80.88 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 
       13.08         0.43         4.01        48.62        11.05        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.15        13.68        25.84        17.33        16.90        80.65 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A40U 
       11.21         4.60        13.41        56.75        73.25        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A560 
       21.34        16.34        12.36         0.13        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVM 
       15.48        99.78        42.94         6.61        92.58        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL 
       78.90        12.85        14.07        47.90        47.44        27.06 
TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PM TCGA-UZ-A9PN 
       11.93        38.63        43.76        18.02        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-WN-A9G9 
        0.53        86.27        38.86        52.11        30.67        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       29.00        18.64        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  AMP PEAK 10(XP22.2) MUTATED AMP PEAK 10(XP22.2) WILD-TYPE 
                         0.07                          0.10 
  AMP PEAK 10(XP22.2) MUTATED AMP PEAK 10(XP22.2) WILD-TYPE 
                       194.79                        151.96 
  AMP PEAK 10(XP22.2) MUTATED AMP PEAK 10(XP22.2) WILD-TYPE 
                       24.265                        31.270 
[1] "0.1 - 194.8 (24.3)" "0.1 - 152.0 (31.3)"
[1] "hr=" "1.3"
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 10(XP22.2) MUTATED        72       14        14       15
  AMP PEAK 10(XP22.2) WILD-TYPE     376       89       176       85
D10V3, multiclass
           clus
vv          AMP PEAK 10(XP22.2) MUTATED AMP PEAK 10(XP22.2) WILD-TYPE
  STAGE I                            72                           376
  STAGE II                           14                            89
  STAGE III                          14                           176
  STAGE IV                           15                            85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 10(XP22.2) MUTATED    73  19  24   3
  AMP PEAK 10(XP22.2) WILD-TYPE 389 104 227  12
D10V4, multiclass
    clus
vv   AMP PEAK 10(XP22.2) MUTATED AMP PEAK 10(XP22.2) WILD-TYPE
  T1                          73                           389
  T2                          19                           104
  T3                          24                           227
  T4                           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                             N0  N1  N2
  AMP PEAK 10(XP22.2) MUTATED    34   5   0
  AMP PEAK 10(XP22.2) WILD-TYPE 283  38   6
D10V5, multiclass
    clus
vv   AMP PEAK 10(XP22.2) MUTATED AMP PEAK 10(XP22.2) WILD-TYPE
  N0                          34                           283
  N1                           5                            38
  N2                           0                             6
[1] 3 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
  AMP PEAK 10(XP22.2) MUTATED    51  12
  AMP PEAK 10(XP22.2) WILD-TYPE 491  77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(XP22.2) MUTATED     51   12
  AMP PEAK 10(XP22.2) WILD-TYPE  491   77
   clus
vv  AMP PEAK 10(XP22.2) MUTATED AMP PEAK 10(XP22.2) WILD-TYPE
  0                          51                           491
  1                          12                            77
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(XP22.2) MUTATED    27  94
  AMP PEAK 10(XP22.2) WILD-TYPE 260 478
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(XP22.2) MUTATED     27   94
  AMP PEAK 10(XP22.2) WILD-TYPE  260  478
        clus
vv       AMP PEAK 10(XP22.2) MUTATED AMP PEAK 10(XP22.2) WILD-TYPE
  FEMALE                          27                           260
  MALE                            94                           478
[1] 2 2
[1] FALSE
D10V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  AMP PEAK 10(XP22.2) MUTATED                    7
  AMP PEAK 10(XP22.2) WILD-TYPE                 59
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  AMP PEAK 10(XP22.2) MUTATED                                  30
  AMP PEAK 10(XP22.2) WILD-TYPE                               494
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK 10(XP22.2) MUTATED                                      84
  AMP PEAK 10(XP22.2) WILD-TYPE                                   185
D10V9, multiclass
                                       clus
vv                                      AMP PEAK 10(XP22.2) MUTATED
  KIDNEY CHROMOPHOBE                                              7
  KIDNEY CLEAR CELL RENAL CARCINOMA                              30
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          84
                                       clus
vv                                      AMP PEAK 10(XP22.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               59
  KIDNEY CLEAR CELL RENAL CARCINOMA                               494
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, continuous
D10V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(XP22.2) MUTATED                                  1     3
  AMP PEAK 10(XP22.2) WILD-TYPE                                1    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(XP22.2) MUTATED                          15    96
  AMP PEAK 10(XP22.2) WILD-TYPE                       101   606
D10V12, multiclass
                                  clus
vv                                 AMP PEAK 10(XP22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                     96
                                  clus
vv                                 AMP PEAK 10(XP22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                  101
  WHITE                                                      606
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, binary
                               cls
clus                              0   1
  AMP PEAK 10(XP22.2) MUTATED     5  89
  AMP PEAK 10(XP22.2) WILD-TYPE  37 508
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(XP22.2) MUTATED      5   89
  AMP PEAK 10(XP22.2) WILD-TYPE   37  508
                        clus
vv                       AMP PEAK 10(XP22.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          89
                        clus
vv                       AMP PEAK 10(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                37
  NOT HISPANIC OR LATINO                           508
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(XP11.4) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(XP11.4) MUTATED   102  21
  AMP PEAK 11(XP11.4) WILD-TYPE 530 190
  AMP PEAK 11(XP11.4) MUTATED AMP PEAK 11(XP11.4) WILD-TYPE 
                          123                           720 
  AMP PEAK 11(XP11.4) MUTATED AMP PEAK 11(XP11.4) WILD-TYPE 
                           21                           190 
$`AMP PEAK 11(XP11.4) MUTATED`
TCGA-KL-8346 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8410 
       62.37        23.47        25.91         3.55        11.21        87.78 
TCGA-KO-8413 TCGA-A3-3325 TCGA-A3-3382 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3445 
       86.10        24.69        18.87        66.31        67.20        42.08 
TCGA-AK-3453 TCGA-B0-4696 TCGA-B0-5109 TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4174 
       45.93        28.47        19.30         4.93       101.06        61.78 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4352 TCGA-BP-4756 TCGA-BP-4770 TCGA-BP-4799 
        0.07        93.99        11.31        12.30        10.82        37.25 
TCGA-BP-4969 TCGA-BP-4989 TCGA-BP-5178 TCGA-BP-5199 TCGA-CJ-4644 TCGA-CJ-4885 
       58.98         3.88        62.86        44.55        11.05        69.86 
TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-5681 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-5456 
       50.24        49.97        18.15        74.66        46.16        56.28 
TCGA-CZ-5464 TCGA-CZ-5468 TCGA-EU-5905 TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       57.21         1.94         3.91        75.55        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-A4-7732 TCGA-A4-8311 
       56.91        25.58         5.29        16.18        19.13        23.97 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31         0.76        19.63        14.33        12.46        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 
       16.31        15.75        12.46         9.63        76.64        13.55 
TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-A6W5 
        2.20        21.67        24.56         6.58        30.58        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       50.50        28.18         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5891 TCGA-BQ-5893 
       22.06         0.16        17.49        47.80         0.95         7.92 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7836 
       48.26        96.92        50.40         3.81        13.61        35.93 
TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6133 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 
       14.63        40.77        51.19         2.40         1.18        51.78 
TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-GL-6846 TCGA-GL-A59T TCGA-HE-A5NF 
       39.25         6.38        17.98       194.79        17.95        68.12 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       11.84        56.75         5.49        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A562 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-AAVK 
       34.29        27.78        20.25        87.22        84.95        52.27 
TCGA-P4-AAVL TCGA-PJ-A5Z9 TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP 
       16.01        17.75        33.04        28.80        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PU TCGA-UZ-A9PV 
       41.62        26.47        48.30        60.03        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A895 
       27.39        12.99        15.91 

$`AMP PEAK 11(XP11.4) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 
       24.79        73.91        71.41        28.80        54.74       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       51.06        31.33       129.37        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
      104.52         0.99        52.27        87.12        19.33         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87        76.90        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 
       74.93        79.04        92.71        16.67        80.38       103.27 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        21.86        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       24.16        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 
       73.08        15.78        60.92        72.07        68.61        57.37 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
       46.78        48.36        40.01        58.49        48.69        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       40.70         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
        3.48        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       16.21        18.21        21.44        37.22        14.76        79.17 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        11.77        10.36        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67         9.57         5.75         0.23         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        1.74         8.42        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 
      111.02        85.51        94.72        90.28        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 
       62.07        80.68        37.25        21.21        15.16        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       12.23        31.89        12.33        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        61.68         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       48.95        36.53        20.38        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       25.81        36.95        27.22        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
       52.27         9.63        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       58.95        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       61.91        57.83        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       59.44        56.35        47.67        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5683 
       25.71        18.87        22.32        25.25        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6087 
        5.39        85.78        73.18        66.31        78.18         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 
      105.93        83.90       103.43        18.77        25.45         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
       47.08        69.21        58.75         6.77        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        0.82        23.74        18.44        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       23.90        66.02        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       15.25        10.85         7.04        59.01         4.57        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       75.42        34.85        56.81        54.64        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 
       22.49         0.13        12.82        11.57        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
       61.05         0.10        35.18         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A57E 
       30.48        29.46        25.64        23.28        19.73         8.48 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        8.28        12.99        58.45        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
       49.25        19.56         7.33        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 
        0.46        33.83        10.09        34.49        12.46        26.40 
TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI 
       20.61         2.10        19.23         6.81        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-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-5892 TCGA-BQ-5894 TCGA-BQ-7044 
       13.25        10.88         7.66        11.97         2.76       123.62 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       93.34        44.84        61.28        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-7834 
       11.28         7.63         7.04         7.17        11.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-DZ-6131 
       37.55        24.46        13.78         3.75         3.02        79.86 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 
       10.68        13.08         0.43         4.01        48.62        11.05 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD 
       34.82        25.15        13.68        25.84        17.33        16.90 
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-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40U 
        0.89        11.21         4.60        13.41        73.25        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A560 TCGA-MH-A561 
       21.34        16.34        12.36         0.13        30.38        27.65 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
        0.36        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       42.94         6.61        92.58        50.60        78.90        12.85 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO 
       14.07        47.90        47.44        27.06        11.93        38.63 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       43.76        18.02        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       38.86        52.11        26.01        29.00        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  AMP PEAK 11(XP11.4) MUTATED AMP PEAK 11(XP11.4) WILD-TYPE 
                         0.07                          0.10 
  AMP PEAK 11(XP11.4) MUTATED AMP PEAK 11(XP11.4) WILD-TYPE 
                       194.79                        151.96 
  AMP PEAK 11(XP11.4) MUTATED AMP PEAK 11(XP11.4) WILD-TYPE 
                       24.560                        31.315 
[1] "0.1 - 194.8 (24.6)" "0.1 - 152.0 (31.3)"
[1] "hr=" "1.3"
D11V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 11(XP11.4) MUTATED        78       14        13       16
  AMP PEAK 11(XP11.4) WILD-TYPE     370       89       177       84
D11V3, multiclass
           clus
vv          AMP PEAK 11(XP11.4) MUTATED AMP PEAK 11(XP11.4) WILD-TYPE
  STAGE I                            78                           370
  STAGE II                           14                            89
  STAGE III                          13                           177
  STAGE IV                           16                            84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 11(XP11.4) MUTATED    80  20  24   3
  AMP PEAK 11(XP11.4) WILD-TYPE 382 103 227  12
D11V4, multiclass
    clus
vv   AMP PEAK 11(XP11.4) MUTATED AMP PEAK 11(XP11.4) WILD-TYPE
  T1                          80                           382
  T2                          20                           103
  T3                          24                           227
  T4                           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                             N0  N1  N2
  AMP PEAK 11(XP11.4) MUTATED    34   5   0
  AMP PEAK 11(XP11.4) WILD-TYPE 283  38   6
D11V5, multiclass
    clus
vv   AMP PEAK 11(XP11.4) MUTATED AMP PEAK 11(XP11.4) WILD-TYPE
  N0                          34                           283
  N1                           5                            38
  N2                           0                             6
[1] 3 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
  AMP PEAK 11(XP11.4) MUTATED    51  13
  AMP PEAK 11(XP11.4) WILD-TYPE 491  76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(XP11.4) MUTATED     51   13
  AMP PEAK 11(XP11.4) WILD-TYPE  491   76
   clus
vv  AMP PEAK 11(XP11.4) MUTATED AMP PEAK 11(XP11.4) WILD-TYPE
  0                          51                           491
  1                          13                            76
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(XP11.4) MUTATED    26 103
  AMP PEAK 11(XP11.4) WILD-TYPE 261 469
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(XP11.4) MUTATED     26  103
  AMP PEAK 11(XP11.4) WILD-TYPE  261  469
        clus
vv       AMP PEAK 11(XP11.4) MUTATED AMP PEAK 11(XP11.4) WILD-TYPE
  FEMALE                          26                           261
  MALE                           103                           469
[1] 2 2
[1] FALSE
D11V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  AMP PEAK 11(XP11.4) MUTATED                    7
  AMP PEAK 11(XP11.4) WILD-TYPE                 59
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  AMP PEAK 11(XP11.4) MUTATED                                  32
  AMP PEAK 11(XP11.4) WILD-TYPE                               492
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK 11(XP11.4) MUTATED                                      90
  AMP PEAK 11(XP11.4) WILD-TYPE                                   179
D11V9, multiclass
                                       clus
vv                                      AMP PEAK 11(XP11.4) MUTATED
  KIDNEY CHROMOPHOBE                                              7
  KIDNEY CLEAR CELL RENAL CARCINOMA                              32
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          90
                                       clus
vv                                      AMP PEAK 11(XP11.4) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               59
  KIDNEY CLEAR CELL RENAL CARCINOMA                               492
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, continuous
D11V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(XP11.4) MUTATED                                  1     3
  AMP PEAK 11(XP11.4) WILD-TYPE                                1    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(XP11.4) MUTATED                          20    99
  AMP PEAK 11(XP11.4) WILD-TYPE                        96   603
D11V12, multiclass
                                  clus
vv                                 AMP PEAK 11(XP11.4) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 20
  WHITE                                                     99
                                  clus
vv                                 AMP PEAK 11(XP11.4) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                   96
  WHITE                                                      603
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, binary
                               cls
clus                              0   1
  AMP PEAK 11(XP11.4) MUTATED     5  99
  AMP PEAK 11(XP11.4) WILD-TYPE  37 498
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(XP11.4) MUTATED      5   99
  AMP PEAK 11(XP11.4) WILD-TYPE   37  498
                        clus
vv                       AMP PEAK 11(XP11.4) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          99
                        clus
vv                       AMP PEAK 11(XP11.4) WILD-TYPE
  HISPANIC OR LATINO                                37
  NOT HISPANIC OR LATINO                           498
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(XQ11.2) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 12(XQ11.2) MUTATED   103  19
  AMP PEAK 12(XQ11.2) WILD-TYPE 529 192
  AMP PEAK 12(XQ11.2) MUTATED AMP PEAK 12(XQ11.2) WILD-TYPE 
                          122                           721 
  AMP PEAK 12(XQ11.2) MUTATED AMP PEAK 12(XQ11.2) WILD-TYPE 
                           19                           192 
$`AMP PEAK 12(XQ11.2) MUTATED`
TCGA-KL-8346 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8410 
       62.37        23.47        25.91         3.55        11.21        87.78 
TCGA-KO-8413 TCGA-A3-3363 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3453 TCGA-B0-4696 
       86.10        10.49        66.31        67.20        45.93        28.47 
TCGA-B0-5109 TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 
       19.30         4.93       101.06        61.78         0.07        93.99 
TCGA-BP-4352 TCGA-BP-4762 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4799 TCGA-BP-4969 
       11.31        44.15        61.68        61.97        37.25        58.98 
TCGA-BP-4989 TCGA-BP-5176 TCGA-CJ-4644 TCGA-CJ-4885 TCGA-CJ-4899 TCGA-CW-5591 
        3.88        52.27        11.05        69.86        50.24        74.66 
TCGA-CZ-4854 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5464 TCGA-EU-5905 TCGA-2Z-A9J1 
       46.16        56.28        56.94        57.21         3.91        75.55 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       58.22       100.27        56.91        25.58         5.29        16.18 
TCGA-A4-7732 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 
       19.13        23.97        23.31         0.76        19.63        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3466 
       12.46        16.96        16.31        15.75        12.46         9.63 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A657 
       76.64        13.55         2.20        21.67        24.56         6.58 
TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 
       30.58        10.16        50.50        28.18         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W9 TCGA-B9-A8YH 
       15.12        43.99        22.06         2.10         0.16        17.49 
TCGA-BQ-5881 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 
       47.80        25.35         0.95         7.92        48.26        96.92 
TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7841 TCGA-DW-7963 
       50.40         3.81        13.61        35.93        14.63        40.77 
TCGA-DZ-6133 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A4TM 
       51.19         2.40         1.18        51.78        39.25         6.38 
TCGA-G7-A8LB TCGA-GL-6846 TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ 
       17.98       194.79        17.95        68.12        11.84        56.75 
TCGA-HE-A5NL TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        5.49        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A562 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVL TCGA-PJ-A5Z9 
       20.25        87.22        84.95        52.27        16.01        17.75 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       33.04        28.80        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       48.30        60.03        38.86        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-Y8-A895 
       12.99        15.91 

$`AMP PEAK 12(XQ11.2) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 
       24.79        73.91        71.41        28.80        54.74       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       51.06        31.33       129.37        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
      104.52         0.99        52.27        87.12        19.33         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87        76.90        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 
       74.93        79.04        92.71        16.67        80.38       103.27 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       42.97        82.32        51.25        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       24.16        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       84.36        73.08        15.78        60.92        72.07        68.61 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       57.37        46.78        48.36        42.08        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       48.69        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       28.04        12.13        40.70         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
        4.57         2.53         3.48        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       30.48        29.95        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67         9.57         5.75         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        14.27         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K 
       29.88        17.06         1.74         8.42        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       77.03        62.24        64.27        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       15.16        18.48        52.24        74.17        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 
       31.30        25.81        36.95        27.22        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       30.64         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        53.52        58.95        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 
       71.87        66.21        61.91        57.83        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       27.65        39.45        59.44        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       73.18        66.31        78.18         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
      103.43        18.77        25.45         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       18.44        55.33        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        47.54        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        43.69        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       11.67        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
       18.12         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
        7.04        59.01         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       56.81        54.64        51.52        35.67        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JT TCGA-4A-A93W 
       30.71        24.33        31.20        29.36        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       35.18         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       25.64        23.28        19.73         8.48         8.28        12.99 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 
       58.45        30.35        25.08        44.61        49.25        19.56 
TCGA-B1-7332 TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
        7.33        16.87         3.55        16.77         0.46        33.83 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A5W7 
       10.09        34.49        12.46        26.40        20.61        19.23 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        6.81        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-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 
       30.28        26.04        13.25        10.88         7.66        11.97 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 
        2.76       123.62        93.34        44.84        61.28        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-DW-5560 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       11.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        3.02        79.86        80.88        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 
       19.00        24.89        10.68        13.08         0.43         4.01 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       48.62        11.05        34.82        25.15        13.68        25.84 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       17.33        16.90        80.65        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH 
        1.05        12.43         0.89        11.21         4.60        13.41 
TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       73.25        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       30.38        27.65         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVM 
       15.48        99.78        42.94         6.61        92.58        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL 
       78.90        12.85        14.07        47.90        47.44        27.06 
TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PM TCGA-UZ-A9PN 
       11.93        38.63        43.76        18.02        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
        0.53        86.27        52.11        26.01        29.00        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  AMP PEAK 12(XQ11.2) MUTATED AMP PEAK 12(XQ11.2) WILD-TYPE 
                         0.07                          0.10 
  AMP PEAK 12(XQ11.2) MUTATED AMP PEAK 12(XQ11.2) WILD-TYPE 
                       194.79                        151.96 
  AMP PEAK 12(XQ11.2) MUTATED AMP PEAK 12(XQ11.2) WILD-TYPE 
                        25.63                         31.27 
[1] "0.1 - 194.8 (25.6)" "0.1 - 152.0 (31.3)"
[1] "hr=" "1.5"
D12V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 12(XQ11.2) MUTATED        80       14        14       12
  AMP PEAK 12(XQ11.2) WILD-TYPE     368       89       176       88
D12V3, multiclass
           clus
vv          AMP PEAK 12(XQ11.2) MUTATED AMP PEAK 12(XQ11.2) WILD-TYPE
  STAGE I                            80                           368
  STAGE II                           14                            89
  STAGE III                          14                           176
  STAGE IV                           12                            88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 12(XQ11.2) MUTATED    82  20  22   2
  AMP PEAK 12(XQ11.2) WILD-TYPE 380 103 229  13
D12V4, multiclass
    clus
vv   AMP PEAK 12(XQ11.2) MUTATED AMP PEAK 12(XQ11.2) WILD-TYPE
  T1                          82                           380
  T2                          20                           103
  T3                          22                           229
  T4                           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                             N0  N1  N2
  AMP PEAK 12(XQ11.2) MUTATED    33   5   0
  AMP PEAK 12(XQ11.2) WILD-TYPE 284  38   6
D12V5, multiclass
    clus
vv   AMP PEAK 12(XQ11.2) MUTATED AMP PEAK 12(XQ11.2) WILD-TYPE
  N0                          33                           284
  N1                           5                            38
  N2                           0                             6
[1] 3 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
  AMP PEAK 12(XQ11.2) MUTATED    51  10
  AMP PEAK 12(XQ11.2) WILD-TYPE 491  79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(XQ11.2) MUTATED     51   10
  AMP PEAK 12(XQ11.2) WILD-TYPE  491   79
   clus
vv  AMP PEAK 12(XQ11.2) MUTATED AMP PEAK 12(XQ11.2) WILD-TYPE
  0                          51                           491
  1                          10                            79
[1] 2 2
[1] FALSE
D12V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(XQ11.2) MUTATED    25 103
  AMP PEAK 12(XQ11.2) WILD-TYPE 262 469
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(XQ11.2) MUTATED     25  103
  AMP PEAK 12(XQ11.2) WILD-TYPE  262  469
        clus
vv       AMP PEAK 12(XQ11.2) MUTATED AMP PEAK 12(XQ11.2) WILD-TYPE
  FEMALE                          25                           262
  MALE                           103                           469
[1] 2 2
[1] FALSE
D12V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  AMP PEAK 12(XQ11.2) MUTATED                    7
  AMP PEAK 12(XQ11.2) WILD-TYPE                 59
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  AMP PEAK 12(XQ11.2) MUTATED                                  28
  AMP PEAK 12(XQ11.2) WILD-TYPE                               496
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK 12(XQ11.2) MUTATED                                      93
  AMP PEAK 12(XQ11.2) WILD-TYPE                                   176
D12V9, multiclass
                                       clus
vv                                      AMP PEAK 12(XQ11.2) MUTATED
  KIDNEY CHROMOPHOBE                                              7
  KIDNEY CLEAR CELL RENAL CARCINOMA                              28
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          93
                                       clus
vv                                      AMP PEAK 12(XQ11.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               59
  KIDNEY CLEAR CELL RENAL CARCINOMA                               496
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, continuous
D12V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(XQ11.2) MUTATED                                  1     3
  AMP PEAK 12(XQ11.2) WILD-TYPE                                1    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(XQ11.2) MUTATED                          21    97
  AMP PEAK 12(XQ11.2) WILD-TYPE                        95   605
D12V12, multiclass
                                  clus
vv                                 AMP PEAK 12(XQ11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 21
  WHITE                                                     97
                                  clus
vv                                 AMP PEAK 12(XQ11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                   95
  WHITE                                                      605
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, binary
                               cls
clus                              0   1
  AMP PEAK 12(XQ11.2) MUTATED     5  96
  AMP PEAK 12(XQ11.2) WILD-TYPE  37 501
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(XQ11.2) MUTATED      5   96
  AMP PEAK 12(XQ11.2) WILD-TYPE   37  501
                        clus
vv                       AMP PEAK 12(XQ11.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          96
                        clus
vv                       AMP PEAK 12(XQ11.2) WILD-TYPE
  HISPANIC OR LATINO                                37
  NOT HISPANIC OR LATINO                           501
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(XQ28) MUTATION ANALYSIS
D13V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 13(XQ28) MUTATED   106  20
  AMP PEAK 13(XQ28) WILD-TYPE 526 191
  AMP PEAK 13(XQ28) MUTATED AMP PEAK 13(XQ28) WILD-TYPE 
                        126                         717 
  AMP PEAK 13(XQ28) MUTATED AMP PEAK 13(XQ28) WILD-TYPE 
                         20                         191 
$`AMP PEAK 13(XQ28) MUTATED`
TCGA-KL-8337 TCGA-KL-8346 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 
       44.84        62.37        23.47        25.91         3.55        11.21 
TCGA-KO-8410 TCGA-KO-8413 TCGA-A3-3336 TCGA-A3-3383 TCGA-AK-3428 TCGA-AK-3436 
       87.78        86.10        34.29        28.31        73.08        67.20 
TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4713 TCGA-B0-4827 TCGA-B0-5080 TCGA-B0-5109 
       45.93         3.32         6.64        29.10        11.24        19.30 
TCGA-B0-5120 TCGA-B0-5705 TCGA-B8-5159 TCGA-B8-A54D TCGA-B8-A54I TCGA-BP-4162 
       16.21       120.59        23.74        27.29         4.93       101.06 
TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4352 TCGA-BP-4799 TCGA-BP-4959 
       61.78         0.07        93.99        11.31        37.25        87.45 
TCGA-BP-4969 TCGA-BP-4989 TCGA-BP-5176 TCGA-CJ-4885 TCGA-CJ-5681 TCGA-CJ-6031 
       58.98         3.88        52.27        69.86        18.15        62.66 
TCGA-CW-5581 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5461 
       92.02        74.66        46.16        56.28        56.94        10.85 
TCGA-CZ-5464 TCGA-EU-5905 TCGA-MM-A84U TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       57.21         3.91        15.25        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JQ TCGA-A4-7732 TCGA-A4-8311 TCGA-A4-8630 
      100.27        56.91        25.58        19.13        23.97        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3468 TCGA-AL-3471 
       12.46        16.96        16.31        15.75        76.64        13.55 
TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-4103 
        2.20        21.67        24.56         0.46         6.58        30.58 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       10.16        50.50        28.18        20.61         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W9 TCGA-B9-A8YH 
       15.12        43.99        22.06         2.10         0.16        17.49 
TCGA-BQ-5881 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 
       47.80        25.35         0.95         7.92        48.26        96.92 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7841 TCGA-DW-7842 
        7.04         3.81        13.61        35.93        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6133 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       40.77        79.86        51.19         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-GL-6846 TCGA-GL-A59T 
       51.78        39.25         6.38        17.98       194.79        17.95 
TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-KV-A6GD TCGA-KV-A6GE 
       68.12        11.84        56.75         5.49        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-AAVL TCGA-PJ-A5Z9 
       11.41        34.29        87.22        84.95        16.01        17.75 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       33.04        28.80        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PU TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A895 
       48.30        60.03        30.67        27.39        12.99        15.91 

$`AMP PEAK 13(XQ28) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       92.55        30.25        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 
       73.91        71.41        28.80        54.74       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
       31.33       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
        0.99        52.27        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 
       79.04        92.71        16.67        80.38       103.27        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
       57.17        61.58        63.95        12.66        12.16        36.82 
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       47.21         0.53        39.16        24.16        49.08        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       37.15        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       37.38        48.82        21.86        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       53.29        43.20        55.76        20.71        18.64        18.87 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       65.52        20.28        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3429 
       11.18        10.62       109.91        29.10        84.36        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 
       15.78        60.92        72.07        68.61        57.37        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
       48.36        42.08        40.01        58.49        48.69        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
       28.47        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 
        5.98         2.14        19.73         3.16        43.96         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       20.25        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       14.93        54.48        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5084 
       36.85        70.52        20.94        43.30        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       52.54        30.48        29.95        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       21.60        17.59         1.94        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       52.77        39.55        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5163 
       25.55        25.91        23.01        20.91         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
        0.53        34.39        14.30        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        8.42        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       85.51        94.72        90.28        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 
        0.43        89.36        23.05        77.03        62.24        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 
       80.68        37.25        21.21        15.16        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       48.07        13.15        61.68        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       25.81        36.95        27.22        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       53.52        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 
       71.87        66.21        61.91        57.83        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       22.32        25.25        61.91        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6032 TCGA-CJ-6033 
       53.26        60.99        53.42        75.58        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       64.57        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       25.45         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
       63.42        58.82         0.82        23.74        18.44        55.33 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       55.33        47.01        10.22        21.76        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 
       56.84        23.90        66.02        18.12         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       19.96        10.85         7.04         4.57        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK 
       34.85        56.81        54.64        51.52        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       26.43        30.71        24.33        31.20        29.36         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 
       16.18        22.49         0.13        12.82        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7734 TCGA-A4-7915 
       19.63        61.05         0.10        35.18         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8515 
       16.64        30.48        29.46        25.64        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 
        0.76        19.63        19.73         8.48         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        58.45        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
       49.25        19.56         7.33        16.87         3.55        16.77 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-A5W7 
       33.83        10.09        34.49        12.46        26.40        19.23 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        6.81        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-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 
       30.28        26.04        13.25        10.88         7.66        11.97 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        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-7061 
       49.84        26.27        20.12        11.28         7.63         7.17 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       11.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 
       10.68        13.08         4.01        48.62        11.05        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.15        13.68        25.84        17.33        16.90        80.65 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X 
       11.21         4.60        13.41        73.25        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       16.34        12.36         0.13        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM 
       99.78        42.94         6.61        92.58        52.27        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL 
       78.90        12.85        14.07        47.90        47.44        27.06 
TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PM TCGA-UZ-A9PN 
       11.93        38.63        43.76        18.02        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PV TCGA-WN-A9G9 
        0.53        86.27        38.86        52.11        25.68        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       29.00        18.64        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  AMP PEAK 13(XQ28) MUTATED AMP PEAK 13(XQ28) WILD-TYPE 
                       0.07                        0.10 
  AMP PEAK 13(XQ28) MUTATED AMP PEAK 13(XQ28) WILD-TYPE 
                     194.79                      151.96 
  AMP PEAK 13(XQ28) MUTATED AMP PEAK 13(XQ28) WILD-TYPE 
                     25.465                      31.300 
[1] "0.1 - 194.8 (25.5)" "0.1 - 152.0 (31.3)"
[1] "hr=" "1.5"
D13V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 13(XQ28) MUTATED        80       12        18       14
  AMP PEAK 13(XQ28) WILD-TYPE     368       91       172       86
D13V3, multiclass
           clus
vv          AMP PEAK 13(XQ28) MUTATED AMP PEAK 13(XQ28) WILD-TYPE
  STAGE I                          80                         368
  STAGE II                         12                          91
  STAGE III                        18                         172
  STAGE IV                         14                          86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 13(XQ28) MUTATED    83  19  26   3
  AMP PEAK 13(XQ28) WILD-TYPE 379 104 225  12
D13V4, multiclass
    clus
vv   AMP PEAK 13(XQ28) MUTATED AMP PEAK 13(XQ28) WILD-TYPE
  T1                        83                         379
  T2                        19                         104
  T3                        26                         225
  T4                         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                           N0  N1  N2
  AMP PEAK 13(XQ28) MUTATED    39   4   0
  AMP PEAK 13(XQ28) WILD-TYPE 278  39   6
D13V5, multiclass
    clus
vv   AMP PEAK 13(XQ28) MUTATED AMP PEAK 13(XQ28) WILD-TYPE
  N0                        39                         278
  N1                         4                          39
  N2                         0                           6
[1] 3 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
  AMP PEAK 13(XQ28) MUTATED    58  12
  AMP PEAK 13(XQ28) WILD-TYPE 484  77
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(XQ28) MUTATED     58   12
  AMP PEAK 13(XQ28) WILD-TYPE  484   77
   clus
vv  AMP PEAK 13(XQ28) MUTATED AMP PEAK 13(XQ28) WILD-TYPE
  0                        58                         484
  1                        12                          77
[1] 2 2
[1] FALSE
D13V7, binary
                             cls
clus                            0   1
  AMP PEAK 13(XQ28) MUTATED    32 100
  AMP PEAK 13(XQ28) WILD-TYPE 255 472
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(XQ28) MUTATED     32  100
  AMP PEAK 13(XQ28) WILD-TYPE  255  472
        clus
vv       AMP PEAK 13(XQ28) MUTATED AMP PEAK 13(XQ28) WILD-TYPE
  FEMALE                        32                         255
  MALE                         100                         472
[1] 2 2
[1] FALSE
D13V8, continuous
                             vv
clus                          KIDNEY CHROMOPHOBE
  AMP PEAK 13(XQ28) MUTATED                    8
  AMP PEAK 13(XQ28) WILD-TYPE                 58
                             vv
clus                          KIDNEY CLEAR CELL RENAL CARCINOMA
  AMP PEAK 13(XQ28) MUTATED                                  37
  AMP PEAK 13(XQ28) WILD-TYPE                               487
                             vv
clus                          KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK 13(XQ28) MUTATED                                      87
  AMP PEAK 13(XQ28) WILD-TYPE                                   182
D13V9, multiclass
                                       clus
vv                                      AMP PEAK 13(XQ28) MUTATED
  KIDNEY CHROMOPHOBE                                            8
  KIDNEY CLEAR CELL RENAL CARCINOMA                            37
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                        87
                                       clus
vv                                      AMP PEAK 13(XQ28) WILD-TYPE
  KIDNEY CHROMOPHOBE                                             58
  KIDNEY CLEAR CELL RENAL CARCINOMA                             487
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                         182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, continuous
D13V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(XQ28) MUTATED                                  1     2
  AMP PEAK 13(XQ28) WILD-TYPE                                1    13
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(XQ28) MUTATED                          23   100
  AMP PEAK 13(XQ28) WILD-TYPE                        93   602
D13V12, multiclass
                                  clus
vv                                 AMP PEAK 13(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                               23
  WHITE                                                  100
                                  clus
vv                                 AMP PEAK 13(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     13
  BLACK OR AFRICAN AMERICAN                                 93
  WHITE                                                    602
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, binary
                             cls
clus                            0   1
  AMP PEAK 13(XQ28) MUTATED     4 102
  AMP PEAK 13(XQ28) WILD-TYPE  38 495
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(XQ28) MUTATED      4  102
  AMP PEAK 13(XQ28) WILD-TYPE   38  495
                        clus
vv                       AMP PEAK 13(XQ28) MUTATED AMP PEAK 13(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             4                          38
  NOT HISPANIC OR LATINO                       102                         495
[1] 2 2
[1] FALSE

Clustering(14) Variable = DEL PEAK  1(1P36.31) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.31) MUTATED   139  63
  DEL PEAK  1(1P36.31) WILD-TYPE 493 148
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           202                            641 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            63                            148 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 
      151.96        44.91        47.24        49.97       123.12       129.37 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8429 
       87.91        25.48        65.19       104.52         0.99        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 
       19.33         2.50        59.08       115.00        42.35        76.90 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 
       74.93        79.04        92.71        16.67        80.38       103.27 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3313 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        24.16        49.08 
TCGA-A3-3347 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3380 TCGA-AK-3427 TCGA-AK-3433 
       52.93        53.29        43.20        18.64        84.36        72.07 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3465 TCGA-AS-3777 
       67.20        57.37        40.01        45.93        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4718 
        1.41         4.57         1.38         3.62        65.10        20.25 
TCGA-B0-4813 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4834 TCGA-B0-4843 TCGA-B0-4845 
        0.59        40.44        36.53        68.71        11.64        65.29 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5098 TCGA-B0-5102 
       36.85        70.52         7.30        15.09        52.08        90.87 
TCGA-B0-5117 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5709 TCGA-B2-3923 TCGA-B2-4098 
       17.59        56.94        39.55       102.48        32.61         1.68 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4619 
       21.57         0.23         0.53         5.46        23.31        17.19 
TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-BP-4176 
        1.18         0.85         6.38        14.27         0.53        64.27 
TCGA-BP-4334 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4352 
       21.21        93.99        18.48        74.17        62.86        11.31 
TCGA-BP-4353 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4965 
       12.33        13.15         5.33        60.59        68.38        61.51 
TCGA-BP-4968 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-5004 
       57.40        31.30        25.81         3.88        43.00        37.02 
TCGA-BP-5173 TCGA-BP-5185 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4640 
        1.78        37.22        31.27        46.55        73.22        65.69 
TCGA-CJ-4641 TCGA-CJ-4869 TCGA-CJ-4876 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4901 
       54.61        83.97        64.27        27.65        59.44        47.67 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-6027 TCGA-CJ-6030 
       51.29        49.28        18.87        22.32        60.99        75.58 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 
        7.36        64.57        66.31        83.90        18.77        47.08 
TCGA-CZ-4860 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5462 TCGA-CZ-5469 
        6.77        93.04        61.41        55.33        10.22        31.10 
TCGA-EU-5907 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI 
        4.18        35.87         2.01        67.30        54.64        51.52 
TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-8098 TCGA-A4-A5XZ TCGA-A4-A5Y1 
       12.82        18.21         0.10        29.46        15.75        12.99 
TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A44B 
        9.63        49.25         7.33        10.09        20.61         2.10 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 
        6.81        14.86        86.76         8.88        22.92        21.63 
TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7055 
       30.28        13.25         7.66         2.76       123.62        26.27 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       10.68        13.08         4.01        25.15        13.68        25.84 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-GL-8500 TCGA-HE-A5NK TCGA-IA-A40Y 
       17.33        16.90         3.68        27.65        73.25         2.04 
TCGA-J7-8537 TCGA-P4-A5EA TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-UN-AAZ9 
        0.13         6.61        78.90        12.85        14.07        18.02 
TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-A9G9 TCGA-Y8-A8RZ 
       21.93        86.27        26.01         6.74 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 
       23.28        28.80        51.06        31.33        23.47        25.91 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8410 
        3.55        52.27        11.21       100.87        10.68        87.78 
TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 
       86.10        12.66        12.16        36.82        47.21         0.53 
TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       39.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        24.69        37.38        48.82        21.86        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
       31.07         4.50        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 
       74.76        24.16        55.76        20.71        18.87        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       65.52        20.28        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3429 
       11.18        10.62       109.91        29.10        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       15.78        60.92        68.61        46.78        48.36        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4693 TCGA-B0-4694 
       31.27        28.04         1.41         3.32         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
       28.47        19.00         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 
        3.16        43.96         6.64         3.25        15.72        46.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4844 
       45.30        27.42        53.88         6.71        56.68        10.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-5075 TCGA-B0-5077 
       39.45        26.07        29.03         2.27        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5094 TCGA-B0-5095 
       11.24        11.90        25.32        18.51        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 
        2.24        21.86        15.95        62.89        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       21.60         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 
       46.68        56.78        60.33        84.92        90.12        52.77 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      120.59        79.36        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       97.41        35.90        12.30        21.30        31.30        11.77 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       10.36        32.98        16.67         9.57         5.75         1.25 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        4.64         0.36         0.23        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       25.05        24.66        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 
       23.74        27.02        24.23        17.16        16.60        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       61.78        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4341 
       62.07        80.68        37.25        15.16         0.07        52.24 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 
       54.77        49.08        44.94        12.23        31.89        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       61.97        13.51        56.91        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4969 
       63.62        58.68        60.30        61.22         6.74        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 
       53.65        14.93        36.07        33.34        46.45        36.95 
TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
       27.22        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       41.62        18.51        38.70        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
       36.23        28.87        48.10         6.35        79.30        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       38.30        42.44        37.25        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
       19.82        44.55        34.95         0.95        59.84        63.25 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       14.17        75.88        53.52        58.95        11.05        21.24 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4904 
       24.66        39.45        50.24        56.35        49.97        58.92 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       25.71        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 
       67.00        53.26        53.42        62.66        83.77        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 
       81.83         5.39        85.78        73.18        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
        1.35       105.93       103.43        25.45        46.16         0.59 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       69.21        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
       56.94        55.33        47.01        10.85        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
       47.54        22.52         2.40         1.94        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       43.69        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       66.28        56.84        23.90        66.02        18.12         3.91 
TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-MM-A563 TCGA-MM-A564 
        6.77         7.96        10.29        70.13        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.25        10.85         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
      100.27        56.91         4.57        75.42        34.85        56.81 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       11.57        19.63        61.05        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
        0.23        16.64        30.48        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 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-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
       16.96         8.48        16.31         8.28        12.46        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       76.64        13.55        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
       19.56        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        0.46         6.58        33.83        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 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-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH 
       15.12        43.99        22.06        19.23         0.16        17.49 
TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       12.30        19.27        63.72        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        26.04        25.35        10.88         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
        7.92        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       34.19        19.00        24.89         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-A4TM 
       51.78        48.62        11.05        39.25        34.82         6.38 
TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-A4EM TCGA-GL-A59R 
       17.98        80.65       194.79        12.92         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       11.84        56.75         5.49        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
       52.27        16.01        50.60        17.75        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK 
       16.31        41.62        26.47        48.30        43.76        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       14.83         0.53        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       27.39        12.99        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.02        13.28 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        151.96                         194.79 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         37.12                          29.10 
[1] "0.1 - 152.0 (37.1)" "0.1 - 194.8 (29.1)"
[1] "hr=" "1.1"
D14V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  1(1P36.31) MUTATED        71       38        60       29
  DEL PEAK  1(1P36.31) WILD-TYPE     377       65       130       71
D14V3, multiclass
           clus
vv          DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  STAGE I                             71                            377
  STAGE II                            38                             65
  STAGE III                           60                            130
  STAGE IV                            29                             71
[1] 4 2
[1] 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    77  45  73   6
  DEL PEAK  1(1P36.31) WILD-TYPE 385  78 178   9
D14V4, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T1                           77                            385
  T2                           45                             78
  T3                           73                            178
  T4                            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                              N0  N1  N2
  DEL PEAK  1(1P36.31) MUTATED    92  19   3
  DEL PEAK  1(1P36.31) WILD-TYPE 225  24   3
D14V5, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  N0                           92                            225
  N1                           19                             24
  N2                            3                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED   126  24
  DEL PEAK  1(1P36.31) WILD-TYPE 416  65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED    126   24
  DEL PEAK  1(1P36.31) WILD-TYPE  416   65
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                          126                            416
  1                           24                             65
[1] 2 2
[1] FALSE
D14V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    72 131
  DEL PEAK  1(1P36.31) WILD-TYPE 215 441
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     72  131
  DEL PEAK  1(1P36.31) WILD-TYPE  215  441
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                           72                            215
  MALE                            131                            441
[1] 2 2
[1] FALSE
D14V8, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  DEL PEAK  1(1P36.31) MUTATED                   53
  DEL PEAK  1(1P36.31) WILD-TYPE                 13
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK  1(1P36.31) MUTATED                                 101
  DEL PEAK  1(1P36.31) WILD-TYPE                               423
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  1(1P36.31) MUTATED                                      49
  DEL PEAK  1(1P36.31) WILD-TYPE                                   220
D14V9, multiclass
                                       clus
vv                                      DEL PEAK  1(1P36.31) MUTATED
  KIDNEY CHROMOPHOBE                                              53
  KIDNEY CLEAR CELL RENAL CARCINOMA                              101
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           49
                                       clus
vv                                      DEL PEAK  1(1P36.31) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                13
  KIDNEY CLEAR CELL RENAL CARCINOMA                                423
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            220
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, continuous
D14V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.31) MUTATED                                  0     5
  DEL PEAK  1(1P36.31) WILD-TYPE                                2    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.31) MUTATED                          24   168
  DEL PEAK  1(1P36.31) WILD-TYPE                        92   534
D14V12, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  24
  WHITE                                                     168
                                  clus
vv                                 DEL PEAK  1(1P36.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    92
  WHITE                                                       534
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V13, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    12 129
  DEL PEAK  1(1P36.31) WILD-TYPE  30 468
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     12  129
  DEL PEAK  1(1P36.31) WILD-TYPE   30  468
                        clus
vv                       DEL PEAK  1(1P36.31) MUTATED
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          129
                        clus
vv                       DEL PEAK  1(1P36.31) WILD-TYPE
  HISPANIC OR LATINO                                 30
  NOT HISPANIC OR LATINO                            468
[1] 2 2
[1] FALSE

Clustering(15) Variable = DEL PEAK  2(1P31.1) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P31.1) MUTATED   116  44
  DEL PEAK  2(1P31.1) WILD-TYPE 516 167
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                          160                           683 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                           44                           167 
$`DEL PEAK  2(1P31.1) MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 
      151.96        44.91        47.24        49.97       123.12       129.37 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8429 
       87.91        25.48        65.19       104.52         0.99        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 
       19.33         2.50        59.08       115.00        42.35        76.90 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 
       74.93        79.04        92.71        16.67        80.38       103.27 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3313 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        24.16        49.08 
TCGA-A3-3319 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3380 TCGA-AK-3427 TCGA-AK-3433 
       37.15        53.29        43.20        18.64        84.36        72.07 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4698 
       67.20        57.37        40.01        12.13        40.70         1.38 
TCGA-B0-4699 TCGA-B0-4712 TCGA-B0-4718 TCGA-B0-4814 TCGA-B0-4821 TCGA-B0-4822 
        3.62        43.96        20.25         5.52        40.44        36.53 
TCGA-B0-4834 TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5094 
       68.71        65.29        36.85         7.30        15.09        10.95 
TCGA-B0-5098 TCGA-B0-5102 TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5703 
       52.08        90.87        19.30        17.59        14.76        39.55 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4619 
       32.61         1.68         0.23         0.53         5.46        17.19 
TCGA-B8-5549 TCGA-BP-4176 TCGA-BP-4334 TCGA-BP-4340 TCGA-BP-4342 TCGA-BP-4353 
        6.38        64.27        21.21        18.48        74.17        12.33 
TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4968 TCGA-BP-4983 TCGA-BP-4985 
       13.15        60.59        68.38        57.40        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5201 
       25.81        43.00        37.02         1.78        30.64        31.27 
TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4869 TCGA-CJ-4876 TCGA-CJ-4894 TCGA-CJ-4897 
       46.55        65.69        83.97        64.27        27.65        59.44 
TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CW-5588 TCGA-CW-5591 
       47.67        49.28        18.87        22.32        66.31        74.66 
TCGA-CW-6090 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5462 TCGA-CZ-5469 
       83.90         6.77        61.41        55.33        10.22        31.10 
TCGA-EU-5907 TCGA-G6-A8L8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7286 
        4.18        35.87        54.64        51.52        12.82        18.21 
TCGA-A4-7583 TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-A5W8 
        0.10        29.46        12.99         7.33        10.09         6.81 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5894 TCGA-BQ-7044 
       14.86        86.76         8.88        21.63         2.76       123.62 
TCGA-BQ-7055 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6797 TCGA-G7-7502 
       26.27        10.68        13.08         4.01        25.15        25.84 
TCGA-G7-A8LC TCGA-GL-7966 TCGA-GL-8500 TCGA-HE-A5NK TCGA-IA-A40Y TCGA-P4-A5EA 
       17.33         3.68        27.65        73.25         2.04         6.61 
TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       12.85        14.07        18.02        86.27 

$`DEL PEAK  2(1P31.1) WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 
       23.28        28.80        51.06        31.33        23.47        25.91 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8410 
        3.55        52.27        11.21       100.87        10.68        87.78 
TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 
       86.10        12.66        12.16        36.82        47.21         0.53 
TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       39.16        49.02        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 
       74.76        24.16        55.76        20.71        18.87        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       65.52        20.28        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3429 
       11.18        10.62       109.91        29.10        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       15.78        60.92        68.61        46.78        48.36        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       38.40        31.27        28.04         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4700 
        4.57         2.53         3.48        28.47        19.00        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4713 
        7.82         5.98         2.14        19.73         3.16         6.64 
TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 
        3.25        15.72        46.59         0.59        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       33.50        16.77         6.02        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 
        6.71        56.68        11.64        10.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
       29.03         2.27        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       11.90        25.32        18.51         8.05         2.24        21.86 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       15.95        62.89        90.48        52.54        30.48        29.95 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       35.90        11.80        26.20        21.60         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       18.21        21.44        37.22        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       90.12        56.94        52.77       120.59        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
       47.97        96.36        89.49        61.32        97.41        35.90 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 
       21.57        16.67         9.57         5.75         1.25         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       25.05        24.66        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60        14.27         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 
       89.36        23.05        77.03        62.24        61.78        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4341 TCGA-BP-4343 
       37.25        15.16         0.07        93.99        52.24        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       54.77        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
       10.82         5.33        61.97        13.51        56.91        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       33.34        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        6.35        79.30        74.20        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95        59.84        63.25        73.22        14.17        75.88 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 
       54.61        53.52        58.95        11.05        21.24        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 
       79.66        47.18        74.27        75.06        77.36        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       39.45        50.24        56.35        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       25.71        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       67.00        53.26        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       83.77         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 
       85.78        73.18        78.18         1.35       105.93       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
       58.75        14.66        60.59        63.39        93.04         5.46 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
       56.94        55.33        47.01        10.85        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
       47.54        22.52         2.40         1.94        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       43.69        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       66.28        56.84        23.90        66.02        18.12         3.91 
TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
        6.77         7.96        10.29        70.13         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        15.25        10.85         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       58.22       100.27        56.91         4.57        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       34.85        56.81        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       24.33        31.20        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 
       22.49         0.13        11.57        19.63        61.05        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
       19.13         0.89         0.23        16.64        30.48        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        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       30.35        25.08        44.61        49.25         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        6.58        33.83        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 
       15.12        43.99        22.06         2.10        19.23         0.16 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       17.49        12.30        19.27        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         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        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       19.00        24.89         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A4TM 
       48.62        11.05        39.25        34.82        13.68         6.38 
TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-A4EM 
       17.98        16.90        80.65       194.79        12.92         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       13.41        11.84        56.75         5.49        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       48.30        43.76        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                       151.96                        194.79 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                       40.225                        29.000 
[1] "0.1 - 152.0 (40.2)" "0.1 - 194.8 (29.0)"
[1] "hr=" "1.1"
D15V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  2(1P31.1) MUTATED        59       34        43       22
  DEL PEAK  2(1P31.1) WILD-TYPE     389       69       147       78
D15V3, multiclass
           clus
vv          DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  STAGE I                            59                           389
  STAGE II                           34                            69
  STAGE III                          43                           147
  STAGE IV                           22                            78
[1] 4 2
[1] 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(1P31.1) MUTATED    64  38  52   6
  DEL PEAK  2(1P31.1) WILD-TYPE 398  85 199   9
D15V4, multiclass
    clus
vv   DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  T1                          64                           398
  T2                          38                            85
  T3                          52                           199
  T4                           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                             N0  N1  N2
  DEL PEAK  2(1P31.1) MUTATED    72  14   3
  DEL PEAK  2(1P31.1) WILD-TYPE 245  29   3
D15V5, multiclass
    clus
vv   DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  N0                          72                           245
  N1                          14                            29
  N2                           3                             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"
D15V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P31.1) MUTATED   104  16
  DEL PEAK  2(1P31.1) WILD-TYPE 438  73
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED    104   16
  DEL PEAK  2(1P31.1) WILD-TYPE  438   73
   clus
vv  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  0                         104                           438
  1                          16                            73
[1] 2 2
[1] FALSE
D15V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P31.1) MUTATED    54 107
  DEL PEAK  2(1P31.1) WILD-TYPE 233 465
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED     54  107
  DEL PEAK  2(1P31.1) WILD-TYPE  233  465
        clus
vv       DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  FEMALE                          54                           233
  MALE                           107                           465
[1] 2 2
[1] FALSE
D15V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK  2(1P31.1) MUTATED                   53
  DEL PEAK  2(1P31.1) WILD-TYPE                 13
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK  2(1P31.1) MUTATED                                  76
  DEL PEAK  2(1P31.1) WILD-TYPE                               448
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  2(1P31.1) MUTATED                                      32
  DEL PEAK  2(1P31.1) WILD-TYPE                                   237
D15V9, multiclass
                                       clus
vv                                      DEL PEAK  2(1P31.1) MUTATED
  KIDNEY CHROMOPHOBE                                             53
  KIDNEY CLEAR CELL RENAL CARCINOMA                              76
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          32
                                       clus
vv                                      DEL PEAK  2(1P31.1) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               13
  KIDNEY CLEAR CELL RENAL CARCINOMA                               448
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           237
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, continuous
D15V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P31.1) MUTATED                                  0     5
  DEL PEAK  2(1P31.1) WILD-TYPE                                2    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P31.1) MUTATED                          19   131
  DEL PEAK  2(1P31.1) WILD-TYPE                        97   571
D15V12, multiclass
                                  clus
vv                                 DEL PEAK  2(1P31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                    131
                                  clus
vv                                 DEL PEAK  2(1P31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   97
  WHITE                                                      571
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P31.1) MUTATED    11  94
  DEL PEAK  2(1P31.1) WILD-TYPE  31 503
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED     11   94
  DEL PEAK  2(1P31.1) WILD-TYPE   31  503
                        clus
vv                       DEL PEAK  2(1P31.1) MUTATED
  HISPANIC OR LATINO                              11
  NOT HISPANIC OR LATINO                          94
                        clus
vv                       DEL PEAK  2(1P31.1) WILD-TYPE
  HISPANIC OR LATINO                                31
  NOT HISPANIC OR LATINO                           503
[1] 2 2
[1] FALSE

Clustering(16) Variable = DEL PEAK  3(1Q43) MUTATION ANALYSIS
D16V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  3(1Q43) MUTATED    85  26
  DEL PEAK  3(1Q43) WILD-TYPE 547 185
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                        111                         732 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         26                         185 
$`DEL PEAK  3(1Q43) MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 
       73.91        71.41        28.80        54.74       151.96        44.91 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
       47.24        49.97       123.12       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8434 
       65.19       104.52        52.27        87.12        19.33        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
      115.00        42.35        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 
       92.71        16.67        80.38       103.27        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-A8OV 
       61.58        63.95        74.76        43.20        18.64        11.18 
TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4696 
       84.36        72.07        57.37        12.13        40.70        28.47 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4821 TCGA-B0-4834 TCGA-B0-4845 TCGA-B0-4852 
        1.38         3.62        40.44        68.71        65.29        36.85 
TCGA-B0-5102 TCGA-B0-5117 TCGA-B0-5703 TCGA-B2-3923 TCGA-B4-5838 TCGA-B8-4619 
       90.87        17.59        39.55        32.61         5.46        17.19 
TCGA-B8-5549 TCGA-BP-4329 TCGA-BP-4334 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4768 
        6.38        27.78        21.21        11.31        12.33        13.15 
TCGA-BP-4775 TCGA-BP-4968 TCGA-BP-4994 TCGA-CJ-4878 TCGA-CJ-4897 TCGA-CJ-4901 
       60.59        57.40        43.00        71.87        59.44        47.67 
TCGA-CJ-4907 TCGA-CW-5585 TCGA-CW-5588 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5457 
       49.28        85.78        66.31         6.77        61.41        55.33 
TCGA-CZ-5469 TCGA-G6-A8L8 TCGA-2Z-A9JG TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7583 
       31.10        35.87        54.64        12.82        18.21         0.10 
TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5894 
        7.33        16.77        10.09         6.81         0.16         2.76 
TCGA-F9-A7Q0 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-8500 TCGA-HE-A5NK TCGA-P4-A5EA 
       13.08        25.84        17.33        27.65        73.25         6.61 
TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-UN-AAZ9 
       16.01        12.85        18.02 

$`DEL PEAK  3(1Q43) WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 
      109.22        62.37        23.28        28.80        51.06        31.33 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8432 TCGA-KN-8433 
       23.47        25.91         3.55         0.99         2.50        11.21 
TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
      100.87        87.78        86.10        12.66        12.16        36.82 
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       47.21         0.53        39.16        24.16        49.08        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       37.15        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        21.86        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3372 
       82.32        51.25        10.49        28.70        74.63        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       53.29        55.76        20.71        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OW 
       20.28        15.39        22.65         0.10         0.10        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91        29.10        73.08        66.31        15.78        60.92 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       68.61        67.20        46.78        48.36        42.08        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       38.40        31.27        28.04         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 
        4.57         2.53         3.48        19.00        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
       52.21        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 
       10.29        39.45        26.07        29.03         2.27        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       52.08        15.95        62.89        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       61.32        97.41        35.90         1.68        12.30        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        11.77        10.36        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
        9.57         5.75         0.23         1.25         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       25.05        24.66        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60        14.27         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4330 TCGA-BP-4331 
       54.90        97.45        53.42         3.58        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       37.25        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       31.89        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       61.68        10.82         5.33        61.97        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       53.52        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       27.65        39.45        50.24        56.35        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       58.92        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       61.91        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83         5.39        73.18        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39        93.04         5.46        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 
        0.82        23.74        18.44        56.28        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       47.01        10.85        10.22        21.76        57.21        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
       22.52         2.40         1.94        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       56.84        23.90        66.02        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
        4.18         7.96        10.29        70.13         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        15.25        10.85         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       58.22       100.27        56.91         4.57        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       34.85        56.81        51.52        35.67        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 
       16.18        22.49         0.13        11.57        19.63        61.05 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-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 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       49.25         2.20        19.56        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
        3.55         0.46         6.58        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       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-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
       19.23        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 
       10.88         7.66         0.95        11.97         7.92       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY 
       34.19        19.00        24.89        10.68         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
       34.82        25.15        13.68         6.38        17.98        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65       194.79        12.92         3.68         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       11.84        56.75         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 
       84.95        92.58        52.27        50.60        78.90        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       48.30        43.76        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                       0.10                        0.07 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                     151.96                      194.79 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                     47.240                      29.015 
[1] "0.1 - 152.0 (47.2)" "0.1 - 194.8 (29.0)"
[1] "hr=" "1.5"
D16V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  3(1Q43) MUTATED        46       28        23       11
  DEL PEAK  3(1Q43) WILD-TYPE     402       75       167       89
D16V3, multiclass
           clus
vv          DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  STAGE I                          46                         402
  STAGE II                         28                          75
  STAGE III                        23                         167
  STAGE IV                         11                          89
[1] 4 2
[1] 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(1Q43) MUTATED    47  28  31   4
  DEL PEAK  3(1Q43) WILD-TYPE 415  95 220  11
D16V4, multiclass
    clus
vv   DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  T1                        47                         415
  T2                        28                          95
  T3                        31                         220
  T4                         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                           N0  N1  N2
  DEL PEAK  3(1Q43) MUTATED    58   5   2
  DEL PEAK  3(1Q43) WILD-TYPE 259  38   4
D16V5, multiclass
    clus
vv   DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  N0                        58                         259
  N1                         5                          38
  N2                         2                           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"
D16V6, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED    72   7
  DEL PEAK  3(1Q43) WILD-TYPE 470  82
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED     72    7
  DEL PEAK  3(1Q43) WILD-TYPE  470   82
   clus
vv  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  0                        72                         470
  1                         7                          82
[1] 2 2
[1] FALSE
D16V7, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED    44  68
  DEL PEAK  3(1Q43) WILD-TYPE 243 504
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED     44   68
  DEL PEAK  3(1Q43) WILD-TYPE  243  504
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  FEMALE                        44                         243
  MALE                          68                         504
[1] 2 2
[1] FALSE
D16V8, continuous
                             vv
clus                          KIDNEY CHROMOPHOBE
  DEL PEAK  3(1Q43) MUTATED                   51
  DEL PEAK  3(1Q43) WILD-TYPE                 15
                             vv
clus                          KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK  3(1Q43) MUTATED                                  42
  DEL PEAK  3(1Q43) WILD-TYPE                               482
                             vv
clus                          KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  3(1Q43) MUTATED                                      19
  DEL PEAK  3(1Q43) WILD-TYPE                                   250
D16V9, multiclass
                                       clus
vv                                      DEL PEAK  3(1Q43) MUTATED
  KIDNEY CHROMOPHOBE                                           51
  KIDNEY CLEAR CELL RENAL CARCINOMA                            42
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                        19
                                       clus
vv                                      DEL PEAK  3(1Q43) WILD-TYPE
  KIDNEY CHROMOPHOBE                                             15
  KIDNEY CLEAR CELL RENAL CARCINOMA                             482
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                         250
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, continuous
D16V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(1Q43) MUTATED                                  0     4
  DEL PEAK  3(1Q43) WILD-TYPE                                2    11
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q43) MUTATED                          11    92
  DEL PEAK  3(1Q43) WILD-TYPE                       105   610
D16V12, multiclass
                                  clus
vv                                 DEL PEAK  3(1Q43) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               11
  WHITE                                                   92
                                  clus
vv                                 DEL PEAK  3(1Q43) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                     11
  BLACK OR AFRICAN AMERICAN                                105
  WHITE                                                    610
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED     8  69
  DEL PEAK  3(1Q43) WILD-TYPE  34 528
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      8   69
  DEL PEAK  3(1Q43) WILD-TYPE   34  528
                        clus
vv                       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  HISPANIC OR LATINO                             8                          34
  NOT HISPANIC OR LATINO                        69                         528
[1] 2 2
[1] FALSE

Clustering(17) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.3) MUTATED    87  21
  DEL PEAK  4(2Q37.3) WILD-TYPE 545 190
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                          108                           735 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           21                           190 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       73.91        54.74       151.96        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 
      123.12       129.37        65.19       104.52         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       87.12        19.33         2.50        59.08       115.00        42.35 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       80.38       103.27        77.85        57.17        61.58        63.95 
TCGA-A3-3311 TCGA-A3-3323 TCGA-A3-3336 TCGA-A3-3374 TCGA-AK-3425 TCGA-AK-3433 
       39.16        36.36        34.29        43.20       109.91        72.07 
TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4696 TCGA-B0-4699 
       57.37        40.01        12.13        40.70        28.47         3.62 
TCGA-B0-4703 TCGA-B0-4821 TCGA-B0-4841 TCGA-B0-5095 TCGA-B0-5099 TCGA-B0-5116 
        5.98        40.44         6.71         8.05        15.95        21.60 
TCGA-B0-5117 TCGA-B0-5120 TCGA-B2-3923 TCGA-B2-5641 TCGA-B8-4620 TCGA-B8-5549 
       17.59        16.21        32.61        21.57        25.55         6.38 
TCGA-B8-A54F TCGA-B8-A54G TCGA-BP-4166 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4761 
       17.06         1.74         0.43        37.25        21.21         5.98 
TCGA-BP-4782 TCGA-BP-4991 TCGA-BP-4994 TCGA-BP-5008 TCGA-BP-5175 TCGA-BP-5177 
       11.64        46.45        43.00        35.21        30.64         9.63 
TCGA-BP-5199 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4881 TCGA-CJ-4902 
       44.55        58.95        21.24        49.25        66.21        49.97 
TCGA-CJ-6027 TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-5453 TCGA-CZ-5468 TCGA-CZ-5985 
       60.99        83.90        46.16         0.82         1.94        65.65 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-4A-A93X TCGA-A4-7585 TCGA-A4-A5Y0 TCGA-B3-4104 
       22.78        62.63        12.82        35.18         8.28        34.49 
TCGA-B9-4117 TCGA-B9-A69E TCGA-BQ-5878 TCGA-MH-A855 TCGA-Q2-A5QZ TCGA-Y8-A8RZ 
        0.46        14.86        63.72        12.13        14.07         6.74 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 
      109.22        71.41        28.80        62.37        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       51.06        31.33        23.47        87.91        25.48        25.91 
TCGA-KN-8426 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z 
        3.55        11.21       100.87        87.78        86.10        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
       12.16        36.82        47.21         0.53        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 
       49.02        37.15        49.58        48.59        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       37.38        48.82        21.86        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
       53.29        55.76        20.71        18.64        18.87        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       65.52        20.28        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       11.18        10.62        29.10        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
       15.78        60.92        68.61        67.20        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       42.08        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 
       37.58        38.40        31.27        28.04         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 
        1.41         4.57         2.53         3.48        19.00         1.38 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         7.82         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4842 
       68.71        40.70        45.30        27.42        53.88        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.90         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        2.24        21.86        52.08        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       26.20         1.94        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        61.32        97.41        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR 
       21.30        31.30        11.77        10.36        32.98        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
        9.57         5.75         0.23         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 
       27.55        25.05        24.66        17.19        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       17.16        16.60        14.27         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       27.29        29.88         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        32.61        99.85        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4335 
       53.42         3.58        27.78        62.07        80.68        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       54.77        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.33        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.62        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4993 
       25.81        36.95        27.22         3.88        16.47         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       27.62        37.48        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 
       79.30         1.78        74.20        52.27        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       24.62        33.47        19.82        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4871 
       65.69        54.61        53.52        11.05        83.97        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4903 
       39.45        59.44        50.24        56.35        47.67        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15        61.91        62.10        73.35        67.00        53.26 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 TCGA-CW-6097 
       78.18        74.66         1.35       105.93       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       25.45         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       63.42        58.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 
       57.21        47.54        22.52         2.40        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-DV-5565 TCGA-DV-5566 
       80.19        67.96        12.26        14.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        15.25        10.85         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       58.22       100.27        56.91         4.57        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK 
       34.85        56.81        54.64        51.52        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 
        5.29        16.18        22.49         0.13        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       19.63        61.05         0.10        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y1 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       33.83        10.09        30.58        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       28.18        26.40        20.61         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH 
       22.06         2.10        19.23         6.81         0.16        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 
       12.30        86.76        19.27         8.88        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       13.68        25.84         6.38        17.98        17.33        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
        0.36        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
       50.60        78.90        12.85        17.75        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         0.43                          0.07 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       151.96                        194.79 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       42.675                        29.000 
[1] "0.4 - 152.0 (42.7)" "0.1 - 194.8 (29.0)"
[1] "hr=" "1.7"
D17V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  4(2Q37.3) MUTATED        38       32        28       10
  DEL PEAK  4(2Q37.3) WILD-TYPE     410       71       162       90
D17V3, multiclass
           clus
vv          DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  STAGE I                            38                           410
  STAGE II                           32                            71
  STAGE III                          28                           162
  STAGE IV                           10                            90
[1] 4 2
[1] 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    38  34  34   3
  DEL PEAK  4(2Q37.3) WILD-TYPE 424  89 217  12
D17V4, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  T1                          38                           424
  T2                          34                            89
  T3                          34                           217
  T4                           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                             N0  N1  N2
  DEL PEAK  4(2Q37.3) MUTATED    55   5   2
  DEL PEAK  4(2Q37.3) WILD-TYPE 262  38   4
D17V5, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  N0                          55                           262
  N1                           5                            38
  N2                           2                             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"
D17V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    75   6
  DEL PEAK  4(2Q37.3) WILD-TYPE 467  83
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     75    6
  DEL PEAK  4(2Q37.3) WILD-TYPE  467   83
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                          75                           467
  1                           6                            83
[1] 2 2
[1] FALSE
D17V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    40  70
  DEL PEAK  4(2Q37.3) WILD-TYPE 247 502
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     40   70
  DEL PEAK  4(2Q37.3) WILD-TYPE  247  502
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                          40                           247
  MALE                            70                           502
[1] 2 2
[1] FALSE
D17V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK  4(2Q37.3) MUTATED                   49
  DEL PEAK  4(2Q37.3) WILD-TYPE                 17
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK  4(2Q37.3) MUTATED                                  50
  DEL PEAK  4(2Q37.3) WILD-TYPE                               474
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  4(2Q37.3) MUTATED                                      11
  DEL PEAK  4(2Q37.3) WILD-TYPE                                   258
D17V9, multiclass
                                       clus
vv                                      DEL PEAK  4(2Q37.3) MUTATED
  KIDNEY CHROMOPHOBE                                             49
  KIDNEY CLEAR CELL RENAL CARCINOMA                              50
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          11
                                       clus
vv                                      DEL PEAK  4(2Q37.3) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               17
  KIDNEY CLEAR CELL RENAL CARCINOMA                               474
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           258
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, continuous
D17V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2Q37.3) MUTATED                                  0     3
  DEL PEAK  4(2Q37.3) WILD-TYPE                                2    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED                          11    92
  DEL PEAK  4(2Q37.3) WILD-TYPE                       105   610
D17V12, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     92
                                  clus
vv                                 DEL PEAK  4(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                  105
  WHITE                                                      610
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     4  64
  DEL PEAK  4(2Q37.3) WILD-TYPE  38 533
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      4   64
  DEL PEAK  4(2Q37.3) WILD-TYPE   38  533
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          64
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           533
[1] 2 2
[1] FALSE

Clustering(18) Variable = DEL PEAK  5(3P26.3) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(3P26.3) MUTATED   335 150
  DEL PEAK  5(3P26.3) WILD-TYPE 297  61
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                          485                           358 
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                          150                            61 
$`DEL PEAK  5(3P26.3) MUTATED`
TCGA-KL-8324 TCGA-KL-8333 TCGA-KL-8335 TCGA-KN-8421 TCGA-KN-8425 TCGA-KN-8427 
      141.73        98.33        92.55        87.91       104.52         0.99 
TCGA-KN-8432 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-3Z-A93Z TCGA-A3-3306 
        2.50        80.38        77.85        57.17        12.66        36.82 
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       47.21         0.53        39.16        24.16        49.08        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       37.15        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        21.86        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       82.32        51.25        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
       53.29        55.76        20.71        18.64        18.87        28.31 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       10.62       109.91        29.10        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 
       60.92        72.07        68.61        67.20        48.36        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3458 TCGA-AK-3460 
       58.49        48.69        28.73        22.45        38.40        31.27 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       28.04         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
       28.47        19.00         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4847 TCGA-B0-4848 
        6.71        56.68        11.64        65.29        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 
        2.27        36.85        70.52        20.94        43.30        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5107 
       21.86        52.08        15.95        90.87        90.48        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       29.95        35.90        11.80        26.20        21.60         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       16.21        18.21        21.44        14.76        79.17       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       97.41        35.90        12.30        21.30        31.30        11.77 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       32.98        21.57        16.67         9.57         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 
       16.80        27.16        27.55        25.05        24.66        25.55 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
        6.38         0.53        34.39        14.30        27.29        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 
        1.74         8.42         4.93        17.36        16.27       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4176 
        0.43        89.36        23.05        77.03        61.78        64.27 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       37.25        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       31.89        11.31        12.33        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.98         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       13.15         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       68.38        11.64        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       10.98        36.95         6.71         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 
       63.62        58.68        60.30        61.22        61.51        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       25.81        36.95         3.88        46.45        16.47         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       47.18        74.27        75.06        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        3.06        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5683 
       25.71        18.87        22.32        25.25        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        5.39        85.78        73.18        66.31        78.18        74.66 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
      105.93        83.90        25.45         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
       58.75         6.77        14.66        63.39        93.04         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        57.21        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-A4W0 
       12.16        11.67        37.15        66.28        56.84        66.02 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
       18.12         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        15.25        10.85 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3473 
       54.64        51.52        38.99         8.48        12.99        25.08 
TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5892 TCGA-DZ-6131 
        2.10        14.86         8.88        21.63        11.97        79.86 
TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 
        4.01        13.68        17.33         3.68         2.04         0.13 
TCGA-Q2-A5QZ TCGA-SX-A7SU TCGA-UZ-A9PQ TCGA-WN-A9G9 TCGA-Y8-A8RZ 
       14.07        43.76        86.27        26.01         6.74 

$`DEL PEAK  5(3P26.3) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8336 TCGA-KL-8337 
      108.62        98.96        84.89        96.95        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       86.56        28.11        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       28.80        54.74        62.37       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       28.80        47.24        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 
      129.37        23.47        25.48        25.91        65.19         3.55 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12        19.33        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8416 
       92.71        16.67        87.78       103.27        86.10        61.58 
TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3385 TCGA-AK-3427 
       63.95        12.16        10.49        43.20        65.52        84.36 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 
       57.37        46.78        40.01        45.93        37.58        12.13 
TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4834 
       40.70         3.32         1.38         3.62        65.10        68.71 
TCGA-B0-4839 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-5080 TCGA-B0-5096 TCGA-B0-5100 
       53.88        10.29        39.45        11.24         2.24        62.89 
TCGA-B0-5106 TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5400 TCGA-B2-3923 TCGA-B2-4098 
       52.54        19.30        17.59        37.22        32.61         1.68 
TCGA-B2-5635 TCGA-B4-5378 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5545 
       10.36         5.75        17.19        25.91        23.01        17.16 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-A54E TCGA-B8-A54K TCGA-B8-A8YJ TCGA-BP-4165 
       16.60        14.27        29.88        15.42        14.17        99.85 
TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4334 TCGA-BP-4756 TCGA-BP-4760 TCGA-BP-4769 
       62.24        54.90        21.21        12.30        77.62        61.68 
TCGA-BP-4770 TCGA-BP-4784 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4967 
       10.82        60.95        20.38        37.25        47.97         6.74 
TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4994 TCGA-BP-5191 TCGA-CJ-4875 TCGA-CJ-4889 
       53.65        27.22        43.00        31.79        77.36        63.98 
TCGA-CJ-4890 TCGA-CJ-4920 TCGA-CJ-5681 TCGA-CW-6087 TCGA-CW-6093 TCGA-CW-6097 
       68.55         4.57        18.15         1.35       103.43        18.77 
TCGA-CZ-4854 TCGA-CZ-4862 TCGA-DV-5567 TCGA-DV-5576 TCGA-EU-5905 TCGA-2K-A9WE 
       46.16        60.59        65.88        23.90         3.91         7.04 
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-A9JJ TCGA-2Z-A9JL 
       67.30        75.42        34.85        56.81        35.67        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 
       16.18        22.49         0.13        12.82        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       12.46        16.96        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 
        9.63        58.45        76.64        13.55        30.35        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH 
       43.99        22.06        19.23         6.81         0.16        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       12.30        86.76        19.27        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       13.25        10.88         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        40.77        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        1.18         0.43        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
       34.82        25.15        25.84         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         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       26.47        48.30        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
        0.53        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       12.99        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.02        13.28 

  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                         0.07                          0.10 
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                       141.73                        194.79 
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                        36.36                         25.94 
[1] "0.1 - 141.7 (36.4)" "0.1 - 194.8 (25.9)"
[1] "hr=" "1.6"
D18V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  5(3P26.3) MUTATED       227       57       131       71
  DEL PEAK  5(3P26.3) WILD-TYPE     221       46        59       29
D18V3, multiclass
           clus
vv          DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  STAGE I                           227                           221
  STAGE II                           57                            46
  STAGE III                         131                            59
  STAGE IV                           71                            29
[1] 4 2
[1] 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(3P26.3) MUTATED   233  71 175   7
  DEL PEAK  5(3P26.3) WILD-TYPE 229  52  76   8
D18V4, multiclass
    clus
vv   DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  T1                         233                           229
  T2                          71                            52
  T3                         175                            76
  T4                           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                             N0  N1  N2
  DEL PEAK  5(3P26.3) MUTATED   212  23   1
  DEL PEAK  5(3P26.3) WILD-TYPE 105  20   5
D18V5, multiclass
    clus
vv   DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  N0                         212                           105
  N1                          23                            20
  N2                           1                             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"
D18V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P26.3) MUTATED   374  69
  DEL PEAK  5(3P26.3) WILD-TYPE 168  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.3) MUTATED    374   69
  DEL PEAK  5(3P26.3) WILD-TYPE  168   20
   clus
vv  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  0                         374                           168
  1                          69                            20
[1] 2 2
[1] FALSE
D18V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P26.3) MUTATED   175 311
  DEL PEAK  5(3P26.3) WILD-TYPE 112 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.3) MUTATED    175  311
  DEL PEAK  5(3P26.3) WILD-TYPE  112  261
        clus
vv       DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  FEMALE                         175                           112
  MALE                           311                           261
[1] 2 2
[1] FALSE
D18V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK  5(3P26.3) MUTATED                   10
  DEL PEAK  5(3P26.3) WILD-TYPE                 56
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK  5(3P26.3) MUTATED                                 453
  DEL PEAK  5(3P26.3) WILD-TYPE                                71
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  5(3P26.3) MUTATED                                      23
  DEL PEAK  5(3P26.3) WILD-TYPE                                   246
D18V9, multiclass
                                       clus
vv                                      DEL PEAK  5(3P26.3) MUTATED
  KIDNEY CHROMOPHOBE                                             10
  KIDNEY CLEAR CELL RENAL CARCINOMA                             453
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          23
                                       clus
vv                                      DEL PEAK  5(3P26.3) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               56
  KIDNEY CLEAR CELL RENAL CARCINOMA                                71
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           246
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, continuous
D18V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(3P26.3) MUTATED                                  0     7
  DEL PEAK  5(3P26.3) WILD-TYPE                                2     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P26.3) MUTATED                          41   429
  DEL PEAK  5(3P26.3) WILD-TYPE                        75   273
D18V12, multiclass
                                  clus
vv                                 DEL PEAK  5(3P26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 41
  WHITE                                                    429
                                  clus
vv                                 DEL PEAK  5(3P26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   75
  WHITE                                                      273
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P26.3) MUTATED    26 315
  DEL PEAK  5(3P26.3) WILD-TYPE  16 282
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.3) MUTATED     26  315
  DEL PEAK  5(3P26.3) WILD-TYPE   16  282
                        clus
vv                       DEL PEAK  5(3P26.3) MUTATED
  HISPANIC OR LATINO                              26
  NOT HISPANIC OR LATINO                         315
                        clus
vv                       DEL PEAK  5(3P26.3) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           282
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEL PEAK  6(3P21.2) MUTATION ANALYSIS
D19V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P21.2) MUTATED   338 160
  DEL PEAK  6(3P21.2) WILD-TYPE 294  51
  DEL PEAK  6(3P21.2) MUTATED DEL PEAK  6(3P21.2) WILD-TYPE 
                          498                           345 
  DEL PEAK  6(3P21.2) MUTATED DEL PEAK  6(3P21.2) WILD-TYPE 
                          160                            51 
$`DEL PEAK  6(3P21.2) MUTATED`
TCGA-KL-8324 TCGA-KL-8333 TCGA-KL-8341 TCGA-KN-8421 TCGA-KN-8425 TCGA-KN-8427 
      141.73        98.33        24.79        87.91       104.52         0.99 
TCGA-KN-8432 TCGA-KN-8436 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-3Z-A93Z 
        2.50        42.35        80.38        77.85        57.17        12.66 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       42.97        82.32        51.25        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       24.16        53.29        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       28.31        20.28        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3429 
       11.18        10.62       109.91        29.10        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 
       15.78        60.92        72.07        68.61        67.20        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3458 TCGA-AK-3460 
       58.49        48.69        28.73        22.45        38.40        31.27 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       28.04         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
       28.47        19.00         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       43.30        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
       90.87        90.48        30.48        29.95        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       26.20        21.60         1.94        16.21        18.21        21.44 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76        79.17        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 
       89.49        61.32        97.41        35.90        12.30        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        11.77        32.98        21.57        16.67         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       24.66        25.55        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       27.02         0.85        24.23         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       34.39        14.30        27.29        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
        4.93        17.36        16.27       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 
       89.36        23.05        77.03        61.78        64.27        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       31.89        11.31        12.33        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.98         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       13.15         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4798 
       68.38        11.64        15.78        48.95        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4969 
       58.68        60.30        61.22        61.51        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       36.95         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       51.52        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 
       58.92        49.18        49.28        50.33        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       61.91        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18        74.66       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
        6.77        14.66        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        57.21        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-A4W0 TCGA-EU-5904 
       11.67        37.15        66.28        56.84        66.02        18.12 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9JG 
        2.01        19.43        19.96        15.25        10.85        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3473 
       51.52        38.99         8.48        12.99         9.63        25.08 
TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5890 TCGA-BQ-5892 
        2.10        14.86         8.88        21.63         7.66        11.97 
TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 
       79.86         4.01        13.68        17.33        16.90         3.68 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UZ-A9PQ TCGA-WN-A9G9 TCGA-Y8-A8RZ 
        2.04         0.13        14.07        86.27        26.01         6.74 

$`DEL PEAK  6(3P21.2) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        28.11        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       28.80        54.74        62.37       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       28.80        47.24        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 
      129.37        23.47        25.48        25.91        65.19         3.55 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12        19.33        11.21        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8416 TCGA-KO-8417 
       16.67        87.78       103.27        86.10        61.58        63.95 
TCGA-6D-AA2E TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3440 
       12.16        10.49        43.20        65.52        84.36        57.37 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 
       46.78        48.36        40.01        45.93        37.58        12.13 
TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4834 
       40.70         3.32         1.38         3.62        65.10        68.71 
TCGA-B0-4839 TCGA-B0-5080 TCGA-B0-5100 TCGA-B0-5106 TCGA-B0-5109 TCGA-B0-5117 
       53.88        11.24        62.89        52.54        19.30        17.59 
TCGA-B0-5400 TCGA-B0-5691 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-5635 TCGA-B4-5378 
       37.22       112.80        32.61         1.68        10.36         5.75 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-A54E TCGA-B8-A54K 
       17.19        25.91        17.16        16.60        29.88        15.42 
TCGA-B8-A8YJ TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4756 TCGA-BP-4760 TCGA-BP-4769 
       14.17        62.24        54.90        12.30        77.62        61.68 
TCGA-BP-4770 TCGA-BP-4784 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4804 
       10.82        60.95        36.53        20.38        37.25        47.97 
TCGA-BP-4967 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4994 TCGA-CJ-4889 TCGA-CJ-4890 
        6.74        53.65        27.22        43.00        63.98        68.55 
TCGA-CJ-4912 TCGA-CW-6087 TCGA-CZ-4862 TCGA-DV-5567 TCGA-DV-5576 TCGA-EU-5905 
       54.48         1.35        60.59        65.88        23.90         3.91 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ 
        4.57        67.30        75.42        34.85        56.81        35.67 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
        5.29        16.18        22.49         0.13        12.82        11.57 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       14.33        12.46        16.96        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 
       12.46        58.45        76.64        13.55        30.35        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH 
       43.99        22.06        19.23         6.81         0.16        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       12.30        86.76        19.27        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-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       13.25        10.88         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        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-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        48.62        11.05        39.25        34.82 
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         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25         5.49        16.80        19.99        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
       67.17        22.26        21.34        16.34        12.36        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  DEL PEAK  6(3P21.2) MUTATED DEL PEAK  6(3P21.2) WILD-TYPE 
                         0.07                          0.10 
  DEL PEAK  6(3P21.2) MUTATED DEL PEAK  6(3P21.2) WILD-TYPE 
                       141.73                        194.79 
  DEL PEAK  6(3P21.2) MUTATED DEL PEAK  6(3P21.2) WILD-TYPE 
                        35.08                         26.43 
[1] "0.1 - 141.7 (35.1)" "0.1 - 194.8 (26.4)"
[1] "hr=" "2"  
D19V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  6(3P21.2) MUTATED       227       57       137       78
  DEL PEAK  6(3P21.2) WILD-TYPE     221       46        53       22
D19V3, multiclass
           clus
vv          DEL PEAK  6(3P21.2) MUTATED DEL PEAK  6(3P21.2) WILD-TYPE
  STAGE I                           227                           221
  STAGE II                           57                            46
  STAGE III                         137                            53
  STAGE IV                           78                            22
[1] 4 2
[1] 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(3P21.2) MUTATED   233  71 188   7
  DEL PEAK  6(3P21.2) WILD-TYPE 229  52  63   8
D19V4, multiclass
    clus
vv   DEL PEAK  6(3P21.2) MUTATED DEL PEAK  6(3P21.2) WILD-TYPE
  T1                         233                           229
  T2                          71                            52
  T3                         188                            63
  T4                           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                             N0  N1  N2
  DEL PEAK  6(3P21.2) MUTATED   218  26   2
  DEL PEAK  6(3P21.2) WILD-TYPE  99  17   4
D19V5, multiclass
    clus
vv   DEL PEAK  6(3P21.2) MUTATED DEL PEAK  6(3P21.2) WILD-TYPE
  N0                         218                            99
  N1                          26                            17
  N2                           2                             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"
D19V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P21.2) MUTATED   379  75
  DEL PEAK  6(3P21.2) WILD-TYPE 163  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P21.2) MUTATED    379   75
  DEL PEAK  6(3P21.2) WILD-TYPE  163   14
   clus
vv  DEL PEAK  6(3P21.2) MUTATED DEL PEAK  6(3P21.2) WILD-TYPE
  0                         379                           163
  1                          75                            14
[1] 2 2
[1] FALSE
D19V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P21.2) MUTATED   177 322
  DEL PEAK  6(3P21.2) WILD-TYPE 110 250
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P21.2) MUTATED    177  322
  DEL PEAK  6(3P21.2) WILD-TYPE  110  250
        clus
vv       DEL PEAK  6(3P21.2) MUTATED DEL PEAK  6(3P21.2) WILD-TYPE
  FEMALE                         177                           110
  MALE                           322                           250
[1] 2 2
[1] FALSE
D19V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK  6(3P21.2) MUTATED                   11
  DEL PEAK  6(3P21.2) WILD-TYPE                 55
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK  6(3P21.2) MUTATED                                 463
  DEL PEAK  6(3P21.2) WILD-TYPE                                61
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  6(3P21.2) MUTATED                                      25
  DEL PEAK  6(3P21.2) WILD-TYPE                                   244
D19V9, multiclass
                                       clus
vv                                      DEL PEAK  6(3P21.2) MUTATED
  KIDNEY CHROMOPHOBE                                             11
  KIDNEY CLEAR CELL RENAL CARCINOMA                             463
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          25
                                       clus
vv                                      DEL PEAK  6(3P21.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               55
  KIDNEY CLEAR CELL RENAL CARCINOMA                                61
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           244
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, continuous
D19V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(3P21.2) MUTATED                                  0     8
  DEL PEAK  6(3P21.2) WILD-TYPE                                2     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P21.2) MUTATED                          41   442
  DEL PEAK  6(3P21.2) WILD-TYPE                        75   260
D19V12, multiclass
                                  clus
vv                                 DEL PEAK  6(3P21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 41
  WHITE                                                    442
                                  clus
vv                                 DEL PEAK  6(3P21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   75
  WHITE                                                      260
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P21.2) MUTATED    24 328
  DEL PEAK  6(3P21.2) WILD-TYPE  18 269
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P21.2) MUTATED     24  328
  DEL PEAK  6(3P21.2) WILD-TYPE   18  269
                        clus
vv                       DEL PEAK  6(3P21.2) MUTATED
  HISPANIC OR LATINO                              24
  NOT HISPANIC OR LATINO                         328
                        clus
vv                       DEL PEAK  6(3P21.2) WILD-TYPE
  HISPANIC OR LATINO                                18
  NOT HISPANIC OR LATINO                           269
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK  7(3P14.1) MUTATION ANALYSIS
D20V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P14.1) MUTATED   277 128
  DEL PEAK  7(3P14.1) WILD-TYPE 355  83
  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE 
                          405                           438 
  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE 
                          128                            83 
$`DEL PEAK  7(3P14.1) MUTATED`
TCGA-KL-8324 TCGA-KL-8333 TCGA-KL-8341 TCGA-KN-8421 TCGA-KN-8425 TCGA-KN-8427 
      141.73        98.33        24.79        87.91       104.52         0.99 
TCGA-KN-8432 TCGA-KN-8436 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-3Z-A93Z 
        2.50        42.35        80.38        77.85        57.17        12.66 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       36.82        47.21        39.16        24.16        49.08        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       37.15        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3351 
       48.82        21.86        34.29         4.50        52.93        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        42.97        82.32        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       18.87        28.31        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3429 
        0.10        11.18        10.62       109.91        29.10        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 
       15.78        60.92        72.07        68.61        67.20        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3458 TCGA-AK-3460 
       58.49        48.69        28.73        22.45        38.40        31.27 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
       28.04         1.41         1.41         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       19.00         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 
        6.64        15.72        46.59         0.59        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
        6.71        56.68        11.64        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5084 
       29.03         2.27        70.52        20.94        43.30         7.30 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5108 TCGA-B0-5110 
       52.08        15.95        90.87        90.48        29.95        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 
       11.80        26.20        21.60         1.94        16.21        21.44 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5696 
       14.76        79.17        48.89       101.13        15.78        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       35.90        12.30        11.77        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
        9.57         0.23         1.25         0.53         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-4622 
        0.23        23.31        16.80        27.16        25.55        23.01 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5549 TCGA-B8-5551 
       23.74         1.18        27.02         0.85         6.38         0.53 
TCGA-B8-5552 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       34.39        27.29        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4163 TCGA-BP-4164 
       17.36       111.02        85.51        94.72        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4174 
       99.85         0.43        89.36        23.05        77.03        61.78 
TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4331 TCGA-BP-4332 
       64.27        97.45         3.58        27.78        80.68        37.25 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       93.99        18.48        52.24        74.17        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4758 
       49.08        44.94        31.89        11.31        12.33        72.59 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 
        5.98        41.75        71.80        48.07        13.15         5.33 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4789 
       61.97        13.51        56.91        68.38        11.64        48.95 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 
       36.39        10.98        36.95         6.71         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4971 
       71.41        63.62        58.68        60.30        61.51        48.89 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
        7.23        47.11        14.93        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       25.81        36.95         3.88        46.45        16.47         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5006 
       45.07        30.64        41.62        18.51        37.02        27.62 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87        48.10         6.35         1.78        74.20 
TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
       52.27        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.25        37.22        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       34.95        31.27        59.84        46.55        63.25        73.22 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       65.69        54.61        53.52        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 
       83.97        49.25        79.66        74.27        75.06        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       71.87        66.21        61.91        64.18        30.64        51.52 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 
       26.93        50.01        24.66        27.65        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4908 
       56.35        47.67        49.97        51.29        58.92        50.33 
TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       45.14        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5689 
       18.87        22.32        61.91        62.10        73.35        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       60.99        53.42        75.58        83.77         7.36        64.57 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       81.83         5.39        73.18        66.31        78.18        74.66 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
      105.93        83.90        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4863 TCGA-CZ-4864 
       47.08        69.21        58.75         6.77        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5457 
        5.46        63.42        58.82         0.82        18.44        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5982 
       57.21        47.54        22.52         1.94        31.10        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        37.15        66.28        56.84 
TCGA-DV-A4W0 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 
       66.02         6.77         4.18        10.29        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9JG TCGA-2Z-A9JI 
       19.43        19.96        15.25        10.85        54.64        51.52 
TCGA-2Z-A9JK TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3473 TCGA-B9-A44B TCGA-B9-A69E 
       38.99         8.48        12.99        25.08         2.10        14.86 
TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-DZ-6131 TCGA-G7-6789 
        8.88        21.63         7.66        11.97        79.86         4.01 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ 
       17.33        16.90         3.68         2.04         0.13        14.07 
TCGA-UZ-A9PQ TCGA-WN-A9G9 TCGA-Y8-A8RZ 
       86.27        26.01         6.74 

$`DEL PEAK  7(3P14.1) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        28.11        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       28.80        54.74        62.37       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       28.80        47.24        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 
      129.37        23.47        25.48        25.91        65.19         3.55 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12        19.33        11.21        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8416 TCGA-KO-8417 
       16.67        87.78       103.27        86.10        61.58        63.95 
TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3326 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3362 
       12.16         0.53        37.38        31.07        45.53        51.25 
TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3440 
       10.49        43.20        65.52        84.36        73.08        57.37 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 
       46.78        48.36        40.01        45.93        37.58        12.13 
TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
       40.70         3.32         4.57         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4814 TCGA-B0-4819 TCGA-B0-4834 
        7.82         3.25        20.25         5.52         6.02        68.71 
TCGA-B0-4839 TCGA-B0-4844 TCGA-B0-4852 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 
       53.88        10.29        36.85        11.24        11.90        25.32 
TCGA-B0-5100 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5121 
       62.89        52.54        30.48        19.30        17.59        18.21 
TCGA-B0-5400 TCGA-B0-5691 TCGA-B0-5695 TCGA-B0-5705 TCGA-B0-5812 TCGA-B2-3923 
       37.22       112.80        46.68       120.59        97.41        32.61 
TCGA-B2-4098 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B4-5378 TCGA-B4-5838 
        1.68        21.30        31.30        10.36         5.75         5.46 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-5158 
       27.55        25.05        24.66        17.19        25.91        20.91 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5553 TCGA-B8-A54E 
       24.23        17.16        16.60        14.27        14.30        29.88 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4173 
       15.42        16.27        14.17        90.28       101.06        62.24 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       54.90        53.42        62.07        21.21        15.16         0.07 
TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4759 TCGA-BP-4760 
       12.23        33.99        31.33        12.30        77.98        77.62 
TCGA-BP-4762 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4775 TCGA-BP-4784 TCGA-BP-4787 
       44.15        61.68        10.82        60.59        60.95        15.78 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4964 TCGA-BP-4967 
       36.53        20.38        37.25        47.97        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4976 
       57.40        58.98        14.24        49.38        45.50        53.65 
TCGA-BP-4981 TCGA-BP-4988 TCGA-BP-4994 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5009 
       36.07        27.22        43.00        38.70        37.48        36.23 
TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5186 TCGA-BP-5202 TCGA-CJ-4638 
       79.30        30.64         9.63        22.78         0.95        14.17 
TCGA-CJ-4639 TCGA-CJ-4872 TCGA-CJ-4875 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4889 
       75.88        47.18        77.36        57.83        69.86        63.98 
TCGA-CJ-4890 TCGA-CJ-4897 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-4913 
       68.55        59.44        49.18        49.28        54.48        38.56 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5686 
        3.06         4.57        18.81        25.25        18.15        67.00 
TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-6087 TCGA-CW-6093 TCGA-CZ-4861 
       62.66        92.02        85.78         1.35       103.43        14.66 
TCGA-CZ-4862 TCGA-CZ-4866 TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5467 TCGA-CZ-5470 
       60.59        61.41        23.74        56.28         2.40        12.69 
TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-G6-A5PC 
       65.88        11.67        23.90        18.12         3.91         7.96 
TCGA-G6-A8L7 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       70.13         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       56.91         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       35.67        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       25.58         5.29        16.18        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       11.57        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.73        14.33        12.46        16.96        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        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       30.35        44.61        49.25         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        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         6.81 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
        0.16        17.49        12.30        86.76        19.27        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.20        47.80        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5893 
       26.04        25.35        13.25        10.88         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        40.77        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       54.90        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       17.98        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       16.34        12.36        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        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        12.85        17.75        47.90        47.44        33.04 
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        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       41.62        26.47        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       14.83        21.93         0.53        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       25.68        27.39        12.99        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        15.62        25.28         6.02        13.28 

  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE 
                       141.73                        194.79 
  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE 
                        36.36                         27.14 
[1] "0.1 - 141.7 (36.4)" "0.1 - 194.8 (27.1)"
[1] "hr=" "1.5"
D20V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  7(3P14.1) MUTATED       187       49       112       57
  DEL PEAK  7(3P14.1) WILD-TYPE     261       54        78       43
D20V3, multiclass
           clus
vv          DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE
  STAGE I                           187                           261
  STAGE II                           49                            54
  STAGE III                         112                            78
  STAGE IV                           57                            43
[1] 4 2
[1] 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(3P14.1) MUTATED   191  60 149   5
  DEL PEAK  7(3P14.1) WILD-TYPE 271  63 102  10
D20V4, multiclass
    clus
vv   DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE
  T1                         191                           271
  T2                          60                            63
  T3                         149                           102
  T4                           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                             N0  N1  N2
  DEL PEAK  7(3P14.1) MUTATED   177  19   2
  DEL PEAK  7(3P14.1) WILD-TYPE 140  24   4
D20V5, multiclass
    clus
vv   DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE
  N0                         177                           140
  N1                          19                            24
  N2                           2                             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  7(3P14.1) MUTATED   310  54
  DEL PEAK  7(3P14.1) WILD-TYPE 232  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.1) MUTATED    310   54
  DEL PEAK  7(3P14.1) WILD-TYPE  232   35
   clus
vv  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE
  0                         310                           232
  1                          54                            35
[1] 2 2
[1] FALSE
D20V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.1) MUTATED   126 279
  DEL PEAK  7(3P14.1) WILD-TYPE 161 293
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.1) MUTATED    126  279
  DEL PEAK  7(3P14.1) WILD-TYPE  161  293
        clus
vv       DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE
  FEMALE                         126                           161
  MALE                           279                           293
[1] 2 2
[1] FALSE
D20V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK  7(3P14.1) MUTATED                   11
  DEL PEAK  7(3P14.1) WILD-TYPE                 55
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK  7(3P14.1) MUTATED                                 371
  DEL PEAK  7(3P14.1) WILD-TYPE                               153
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  7(3P14.1) MUTATED                                      23
  DEL PEAK  7(3P14.1) WILD-TYPE                                   246
D20V9, multiclass
                                       clus
vv                                      DEL PEAK  7(3P14.1) MUTATED
  KIDNEY CHROMOPHOBE                                             11
  KIDNEY CLEAR CELL RENAL CARCINOMA                             371
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          23
                                       clus
vv                                      DEL PEAK  7(3P14.1) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               55
  KIDNEY CLEAR CELL RENAL CARCINOMA                               153
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           246
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, continuous
D20V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3P14.1) MUTATED                                  0     7
  DEL PEAK  7(3P14.1) WILD-TYPE                                2     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P14.1) MUTATED                          35   356
  DEL PEAK  7(3P14.1) WILD-TYPE                        81   346
D20V12, multiclass
                                  clus
vv                                 DEL PEAK  7(3P14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 35
  WHITE                                                    356
                                  clus
vv                                 DEL PEAK  7(3P14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   81
  WHITE                                                      346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.1) MUTATED    20 267
  DEL PEAK  7(3P14.1) WILD-TYPE  22 330
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.1) MUTATED     20  267
  DEL PEAK  7(3P14.1) WILD-TYPE   22  330
                        clus
vv                       DEL PEAK  7(3P14.1) MUTATED
  HISPANIC OR LATINO                              20
  NOT HISPANIC OR LATINO                         267
                        clus
vv                       DEL PEAK  7(3P14.1) WILD-TYPE
  HISPANIC OR LATINO                                22
  NOT HISPANIC OR LATINO                           330
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK  8(3P12.2) MUTATION ANALYSIS
D21V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3P12.2) MUTATED   225 109
  DEL PEAK  8(3P12.2) WILD-TYPE 407 102
  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE 
                          334                           509 
  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE 
                          109                           102 
$`DEL PEAK  8(3P12.2) MUTATED`
TCGA-KL-8324 TCGA-KL-8333 TCGA-KL-8341 TCGA-KN-8421 TCGA-KN-8425 TCGA-KN-8427 
      141.73        98.33        24.79        87.91       104.52         0.99 
TCGA-KN-8432 TCGA-KN-8436 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-3Z-A93Z 
        2.50        42.35        80.38        77.85        57.17        12.66 
TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
       36.82        39.16        24.16        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3331 TCGA-A3-3335 
       48.59        36.36        38.99        24.69        48.82        21.86 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        4.50        52.93        18.44        88.37        42.97        82.32 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3378 
       28.70        74.63        74.76        24.16        53.29        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.64        18.87        28.31        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3429 
        0.10         0.10        11.18        10.62       109.91        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 
       15.78        60.92        72.07        68.61        67.20        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       58.49        48.69        28.73        38.40        31.27        28.04 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4703 
        1.41         1.41         2.53         3.48        28.47         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4810 TCGA-B0-4811 
        2.14        19.73        43.96         6.64        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
        0.59        52.21        33.50        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 
       27.42         6.71        56.68        11.64        65.29        39.45 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5077 TCGA-B0-5084 TCGA-B0-5092 
       29.03         2.27        70.52        43.30         7.30        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5108 
       10.95         8.05        52.08        15.95        90.87        29.95 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 
       11.80        26.20        21.60         1.94        16.21        21.44 
TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5697 TCGA-B0-5699 
       14.76        48.89       101.13        15.78        60.33        90.12 
TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5712 TCGA-B2-3924 
       39.55        79.36       102.48        47.97        89.49        35.90 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 
       11.77        32.98        21.57        16.67         9.57         0.23 
TCGA-B4-5834 TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
        1.25        27.16        25.55         1.18        27.02         0.85 
TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
        6.38         0.53        34.39        27.29        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4166 
        8.42         4.93       111.02        94.72        32.61         0.43 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4327 
       23.05        77.03        61.78        64.27        97.45         3.58 
TCGA-BP-4329 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4342 
       27.78        80.68        37.25        93.99        18.48        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 
       62.86        54.77        49.08        44.94        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4758 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4768 
       12.33        72.59         5.98        41.75        48.07        13.15 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4789 TCGA-BP-4798 
        5.33        61.97        56.91        68.38        48.95        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4971 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4985 
       58.68        60.30        48.89         7.23        47.11        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       25.81        36.95         3.88        46.45        16.47         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5006 
       45.07        30.64        41.62        18.51        37.02        27.62 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       35.21        28.87        48.10         1.78        74.20        52.27 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5195 
       37.22        13.35        27.02        33.24        31.79        24.62 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4634 TCGA-CJ-4635 
       19.82        44.55        34.95        31.27        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
       63.25        65.69        54.61        53.52        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4881 
       21.24        83.97        49.25        74.27        64.27        66.21 
TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4891 TCGA-CJ-4892 
       61.91        64.18        30.64        51.52        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        27.65        39.45        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5677 
       49.97        51.29        58.92        63.88        72.00        25.71 
TCGA-CJ-5679 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5689 TCGA-CJ-6027 
       22.32        18.15        61.91        62.10        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 
       53.42        75.58        83.77         7.36        64.57        81.83 
TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 
        5.39        73.18        78.18        74.66       105.93        83.90 
TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4863 
       18.77        46.16         0.59        69.21        58.75        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 
       93.04         5.46        63.42        58.82         0.82        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       56.94        55.33        10.85        10.22        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5982 TCGA-CZ-5984 
       47.54        22.52         1.94        31.10        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       45.96        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-A4W0 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 
       66.02         6.77         4.18        10.29        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
       19.43        19.96        10.85        54.64        51.52        38.99 
TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3473 TCGA-B9-A44B TCGA-BQ-5877 TCGA-BQ-5882 
        8.48        12.99        25.08         2.10         8.88        21.63 
TCGA-BQ-5890 TCGA-BQ-5892 TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y 
        7.66        11.97         4.01        17.33         3.68         2.04 
TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UZ-A9PQ TCGA-Y8-A8RZ 
        0.13        14.07        86.27         6.74 

$`DEL PEAK  8(3P12.2) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        28.11        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       28.80        54.74        62.37       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       28.80        47.24        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 
      129.37        23.47        25.48        25.91        65.19         3.55 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12        19.33        11.21        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8416 TCGA-KO-8417 
       16.67        87.78       103.27        86.10        61.58        63.95 
TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3326 TCGA-A3-3336 
       12.16        47.21         0.53        49.08        37.38        34.29 
TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3374 
       31.07        45.53        29.92        51.25        10.49        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3440 
       55.76        65.52        29.10        84.36        73.08        57.37 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3455 TCGA-AK-3456 
       46.78        48.36        40.01        45.93        22.45        37.58 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4697 TCGA-B0-4698 
       12.13        40.70         3.32         4.57        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 
        3.62        65.10         7.82         3.16         3.25        20.25 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4834 TCGA-B0-4839 
        5.52        45.07        16.77         6.02        68.71        53.88 
TCGA-B0-4844 TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5081 
       10.29        26.07        36.85        20.94        11.24        11.90 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5100 TCGA-B0-5104 
       25.32        18.51         2.24        21.86        62.89        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5117 TCGA-B0-5121 
       52.54        30.48        19.30        35.90        17.59        18.21 
TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5698 
       37.22        79.17       112.80        46.68        56.78        84.92 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 
       56.94        52.77       120.59        96.36        61.32        97.41 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 
       32.61         1.68        12.30        21.30        31.30        10.36 
TCGA-B4-5378 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        5.75         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       23.31        16.80        27.55        25.05        24.66        17.19 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5165 TCGA-B8-5545 
       25.91        23.01        20.91        23.74        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5553 TCGA-B8-A54E TCGA-B8-A54J TCGA-B8-A54K 
       16.60        14.27        14.30        29.88        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       16.27        14.17        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4330 
       99.85        89.36        62.24        54.90        53.42        62.07 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4341 TCGA-BP-4349 TCGA-BP-4354 
       21.21        15.16         0.07        52.24        12.23        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4765 
       31.33        12.30        77.98        77.62        44.15        71.80 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 
       61.68        10.82        60.59        13.51        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4799 TCGA-BP-4804 
       15.78        36.53        20.38        36.39        37.25        47.97 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       49.38        45.50        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4988 TCGA-BP-4994 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5009 
       46.45        27.22        43.00        38.70        37.48        36.23 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5186 TCGA-BP-5192 
        6.35        79.30        30.64         9.63        22.78        23.47 
TCGA-BP-5194 TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       13.41        33.47         0.95        73.22        14.17        75.88 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4884 
       79.66        47.18        75.06        77.36        71.87        57.83 
TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4897 TCGA-CJ-4905 TCGA-CJ-4907 
       69.86        63.98        68.55        59.44        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5684 
       18.81        79.89        84.66        18.87        25.25        73.35 
TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-6087 
       67.00        62.66        92.02        85.78        66.31         1.35 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
      103.43        25.45        47.08         6.77        14.66        60.59 
TCGA-CZ-4866 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5467 
       61.41        23.74        18.44        56.28        47.01         2.40 
TCGA-CZ-5470 TCGA-DV-5567 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-G6-A5PC 
       12.69        65.88        23.90        18.12         3.91         7.96 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       70.13        15.25         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
      100.27        56.91         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       56.81        35.67        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU 
       19.63        19.73        14.33        12.46        16.96        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
       15.75         8.28        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       13.55        30.35        44.61        49.25         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-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 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       19.27        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-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95         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 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-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        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       13.68        25.84         6.38        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       56.75        73.25         5.49        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       48.30        43.76        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
        0.53        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.02        13.28 

  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE 
                       141.73                        194.79 
  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE 
                       36.675                        27.650 
[1] "0.1 - 141.7 (36.7)" "0.1 - 194.8 (27.6)"
[1] "hr=" "1.6"
D21V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  8(3P12.2) MUTATED       156       42        89       47
  DEL PEAK  8(3P12.2) WILD-TYPE     292       61       101       53
D21V3, multiclass
           clus
vv          DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE
  STAGE I                           156                           292
  STAGE II                           42                            61
  STAGE III                          89                           101
  STAGE IV                           47                            53
[1] 4 2
[1] 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(3P12.2) MUTATED   160  51 119   4
  DEL PEAK  8(3P12.2) WILD-TYPE 302  72 132  11
D21V4, multiclass
    clus
vv   DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE
  T1                         160                           302
  T2                          51                            72
  T3                         119                           132
  T4                           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                             N0  N1  N2
  DEL PEAK  8(3P12.2) MUTATED   146  16   2
  DEL PEAK  8(3P12.2) WILD-TYPE 171  27   4
D21V5, multiclass
    clus
vv   DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE
  N0                         146                           171
  N1                          16                            27
  N2                           2                             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"
D21V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.2) MUTATED   255  44
  DEL PEAK  8(3P12.2) WILD-TYPE 287  45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.2) MUTATED    255   44
  DEL PEAK  8(3P12.2) WILD-TYPE  287   45
   clus
vv  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE
  0                         255                           287
  1                          44                            45
[1] 2 2
[1] FALSE
D21V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.2) MUTATED   100 234
  DEL PEAK  8(3P12.2) WILD-TYPE 187 338
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.2) MUTATED    100  234
  DEL PEAK  8(3P12.2) WILD-TYPE  187  338
        clus
vv       DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE
  FEMALE                         100                           187
  MALE                           234                           338
[1] 2 2
[1] FALSE
D21V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK  8(3P12.2) MUTATED                   11
  DEL PEAK  8(3P12.2) WILD-TYPE                 55
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK  8(3P12.2) MUTATED                                 304
  DEL PEAK  8(3P12.2) WILD-TYPE                               220
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  8(3P12.2) MUTATED                                      19
  DEL PEAK  8(3P12.2) WILD-TYPE                                   250
D21V9, multiclass
                                       clus
vv                                      DEL PEAK  8(3P12.2) MUTATED
  KIDNEY CHROMOPHOBE                                             11
  KIDNEY CLEAR CELL RENAL CARCINOMA                             304
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          19
                                       clus
vv                                      DEL PEAK  8(3P12.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               55
  KIDNEY CLEAR CELL RENAL CARCINOMA                               220
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           250
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, continuous
D21V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(3P12.2) MUTATED                                  0     6
  DEL PEAK  8(3P12.2) WILD-TYPE                                2     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3P12.2) MUTATED                          30   292
  DEL PEAK  8(3P12.2) WILD-TYPE                        86   410
D21V12, multiclass
                                  clus
vv                                 DEL PEAK  8(3P12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 30
  WHITE                                                    292
                                  clus
vv                                 DEL PEAK  8(3P12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   86
  WHITE                                                      410
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.2) MUTATED    14 223
  DEL PEAK  8(3P12.2) WILD-TYPE  28 374
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.2) MUTATED     14  223
  DEL PEAK  8(3P12.2) WILD-TYPE   28  374
                        clus
vv                       DEL PEAK  8(3P12.2) MUTATED
  HISPANIC OR LATINO                              14
  NOT HISPANIC OR LATINO                         223
                        clus
vv                       DEL PEAK  8(3P12.2) WILD-TYPE
  HISPANIC OR LATINO                                28
  NOT HISPANIC OR LATINO                           374
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK  9(4Q34.3) MUTATION ANALYSIS
D22V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4Q34.3) MUTATED    60  50
  DEL PEAK  9(4Q34.3) WILD-TYPE 572 161
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          110                           733 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                           50                           161 
$`DEL PEAK  9(4Q34.3) MUTATED`
TCGA-KN-8427 TCGA-KN-8428 TCGA-KO-8408 TCGA-A3-3316 TCGA-A3-3320 TCGA-A3-3346 
        0.99        52.27        16.67        49.08        49.58         4.50 
TCGA-A3-3352 TCGA-A3-3367 TCGA-A3-3380 TCGA-AK-3436 TCGA-AK-3458 TCGA-B0-4688 
       18.44        74.63        18.64        67.20        38.40         3.32 
TCGA-B0-4690 TCGA-B0-4698 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4811 
        1.41         1.38        19.73         3.16        43.96        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 
        0.59         5.52        52.21        40.44        36.53        10.09 
TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-5084 TCGA-B0-5095 
       40.70        10.29        65.29        36.85         7.30         8.05 
TCGA-B0-5098 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5691 TCGA-B0-5699 TCGA-B0-5701 
       52.08        11.80        21.60       112.80        90.12        56.94 
TCGA-B0-5709 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-5158 TCGA-B8-5162 
      102.48         5.46        23.31        16.80        20.91         1.18 
TCGA-B8-5549 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4353 
        6.38        90.28        32.61        62.86        31.89        12.33 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4787 TCGA-BP-4985 TCGA-BP-5173 TCGA-BP-5183 
       13.15        10.82        15.78        31.30         1.78        42.44 
TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4636 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4870 
       33.47        19.82        63.25        58.95        11.05        49.25 
TCGA-CJ-4881 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5676 TCGA-CJ-5677 
       66.21        59.44        51.29        49.28        84.66        25.71 
TCGA-CJ-5679 TCGA-CJ-6028 TCGA-CW-5580 TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 
       22.32        53.42        64.57        66.31        83.90        18.77 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5461 
       47.08        69.21         6.77        61.41        55.33        10.85 
TCGA-CZ-5465 TCGA-CZ-5469 TCGA-EU-5907 TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7287 
       47.54        31.10         4.18        51.52        12.82        19.63 
TCGA-A4-8098 TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-3926 
       29.46         8.48        12.99        49.25         7.33        10.09 
TCGA-B3-4104 TCGA-BQ-5876 TCGA-BQ-5882 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-DZ-6131 
       34.49        19.27        21.63         7.66         2.76        79.86 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-7501 TCGA-GL-7966 TCGA-HE-A5NK 
       10.68        13.08         0.43        13.68         3.68        73.25 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-AAVK TCGA-Q2-A5QZ 
        2.04         0.13        42.94         6.61        52.27        14.07 
TCGA-SX-A7SS TCGA-UN-AAZ9 
       48.30        18.02 

$`DEL PEAK  9(4Q34.3) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8429 
       25.48        25.91        65.19       104.52         3.55        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78       103.27        86.10        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       61.58        63.95        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3322 
        0.53        39.16        24.16        49.02        37.15        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        24.69        37.38        48.82        21.86 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
       34.29        31.07        52.93        45.53        29.92        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3370 
       42.97        82.32        51.25        10.49        28.70        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 
       24.16        53.29        43.20        55.76        20.71        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       73.08        66.31        15.78        60.92        72.07        68.61 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       57.37        46.78        48.36        42.08        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 
       48.69        45.93        28.73        22.45        37.58        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 
       28.04        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
        3.48        28.47        19.00         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        5.98         2.14         6.64         3.25        20.25        15.72 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 
       45.07        33.50        16.77         6.02        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       29.10        78.44        68.71        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
        6.71        56.68        11.64        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
        2.27        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 
       25.32        18.51        15.09        10.95         2.24        21.86 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
       29.95        19.30        35.90        26.20        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       16.21        18.21        21.44        37.22        14.76        79.17 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5710 
       84.92        52.77        39.55       120.59        79.36        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67         9.57         5.75         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4148 
        1.25         0.53         4.64         0.36         0.23        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.01        23.74        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60        14.27         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 
       74.17        54.77        49.08        44.94        12.23        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        60.95        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       36.07        33.34        46.45        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
       79.30        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        49.15        38.30        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       53.52        21.24        83.97        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06        77.36        64.27        71.87        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 
       26.93        50.01        24.66        27.65        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
       56.35        47.67        49.97        58.92        49.18        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 
       63.88        72.00        79.89        18.87        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       61.91        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 
       75.58        62.66        83.77         7.36        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
        5.39        85.78        73.18        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 
      105.93       103.43        25.45        46.16         0.59        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       14.66        60.59        63.39        93.04         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 
       58.82         0.82        23.74        18.44        56.28        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
       55.33        47.01        10.22        21.76        57.21        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40         1.94        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC 
       23.90        66.02        18.12         3.91         6.77         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.25        10.85         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
      100.27        56.91         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       56.81        54.64        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       24.33        31.20        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 
       22.49         0.13        11.57        18.21        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8310 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-A5DU TCGA-A4-A5XZ 
       19.73        14.33        12.46        16.96        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        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       33.83        30.58        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        12.30        86.76         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       43.20        47.80        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       25.35        13.25        10.88         0.95        11.97         7.92 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        40.77        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 
       34.19        19.00        24.89         2.40         1.18         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84         6.38        17.98        17.33        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       56.75         5.49        16.80        19.99        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
       67.17        22.26        21.34        16.34        12.36        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM 
       99.78        87.22        84.95        92.58        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       78.90        12.85        17.75        47.90        47.44        33.04 
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        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       41.62        26.47        43.76        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                         0.13                          0.07 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                       112.80                        194.79 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                       22.815                        30.640 
[1] "0.1 - 112.8 (22.8)" "0.1 - 194.8 (30.6)"
[1] "hr=" "2.5"
D22V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  9(4Q34.3) MUTATED        26       10        48       24
  DEL PEAK  9(4Q34.3) WILD-TYPE     422       93       142       76
D22V3, multiclass
           clus
vv          DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  STAGE I                            26                           422
  STAGE II                           10                            93
  STAGE III                          48                           142
  STAGE IV                           24                            76
[1] 4 2
[1] 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(4Q34.3) MUTATED    29  14  59   7
  DEL PEAK  9(4Q34.3) WILD-TYPE 433 109 192   8
D22V4, multiclass
    clus
vv   DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  T1                          29                           433
  T2                          14                           109
  T3                          59                           192
  T4                           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                             N0  N1  N2
  DEL PEAK  9(4Q34.3) MUTATED    40  13   0
  DEL PEAK  9(4Q34.3) WILD-TYPE 277  30   6
D22V5, multiclass
    clus
vv   DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  N0                          40                           277
  N1                          13                            30
  N2                           0                             6
[1] 3 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  9(4Q34.3) MUTATED    71  21
  DEL PEAK  9(4Q34.3) WILD-TYPE 471  68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED     71   21
  DEL PEAK  9(4Q34.3) WILD-TYPE  471   68
   clus
vv  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  0                          71                           471
  1                          21                            68
[1] 2 2
[1] FALSE
D22V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q34.3) MUTATED    38  73
  DEL PEAK  9(4Q34.3) WILD-TYPE 249 499
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED     38   73
  DEL PEAK  9(4Q34.3) WILD-TYPE  249  499
        clus
vv       DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  FEMALE                          38                           249
  MALE                            73                           499
[1] 2 2
[1] FALSE
D22V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK  9(4Q34.3) MUTATED                    3
  DEL PEAK  9(4Q34.3) WILD-TYPE                 63
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                                  78
  DEL PEAK  9(4Q34.3) WILD-TYPE                               446
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                                      30
  DEL PEAK  9(4Q34.3) WILD-TYPE                                   239
D22V9, multiclass
                                       clus
vv                                      DEL PEAK  9(4Q34.3) MUTATED
  KIDNEY CHROMOPHOBE                                              3
  KIDNEY CLEAR CELL RENAL CARCINOMA                              78
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          30
                                       clus
vv                                      DEL PEAK  9(4Q34.3) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               63
  KIDNEY CLEAR CELL RENAL CARCINOMA                               446
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           239
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, continuous
D22V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(4Q34.3) MUTATED                                  0     4
  DEL PEAK  9(4Q34.3) WILD-TYPE                                2    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4Q34.3) MUTATED                           8    93
  DEL PEAK  9(4Q34.3) WILD-TYPE                       108   609
D22V12, multiclass
                                  clus
vv                                 DEL PEAK  9(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     93
                                  clus
vv                                 DEL PEAK  9(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                  108
  WHITE                                                      609
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V13, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q34.3) MUTATED     7  78
  DEL PEAK  9(4Q34.3) WILD-TYPE  35 519
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED      7   78
  DEL PEAK  9(4Q34.3) WILD-TYPE   35  519
                        clus
vv                       DEL PEAK  9(4Q34.3) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                          78
                        clus
vv                       DEL PEAK  9(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                35
  NOT HISPANIC OR LATINO                           519
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK 10(5P15.33) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 10(5P15.33) MUTATED    20   9
  DEL PEAK 10(5P15.33) WILD-TYPE 612 202
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                            29                            814 
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                             9                            202 
$`DEL PEAK 10(5P15.33) MUTATED`
TCGA-KL-8324 TCGA-KL-8330 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8442 
      141.73       108.62        24.79        62.37       151.96        47.24 
TCGA-KN-8431 TCGA-KO-8405 TCGA-KO-8409 TCGA-AK-3433 TCGA-B0-5107 TCGA-B8-4143 
       19.33        74.93        80.38        72.07        30.48        23.31 
TCGA-BP-4332 TCGA-BP-5010 TCGA-CJ-4901 TCGA-CZ-5469 TCGA-CZ-5988 TCGA-2Z-A9J2 
       37.25        28.87        47.67        31.10        22.78        59.01 
TCGA-2Z-A9J8 TCGA-2Z-A9JJ TCGA-A4-7286 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5894 
       67.30        35.67        18.21        63.72        22.92         2.76 
TCGA-F9-A4JJ TCGA-G7-6793 TCGA-GL-7773 TCGA-P4-A5E6 TCGA-P4-A5EA 
       10.68        11.05        12.92        99.78         6.61 

$`DEL PEAK 10(5P15.33) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        28.11        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8443 
       28.80        54.74        23.28        44.91        28.80        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87        76.90        10.68        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67        87.78       103.27        86.10        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       61.58        63.95        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        0.53        39.16        24.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       53.29        43.20        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       57.37        46.78        48.36        42.08        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       48.69        45.93        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       31.27        28.04        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       90.48        52.54        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       21.44        37.22        14.76        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       11.77        10.36        32.98        21.57        16.67         9.57 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.36         0.23        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        80.68        21.21        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 
       44.94        12.23        31.89        11.31        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       44.15        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       54.61        53.52        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        5.39        85.78        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        57.21        47.54        22.52         2.40         1.94 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        75.55        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
       75.42        34.85        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
        5.29        16.18        22.49         0.13        12.82        11.57 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       12.99        12.46         9.63        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       30.35        25.08        44.61        49.25         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23         6.81         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
       86.76        19.27         8.88        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 
       10.88         7.66         0.95        11.97         7.92       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       34.19        19.00        24.89        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        0.43         4.01        51.78        48.62        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        13.68        25.84         6.38        17.98        17.33 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       16.90        80.65       194.79         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E7 
        0.36        12.13        25.97        21.44        15.48        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       78.90        12.85        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                          2.76                           0.07 
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                        151.96                         194.79 
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                        35.670                         30.365 
[1] "2.8 - 152.0 (35.7)" "0.1 - 194.8 (30.4)"
[1] "hr=" "1"  
D23V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 10(5P15.33) MUTATED         7        9         9        5
  DEL PEAK 10(5P15.33) WILD-TYPE     441       94       181       95
D23V3, multiclass
           clus
vv          DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE
  STAGE I                              7                            441
  STAGE II                             9                             94
  STAGE III                            9                            181
  STAGE IV                             5                             95
[1] 4 2
[1] 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(5P15.33) MUTATED     7  11  13   0
  DEL PEAK 10(5P15.33) WILD-TYPE 455 112 238  15
D23V4, multiclass
    clus
vv   DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE
  T1                            7                            455
  T2                           11                            112
  T3                           13                            238
  T4                            0                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 10(5P15.33) MUTATED    13   5   2
  DEL PEAK 10(5P15.33) WILD-TYPE 304  38   4
D23V5, multiclass
    clus
vv   DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE
  N0                           13                            304
  N1                            5                             38
  N2                            2                              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"
D23V6, binary
                                cls
clus                               0   1
  DEL PEAK 10(5P15.33) MUTATED    16   3
  DEL PEAK 10(5P15.33) WILD-TYPE 526  86
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(5P15.33) MUTATED     16    3
  DEL PEAK 10(5P15.33) WILD-TYPE  526   86
   clus
vv  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE
  0                           16                            526
  1                            3                             86
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                               0   1
  DEL PEAK 10(5P15.33) MUTATED    14  17
  DEL PEAK 10(5P15.33) WILD-TYPE 273 555
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(5P15.33) MUTATED     14   17
  DEL PEAK 10(5P15.33) WILD-TYPE  273  555
        clus
vv       DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE
  FEMALE                           14                            273
  MALE                             17                            555
[1] 2 2
[1] FALSE
D23V8, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  DEL PEAK 10(5P15.33) MUTATED                   10
  DEL PEAK 10(5P15.33) WILD-TYPE                 56
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 10(5P15.33) MUTATED                                   8
  DEL PEAK 10(5P15.33) WILD-TYPE                               516
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 10(5P15.33) MUTATED                                      13
  DEL PEAK 10(5P15.33) WILD-TYPE                                   256
D23V9, multiclass
                                       clus
vv                                      DEL PEAK 10(5P15.33) MUTATED
  KIDNEY CHROMOPHOBE                                              10
  KIDNEY CLEAR CELL RENAL CARCINOMA                                8
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           13
                                       clus
vv                                      DEL PEAK 10(5P15.33) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                56
  KIDNEY CLEAR CELL RENAL CARCINOMA                                516
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            256
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, continuous
D23V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(5P15.33) MUTATED                                  0     1
  DEL PEAK 10(5P15.33) WILD-TYPE                                2    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(5P15.33) MUTATED                           3    23
  DEL PEAK 10(5P15.33) WILD-TYPE                       113   679
D23V12, multiclass
                                  clus
vv                                 DEL PEAK 10(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      23
                                  clus
vv                                 DEL PEAK 10(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        14
  BLACK OR AFRICAN AMERICAN                                   113
  WHITE                                                       679
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, binary
                                cls
clus                               0   1
  DEL PEAK 10(5P15.33) MUTATED     3  18
  DEL PEAK 10(5P15.33) WILD-TYPE  39 579
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(5P15.33) MUTATED      3   18
  DEL PEAK 10(5P15.33) WILD-TYPE   39  579
                        clus
vv                       DEL PEAK 10(5P15.33) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           18
                        clus
vv                       DEL PEAK 10(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                 39
  NOT HISPANIC OR LATINO                            579
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK 11(6Q22.31) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 11(6Q22.31) MUTATED   164  59
  DEL PEAK 11(6Q22.31) WILD-TYPE 468 152
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                           223                            620 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                            59                            152 
$`DEL PEAK 11(6Q22.31) MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       73.91        54.74       151.96        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
        0.99        52.27        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
      115.00        42.35        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 
       92.71        16.67        80.38       103.27        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3306 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       61.58        63.95        36.82        24.16        49.08        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3325 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3346 
       37.15        49.58        24.69        21.86        34.29         4.50 
TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-A8CQ 
       52.93        18.44        43.20        18.64        18.87         0.10 
TCGA-AK-3426 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       29.10        15.78        72.07        68.61        67.20        57.37 
TCGA-AK-3447 TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       40.01        28.73        38.40        28.04        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 
        1.41         3.48        28.47         1.38         3.62        19.73 
TCGA-B0-4712 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4828 
       43.96        15.72         0.59        36.53        54.48        10.09 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-5084 
       40.70        45.30        10.29        29.03         2.27         7.30 
TCGA-B0-5102 TCGA-B0-5108 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5402 TCGA-B0-5702 
       90.87        29.95        17.59         1.94        14.76        52.77 
TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 
       32.61        21.57         9.57         0.23         0.53         5.46 
TCGA-B8-4143 TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-A54G TCGA-BP-4164 
       23.31        27.16        25.55        20.91         1.74        32.61 
TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4334 
       89.36        64.27        97.45         3.58        80.68        21.21 
TCGA-BP-4342 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4770 
       74.17        11.31        12.33         5.98        13.15        10.82 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4959 
       60.59        56.91        68.38        15.78        36.39        87.45 
TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4968 TCGA-BP-4983 TCGA-BP-4986 
       71.41        58.68        60.30        57.40        46.45        25.81 
TCGA-BP-4987 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 
       36.95        16.47         5.82        43.00        18.51         6.35 
TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5201 
       30.64        62.86        74.40        37.22        31.79        31.27 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4643 TCGA-CJ-4871 TCGA-CJ-4872 
       59.84        46.55        65.69        58.95        79.66        47.18 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4887 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       71.87        66.21        30.64        24.66        39.45        59.44 
TCGA-CJ-4901 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5679 
       47.67        58.92        49.28        79.89        84.66        22.32 
TCGA-CJ-5680 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5584 TCGA-CW-5585 
       25.25        60.99        53.42        83.77         5.39        85.78 
TCGA-CW-5588 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4866 TCGA-CZ-5452 
       66.31        25.45        69.21        58.75        61.41        58.82 
TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5984 
       56.28        47.01        10.22        47.54        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-5565 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5575 
       65.65        14.63        43.69        12.16        37.15        56.84 
TCGA-EU-5907 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MW-A4EC TCGA-2Z-A9J8 
        4.18        70.13        35.87        19.43        10.85        67.30 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-A4-7286 TCGA-B3-3926 TCGA-B9-A44B 
       54.64        51.52        35.67        18.21        10.09         2.10 
TCGA-BQ-5875 TCGA-BQ-5882 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-7056 TCGA-EV-5902 
       86.76        21.63        13.25        10.88        20.12        19.00 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 
       13.08         4.01        11.05        25.84        17.33         3.68 
TCGA-J7-8537 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
        0.13        84.95        14.07        27.06        18.02        86.27 
TCGA-Y8-A896 
       18.64 

$`DEL PEAK 11(6Q22.31) WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 
      109.22        71.41        28.80        62.37        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 
       51.06        31.33        23.47        25.91         3.55        11.21 
TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 
      100.87        87.78        86.10        12.66        12.16        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
        0.53        39.16        48.59        36.36        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 
       48.82        31.07        45.53        29.92        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3383 TCGA-A3-3385 
       24.16        53.29        55.76        20.71        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV TCGA-A3-A8OW 
       20.28        15.39        22.65         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3443 
      109.91        84.36        73.08        66.31        60.92        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3455 
       48.36        42.08        58.49        48.69        45.93        22.45 
TCGA-AK-3456 TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 
       37.58        31.27         1.41         3.32         4.57         2.53 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
       19.00        65.10         7.82         5.98         2.14         3.16 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4815 
        6.64         3.25        20.25        46.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        40.44        14.93 
TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       29.10        78.44        68.71        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4852 
       56.68        11.64        65.29        39.45        26.07        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 
       70.52        20.94        43.30        11.24        11.90        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       52.08        15.95        62.89        90.48        52.54        30.48 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 
       19.30        35.90        11.80        26.20        21.60        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       18.21        21.44        37.22        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       90.12        56.94        39.55       120.59        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
       47.97        96.36        89.49        61.32        97.41        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 
       32.98        16.67         5.75         1.25         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
        0.23        16.80        27.55        25.05        24.66        17.19 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       25.91        23.01        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54H 
       34.39        14.30        27.29        29.88        17.06         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       85.51        94.72        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 
        0.43        23.05        77.03        62.24        61.78        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 
       53.42        27.78        62.07        37.25        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       93.99        18.48        52.24        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       44.94        12.23        31.89        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       72.59        77.98        77.62        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4782 
       48.07        61.68         5.33        61.97        13.51        11.64 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 
       60.95        48.95        36.53        20.38        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4964 
       36.95         6.71        47.97         6.94        63.62        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4995 
       33.34        31.30        27.22         3.88        46.45        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       30.64        41.62        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 
       35.21        36.23        28.87        48.10        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
       74.20        52.27         9.63        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 
       37.25        22.78        13.35        27.02        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5202 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4641 
        0.95        63.25        73.22        14.17        75.88        54.61 
TCGA-CJ-4642 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 
       53.52        11.05        21.24        83.97        49.25        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       75.06        77.36        64.27        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       64.18        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       27.65        50.24        56.35        49.97        51.29        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5681 
       18.81        63.88        72.00        25.71        18.87        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6030 
       61.91        62.10        73.35        67.00        53.26        75.58 
TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5587 
       62.66         7.36        64.57        92.02        81.83        73.18 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4861 
       18.77        46.16         0.59        47.08         6.77        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5453 
       60.59        63.39        93.04         5.46        63.42         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 
       23.74        18.44        55.33        56.94        55.33        10.85 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        57.21        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 
       12.69        12.26        22.78        62.63        45.96        65.88 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        23.90        66.02        18.12         3.91 
TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U 
        6.77         7.96        10.29         2.01        19.96        15.25 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JL 
        4.57        75.42        34.85        56.81        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 
       16.18        22.49         0.13        12.82        11.57        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       25.08        44.61        49.25         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        6.58        33.83        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       15.12        43.99        22.06        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       14.86        17.49        12.30        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.20        47.80        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       26.04        25.35         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY 
       54.90        34.19        24.89        10.68         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        0.43        51.78        48.62        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       13.68         6.38        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
       12.92        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94         6.61        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        47.44        33.04        28.80        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS 
       60.03        14.83        21.93         0.53        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       18.64        15.91        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                        151.96                         194.79 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                         39.45                          27.98 
[1] "0.1 - 152.0 (39.5)" "0.1 - 194.8 (28.0)"
[1] "hr=" "1.1"
D24V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 11(6Q22.31) MUTATED        93       41        55       35
  DEL PEAK 11(6Q22.31) WILD-TYPE     355       62       135       65
D24V3, multiclass
           clus
vv          DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  STAGE I                             93                            355
  STAGE II                            41                             62
  STAGE III                           55                            135
  STAGE IV                            35                             65
[1] 4 2
[1] 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(6Q22.31) MUTATED    94  44  80   7
  DEL PEAK 11(6Q22.31) WILD-TYPE 368  79 171   8
D24V4, multiclass
    clus
vv   DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  T1                           94                            368
  T2                           44                             79
  T3                           80                            171
  T4                            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                              N0  N1  N2
  DEL PEAK 11(6Q22.31) MUTATED    87  17   4
  DEL PEAK 11(6Q22.31) WILD-TYPE 230  26   2
D24V5, multiclass
    clus
vv   DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  N0                           87                            230
  N1                           17                             26
  N2                            4                              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"
D24V6, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED   156  26
  DEL PEAK 11(6Q22.31) WILD-TYPE 386  63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED    156   26
  DEL PEAK 11(6Q22.31) WILD-TYPE  386   63
   clus
vv  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  0                          156                            386
  1                           26                             63
[1] 2 2
[1] FALSE
D24V7, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED    78 147
  DEL PEAK 11(6Q22.31) WILD-TYPE 209 425
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED     78  147
  DEL PEAK 11(6Q22.31) WILD-TYPE  209  425
        clus
vv       DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  FEMALE                           78                            209
  MALE                            147                            425
[1] 2 2
[1] FALSE
D24V8, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  DEL PEAK 11(6Q22.31) MUTATED                   51
  DEL PEAK 11(6Q22.31) WILD-TYPE                 15
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 11(6Q22.31) MUTATED                                 147
  DEL PEAK 11(6Q22.31) WILD-TYPE                               377
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 11(6Q22.31) MUTATED                                      27
  DEL PEAK 11(6Q22.31) WILD-TYPE                                   242
D24V9, multiclass
                                       clus
vv                                      DEL PEAK 11(6Q22.31) MUTATED
  KIDNEY CHROMOPHOBE                                              51
  KIDNEY CLEAR CELL RENAL CARCINOMA                              147
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           27
                                       clus
vv                                      DEL PEAK 11(6Q22.31) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                15
  KIDNEY CLEAR CELL RENAL CARCINOMA                                377
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            242
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, continuous
D24V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(6Q22.31) MUTATED                                  0     6
  DEL PEAK 11(6Q22.31) WILD-TYPE                                2     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q22.31) MUTATED                          16   195
  DEL PEAK 11(6Q22.31) WILD-TYPE                       100   507
D24V12, multiclass
                                  clus
vv                                 DEL PEAK 11(6Q22.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                     195
                                  clus
vv                                 DEL PEAK 11(6Q22.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                   100
  WHITE                                                       507
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED    13 139
  DEL PEAK 11(6Q22.31) WILD-TYPE  29 458
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED     13  139
  DEL PEAK 11(6Q22.31) WILD-TYPE   29  458
                        clus
vv                       DEL PEAK 11(6Q22.31) MUTATED
  HISPANIC OR LATINO                               13
  NOT HISPANIC OR LATINO                          139
                        clus
vv                       DEL PEAK 11(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                 29
  NOT HISPANIC OR LATINO                            458
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK 12(6Q26) MUTATION ANALYSIS
D25V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 12(6Q26) MUTATED   168  60
  DEL PEAK 12(6Q26) WILD-TYPE 464 151
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        228                         615 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                         60                         151 
$`DEL PEAK 12(6Q26) MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       73.91        54.74       151.96        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
        0.99        52.27        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
      115.00        42.35        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 
       92.71        16.67        80.38       103.27        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3306 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       61.58        63.95        36.82        24.16        49.08        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3347 
       37.15        49.58        21.86        34.29         4.50        52.93 
TCGA-A3-3352 TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3426 
       18.44        43.20        18.64        18.87         0.10        29.10 
TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 
       15.78        72.07        68.61        67.20        57.37        40.01 
TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 
       28.73        38.40        28.04        12.13        40.70         1.41 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4712 
        3.48        28.47         1.38         3.62        19.73        43.96 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4836 
       15.72         0.59        36.53        54.48        10.09        40.70 
TCGA-B0-4837 TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-5084 TCGA-B0-5102 
       45.30        10.29        29.03         2.27         7.30        90.87 
TCGA-B0-5108 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5402 TCGA-B0-5702 TCGA-B2-3923 
       29.95        17.59         1.94        14.76        52.77        32.61 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 
       21.57         9.57         0.23         0.53         5.46        23.31 
TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-A54G TCGA-BP-4160 TCGA-BP-4164 
       27.16        25.55        20.91         1.74        94.72        32.61 
TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4334 
       89.36        64.27        97.45         3.58        80.68        21.21 
TCGA-BP-4342 TCGA-BP-4346 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4761 TCGA-BP-4768 
       74.17        49.08        11.31        12.33         5.98        13.15 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4959 
       60.59        56.91        68.38        15.78        36.39        87.45 
TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4968 TCGA-BP-4974 TCGA-BP-4983 
       71.41        58.68        60.30        57.40         7.23        46.45 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-5000 
       25.81        36.95        16.47         5.82        43.00        18.51 
TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5185 
        6.35        30.64        62.86        74.40        49.15        37.22 
TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4643 TCGA-CJ-4871 
       31.79        31.27        59.84        46.55        58.95        79.66 
TCGA-CJ-4872 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4887 TCGA-CJ-4892 
       47.18        64.27        71.87        66.21        30.64        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4904 TCGA-CJ-4907 
       24.66        39.45        59.44        47.67        58.92        49.28 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-6027 TCGA-CJ-6028 
       79.89        84.66        22.32        25.25        60.99        53.42 
TCGA-CJ-6032 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5588 TCGA-CZ-4853 TCGA-CZ-4858 
       83.77         5.39        85.78        66.31        25.45        69.21 
TCGA-CZ-4859 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5460 
       58.75        93.04        61.41        58.82        56.28        47.01 
TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 
       10.22        47.54        80.19        67.96        65.65        14.63 
TCGA-DV-5565 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5575 TCGA-EU-5907 TCGA-G6-A8L7 
       43.69        12.16        37.15        56.84         4.18        70.13 
TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MW-A4EC TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI 
       35.87        19.43        10.85        67.30        54.64        51.52 
TCGA-2Z-A9JJ TCGA-A4-7286 TCGA-B3-3926 TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5882 
       35.67        18.21        10.09         2.10        86.76        21.63 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-7056 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 
       13.25         7.66        20.12        19.00        13.08         4.01 
TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 
       11.05        25.84        17.33         3.68         2.04         0.13 
TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-UZ-A9PQ TCGA-Y8-A896 
       84.95        14.07        27.06        18.02        86.27        18.64 

$`DEL PEAK 12(6Q26) WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 
      109.22        71.41        28.80        62.37        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 
       51.06        31.33        23.47        25.91         3.55        11.21 
TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 
      100.87        87.78        86.10        12.66        12.16        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        0.53        39.16        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
       37.38        48.82        31.07        45.53        29.92        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3383 
       74.76        24.16        53.29        55.76        20.71        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV 
       65.52        20.28        15.39        22.65         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 
       10.62       109.91        84.36        73.08        66.31        60.92 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       46.78        48.36        42.08        58.49        48.69        45.93 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 
       22.45        37.58        31.27         1.41         3.32         4.57 
TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        2.53        19.00        65.10         7.82         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4814 
        3.16         6.64         3.25        20.25        46.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4823 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4838 TCGA-B0-4839 
       14.93        29.10        78.44        68.71        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
        6.71        56.68        11.64        65.29        39.45        26.07 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 
       21.86        52.08        15.95        62.89        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       30.48        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        79.17       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       84.92        90.12        56.94        39.55       120.59        79.36 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        12.30        21.30        31.30        11.77 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 
       10.36        32.98        16.67         5.75         1.25         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.36         0.23        16.80        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       17.19        25.91        23.01        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
      111.02        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 
        0.43        23.05        77.03        62.24        61.78        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 
       53.42        27.78        62.07        37.25        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4347 
       93.99        18.48        52.24        62.86        54.77        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       12.23        31.89        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.98        77.62        44.15        41.75        71.80        48.07 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4782 
       61.68        10.82         5.33        61.97        13.51        11.64 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 
       60.95        48.95        36.53        20.38        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4964 
       36.95         6.71        47.97         6.94        63.62        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4985 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4995 TCGA-BP-4998 
       31.30        27.22         3.88        46.45        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       41.62        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       36.23        28.87        48.10        79.30         1.78        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
       52.27         9.63        38.30        42.44        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       13.35        27.02        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4636 
       33.47        19.82        44.55        34.95         0.95        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 
       11.05        21.24        83.97        49.25        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4888 
       77.36        61.91        57.83        69.86        64.18        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4900 
       63.98        68.55        26.93        27.65        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       49.97        51.29        49.18        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       25.71        18.87        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.26        75.58        62.66         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       92.02        81.83        73.18        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4856 
      105.93        83.90       103.43        18.77        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       47.08         6.77        14.66        60.59        63.39         5.46 
TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       63.42         0.82        23.74        18.44        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 
       55.33        10.85        21.76        57.21        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
        1.94        31.10        12.69        12.26        22.78        62.63 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5576 TCGA-DV-A4W0 
       45.96        65.88        11.67        66.28        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-GK-A6C7 
       18.12         3.91         6.77         7.96        10.29         2.01 
TCGA-MM-A564 TCGA-MM-A84U TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       19.96        15.25         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
      100.27        56.91         4.57        75.42        34.85        56.81 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       25.58         5.29        16.18        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       11.57        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        8.28        12.99        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       16.77         0.46         6.58        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       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 
        6.81         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        10.88         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-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        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        61.02        54.90        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        48.62        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
       34.82        25.15        13.68         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         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM 
       17.75        47.90        47.44        33.04        28.80        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR 
       43.76        60.03        14.83        21.93         0.53        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       29.00        18.64        15.91        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                       0.10                        0.07 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                     151.96                      194.79 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                      40.70                       27.65 
[1] "0.1 - 152.0 (40.7)" "0.1 - 194.8 (27.6)"
[1] "hr=" "1.2"
D25V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 12(6Q26) MUTATED        94       43        58       34
  DEL PEAK 12(6Q26) WILD-TYPE     354       60       132       66
D25V3, multiclass
           clus
vv          DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  STAGE I                          94                         354
  STAGE II                         43                          60
  STAGE III                        58                         132
  STAGE IV                         34                          66
[1] 4 2
[1] 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(6Q26) MUTATED    95  46  83   6
  DEL PEAK 12(6Q26) WILD-TYPE 367  77 168   9
D25V4, multiclass
    clus
vv   DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  T1                        95                         367
  T2                        46                          77
  T3                        83                         168
  T4                         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                           N0  N1  N2
  DEL PEAK 12(6Q26) MUTATED    92  17   4
  DEL PEAK 12(6Q26) WILD-TYPE 225  26   2
D25V5, multiclass
    clus
vv   DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  N0                        92                         225
  N1                        17                          26
  N2                         4                           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"
D25V6, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED   160  26
  DEL PEAK 12(6Q26) WILD-TYPE 382  63
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED    160   26
  DEL PEAK 12(6Q26) WILD-TYPE  382   63
   clus
vv  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  0                       160                         382
  1                        26                          63
[1] 2 2
[1] FALSE
D25V7, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED    80 150
  DEL PEAK 12(6Q26) WILD-TYPE 207 422
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     80  150
  DEL PEAK 12(6Q26) WILD-TYPE  207  422
        clus
vv       DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  FEMALE                        80                         207
  MALE                         150                         422
[1] 2 2
[1] FALSE
D25V8, continuous
                             vv
clus                          KIDNEY CHROMOPHOBE
  DEL PEAK 12(6Q26) MUTATED                   51
  DEL PEAK 12(6Q26) WILD-TYPE                 15
                             vv
clus                          KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 12(6Q26) MUTATED                                 151
  DEL PEAK 12(6Q26) WILD-TYPE                               373
                             vv
clus                          KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 12(6Q26) MUTATED                                      28
  DEL PEAK 12(6Q26) WILD-TYPE                                   241
D25V9, multiclass
                                       clus
vv                                      DEL PEAK 12(6Q26) MUTATED
  KIDNEY CHROMOPHOBE                                           51
  KIDNEY CLEAR CELL RENAL CARCINOMA                           151
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                        28
                                       clus
vv                                      DEL PEAK 12(6Q26) WILD-TYPE
  KIDNEY CHROMOPHOBE                                             15
  KIDNEY CLEAR CELL RENAL CARCINOMA                             373
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                         241
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, continuous
D25V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(6Q26) MUTATED                                  0     6
  DEL PEAK 12(6Q26) WILD-TYPE                                2     9
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6Q26) MUTATED                          16   200
  DEL PEAK 12(6Q26) WILD-TYPE                       100   502
D25V12, multiclass
                                  clus
vv                                 DEL PEAK 12(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    6
  BLACK OR AFRICAN AMERICAN                               16
  WHITE                                                  200
                                  clus
vv                                 DEL PEAK 12(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      9
  BLACK OR AFRICAN AMERICAN                                100
  WHITE                                                    502
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED    14 141
  DEL PEAK 12(6Q26) WILD-TYPE  28 456
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     14  141
  DEL PEAK 12(6Q26) WILD-TYPE   28  456
                        clus
vv                       DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  HISPANIC OR LATINO                            14                          28
  NOT HISPANIC OR LATINO                       141                         456
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK 13(6Q26) MUTATION ANALYSIS
D26V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 13(6Q26) MUTATED   169  60
  DEL PEAK 13(6Q26) WILD-TYPE 463 151
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                        229                         614 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         60                         151 
$`DEL PEAK 13(6Q26) MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       73.91        54.74       151.96        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
        0.99        52.27        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
      115.00        42.35        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 
       92.71        16.67        80.38       103.27        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3306 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       61.58        63.95        36.82        24.16        49.08        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3347 
       37.15        49.58        21.86        34.29         4.50        52.93 
TCGA-A3-3352 TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3426 
       18.44        43.20        18.64        18.87         0.10        29.10 
TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 
       15.78        72.07        68.61        67.20        57.37        40.01 
TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 
       28.73        38.40        28.04        12.13        40.70         1.41 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4712 
        3.48        28.47         1.38         3.62        19.73        43.96 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4836 
       15.72         0.59        36.53        54.48        10.09        40.70 
TCGA-B0-4837 TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-5084 TCGA-B0-5102 
       45.30        10.29        29.03         2.27         7.30        90.87 
TCGA-B0-5108 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5402 TCGA-B0-5702 TCGA-B2-3923 
       29.95        17.59         1.94        14.76        52.77        32.61 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 
       21.57         9.57         0.23         0.53         5.46        23.31 
TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-A54G TCGA-BP-4160 TCGA-BP-4164 
       27.16        25.55        20.91         1.74        94.72        32.61 
TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4334 
       89.36        64.27        97.45         3.58        80.68        21.21 
TCGA-BP-4342 TCGA-BP-4346 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4761 TCGA-BP-4768 
       74.17        49.08        11.31        12.33         5.98        13.15 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4959 
       60.59        56.91        68.38        15.78        36.39        87.45 
TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4968 TCGA-BP-4974 TCGA-BP-4983 
       71.41        58.68        60.30        57.40         7.23        46.45 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-5000 
       25.81        36.95        16.47         5.82        43.00        18.51 
TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5185 
        6.35        30.64        62.86        74.40        49.15        37.22 
TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4643 TCGA-CJ-4871 
       31.79        31.27        59.84        46.55        58.95        79.66 
TCGA-CJ-4872 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4887 TCGA-CJ-4892 
       47.18        64.27        71.87        66.21        30.64        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4904 TCGA-CJ-4907 
       24.66        39.45        59.44        47.67        58.92        49.28 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6032 
       79.89        84.66        22.32        60.99        53.42        83.77 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5588 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 
        5.39        85.78        66.31        25.45        69.21        58.75 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5462 
       93.04        61.41        58.82        56.28        47.01        10.22 
TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 
       47.54         1.94        80.19        67.96        65.65        14.63 
TCGA-DV-5565 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5575 TCGA-EU-5907 TCGA-G6-A8L7 
       43.69        12.16        37.15        56.84         4.18        70.13 
TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MW-A4EC TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI 
       35.87        19.43        10.85        67.30        54.64        51.52 
TCGA-2Z-A9JJ TCGA-A4-7286 TCGA-B3-3926 TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5882 
       35.67        18.21        10.09         2.10        86.76        21.63 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-7056 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 
       13.25         7.66        20.12        19.00        13.08         4.01 
TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 
       11.05        25.84        17.33         3.68         2.04         0.13 
TCGA-MH-A55W TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       34.29        84.95        14.07        27.06        18.02        86.27 
TCGA-Y8-A896 
       18.64 

$`DEL PEAK 13(6Q26) WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 
      109.22        71.41        28.80        62.37        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 
       51.06        31.33        23.47        25.91         3.55        11.21 
TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 
      100.87        87.78        86.10        12.66        12.16        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        0.53        39.16        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
       37.38        48.82        31.07        45.53        29.92        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3383 
       74.76        24.16        53.29        55.76        20.71        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV 
       65.52        20.28        15.39        22.65         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 
       10.62       109.91        84.36        73.08        66.31        60.92 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       46.78        48.36        42.08        58.49        48.69        45.93 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 
       22.45        37.58        31.27         1.41         3.32         4.57 
TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        2.53        19.00        65.10         7.82         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4814 
        3.16         6.64         3.25        20.25        46.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4823 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4838 TCGA-B0-4839 
       14.93        29.10        78.44        68.71        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
        6.71        56.68        11.64        65.29        39.45        26.07 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 
       21.86        52.08        15.95        62.89        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       30.48        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        79.17       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       84.92        90.12        56.94        39.55       120.59        79.36 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        12.30        21.30        31.30        11.77 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 
       10.36        32.98        16.67         5.75         1.25         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.36         0.23        16.80        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       17.19        25.91        23.01        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
      111.02        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 
        0.43        23.05        77.03        62.24        61.78        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 
       53.42        27.78        62.07        37.25        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4347 
       93.99        18.48        52.24        62.86        54.77        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       12.23        31.89        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.98        77.62        44.15        41.75        71.80        48.07 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4782 
       61.68        10.82         5.33        61.97        13.51        11.64 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 
       60.95        48.95        36.53        20.38        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4964 
       36.95         6.71        47.97         6.94        63.62        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4985 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4995 TCGA-BP-4998 
       31.30        27.22         3.88        46.45        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       41.62        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       36.23        28.87        48.10        79.30         1.78        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
       52.27         9.63        38.30        42.44        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       13.35        27.02        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4636 
       33.47        19.82        44.55        34.95         0.95        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 
       11.05        21.24        83.97        49.25        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4888 
       77.36        61.91        57.83        69.86        64.18        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4900 
       63.98        68.55        26.93        27.65        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       49.97        51.29        49.18        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       25.71        18.87        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 
       73.35        67.00        53.26        75.58        62.66         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 
       64.57        92.02        81.83        73.18        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4854 
        1.35       105.93        83.90       103.43        18.77        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
        0.59        47.08         6.77        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
        5.46        63.42         0.82        23.74        18.44        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
       56.94        55.33        10.85        21.76        57.21        22.52 
TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
        2.40        31.10        12.69        12.26        22.78        62.63 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5576 TCGA-DV-A4W0 
       45.96        65.88        11.67        66.28        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-GK-A6C7 
       18.12         3.91         6.77         7.96        10.29         2.01 
TCGA-MM-A564 TCGA-MM-A84U TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       19.96        15.25         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
      100.27        56.91         4.57        75.42        34.85        56.81 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       25.58         5.29        16.18        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       11.57        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        8.28        12.99        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       16.77         0.46         6.58        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       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 
        6.81         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        10.88         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-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        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        61.02        54.90        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        48.62        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
       34.82        25.15        13.68         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         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A560 
       12.36        11.97        29.10        11.41        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94         6.61        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        47.44        33.04        28.80        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS 
       60.03        14.83        21.93         0.53        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       18.64        15.91        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                       0.10                        0.07 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                     151.96                      194.79 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                      40.70                       27.65 
[1] "0.1 - 152.0 (40.7)" "0.1 - 194.8 (27.6)"
[1] "hr=" "1.2"
D26V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 13(6Q26) MUTATED        95       43        58       34
  DEL PEAK 13(6Q26) WILD-TYPE     353       60       132       66
D26V3, multiclass
           clus
vv          DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  STAGE I                          95                         353
  STAGE II                         43                          60
  STAGE III                        58                         132
  STAGE IV                         34                          66
[1] 4 2
[1] 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(6Q26) MUTATED    96  46  83   6
  DEL PEAK 13(6Q26) WILD-TYPE 366  77 168   9
D26V4, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  T1                        96                         366
  T2                        46                          77
  T3                        83                         168
  T4                         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                           N0  N1  N2
  DEL PEAK 13(6Q26) MUTATED    92  17   4
  DEL PEAK 13(6Q26) WILD-TYPE 225  26   2
D26V5, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  N0                        92                         225
  N1                        17                          26
  N2                         4                           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"
D26V6, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED   160  26
  DEL PEAK 13(6Q26) WILD-TYPE 382  63
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED    160   26
  DEL PEAK 13(6Q26) WILD-TYPE  382   63
   clus
vv  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  0                       160                         382
  1                        26                          63
[1] 2 2
[1] FALSE
D26V7, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED    79 152
  DEL PEAK 13(6Q26) WILD-TYPE 208 420
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     79  152
  DEL PEAK 13(6Q26) WILD-TYPE  208  420
        clus
vv       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  FEMALE                        79                         208
  MALE                         152                         420
[1] 2 2
[1] FALSE
D26V8, continuous
                             vv
clus                          KIDNEY CHROMOPHOBE
  DEL PEAK 13(6Q26) MUTATED                   51
  DEL PEAK 13(6Q26) WILD-TYPE                 15
                             vv
clus                          KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 13(6Q26) MUTATED                                 151
  DEL PEAK 13(6Q26) WILD-TYPE                               373
                             vv
clus                          KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 13(6Q26) MUTATED                                      29
  DEL PEAK 13(6Q26) WILD-TYPE                                   240
D26V9, multiclass
                                       clus
vv                                      DEL PEAK 13(6Q26) MUTATED
  KIDNEY CHROMOPHOBE                                           51
  KIDNEY CLEAR CELL RENAL CARCINOMA                           151
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                        29
                                       clus
vv                                      DEL PEAK 13(6Q26) WILD-TYPE
  KIDNEY CHROMOPHOBE                                             15
  KIDNEY CLEAR CELL RENAL CARCINOMA                             373
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                         240
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, continuous
D26V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(6Q26) MUTATED                                  0     6
  DEL PEAK 13(6Q26) WILD-TYPE                                2     9
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(6Q26) MUTATED                          17   200
  DEL PEAK 13(6Q26) WILD-TYPE                        99   502
D26V12, multiclass
                                  clus
vv                                 DEL PEAK 13(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    6
  BLACK OR AFRICAN AMERICAN                               17
  WHITE                                                  200
                                  clus
vv                                 DEL PEAK 13(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      9
  BLACK OR AFRICAN AMERICAN                                 99
  WHITE                                                    502
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED    14 142
  DEL PEAK 13(6Q26) WILD-TYPE  28 455
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     14  142
  DEL PEAK 13(6Q26) WILD-TYPE   28  455
                        clus
vv                       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  HISPANIC OR LATINO                            14                          28
  NOT HISPANIC OR LATINO                       142                         455
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK 14(8P23.2) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(8P23.2) MUTATED   118  63
  DEL PEAK 14(8P23.2) WILD-TYPE 514 148
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                          181                           662 
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                           63                           148 
$`DEL PEAK 14(8P23.2) MUTATED`
TCGA-KL-8327 TCGA-KL-8337 TCGA-KM-8476 TCGA-KN-8424 TCGA-KN-8432 TCGA-KN-8435 
      137.06        44.84       123.12        65.19         2.50       115.00 
TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
       42.35        10.68       103.27        77.85        61.58        63.95 
TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3365 TCGA-A3-3372 
       37.15        24.69        34.29         4.50        28.70        24.16 
TCGA-A3-3373 TCGA-A3-3382 TCGA-A3-A6NN TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3434 
       53.29        18.87         0.10       109.91        29.10        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3458 TCGA-AS-3777 
       67.20        57.37        42.08        40.01        38.40        40.70 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4699 TCGA-B0-4703 TCGA-B0-4707 
        3.32         1.41         4.57         3.62         5.98        19.73 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 
       43.96         6.64        20.25         0.59        52.21        45.07 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 
        6.02        40.44        36.53        40.70        27.42        53.88 
TCGA-B0-4845 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5094 TCGA-B0-5097 
       65.29         2.27        36.85        70.52        10.95        21.86 
TCGA-B0-5102 TCGA-B0-5108 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5712 TCGA-B0-5713 
       90.87        29.95        46.68        56.78        89.49        61.32 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4151 
       16.67         9.57         0.23         5.46        23.31        27.55 
TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-5551 
       20.91        27.02         0.85        17.16         6.38         0.53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-BP-4164 TCGA-BP-4169 TCGA-BP-4174 TCGA-BP-4176 
        8.42         4.93        32.61        23.05        61.78        64.27 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       53.42         3.58        93.99        18.48        52.24        62.86 
TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4768 TCGA-BP-4775 
       44.94        31.89        11.31        12.33        13.15        60.59 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 
       68.38        11.64        15.78        20.38        10.98        37.25 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
        6.94        87.45        71.41         6.74        57.40        14.24 
TCGA-BP-4973 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-4998 
       45.50        46.45        31.30        25.81        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5169 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5177 
       18.51        37.02         6.35         1.78        30.64         9.63 
TCGA-BP-5182 TCGA-BP-5196 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4637 TCGA-CJ-4640 
       38.30        33.47        34.95        31.27        73.22        65.69 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4876 TCGA-CJ-4878 
       53.52        58.95        21.24        49.25        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4894 
       66.21        57.83        69.86        51.52        63.98        27.65 
TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5672 
       59.44        51.29        58.92        49.28        54.48        72.00 
TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6033 
       25.71        22.32        53.26        60.99        75.58         7.36 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4860 TCGA-CZ-4862 TCGA-CZ-4865 
      105.93        83.90        46.16         6.77        60.59         5.46 
TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
        0.82        55.33        10.22        21.76        47.54        22.52 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-5565 
        1.94        12.69        12.26        14.63        22.78        43.69 
TCGA-DV-5574 TCGA-DV-5575 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-2Z-A9J3 TCGA-A4-A5Y1 
       66.28        56.84        35.87        19.43        58.22        12.99 
TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4117 TCGA-BQ-5889 TCGA-DW-5560 
        9.63         7.33        10.09         0.46        10.88        11.61 
TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-A8LC TCGA-G7-A8LD TCGA-J7-8537 TCGA-SX-A7SO 
       13.08         1.18        17.33        16.90         0.13        38.63 
TCGA-UN-AAZ9 
       18.02 

$`DEL PEAK 14(8P23.2) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 
       44.91        28.80        47.24        49.97        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 
      129.37        23.47        87.91        25.48        25.91       104.52 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 
        3.55         0.99        52.27        87.12        19.33        11.21 
TCGA-KN-8434 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       59.08       100.87        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 TCGA-3Z-A93Z 
       16.67        80.38        87.78        86.10        57.17        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.16        36.82        47.21         0.53        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.08        49.02        49.58        48.59        36.36        38.99 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
       37.38        48.82        21.86        31.07        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       29.92        18.44        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       10.49        74.63        74.76        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.64        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
        0.10        11.18        10.62        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3450 
       15.78        60.92        72.07        46.78        48.36        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 
       48.69        45.93        28.73        22.45        37.58        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
       28.04        12.13         1.41         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4710 
       19.00         1.38        65.10         7.82         2.14         3.16 
TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4818 
        3.25        15.72        46.59         5.52        33.50        16.77 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4837 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 
       45.30         6.71        56.68        11.64        10.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       26.07        29.03        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        18.51        15.09         8.05         2.24 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       52.08        15.95        62.89        90.48        52.54        30.48 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5697 
       79.17       112.80        48.89       101.13        15.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5812 TCGA-B2-3923 
       79.36       102.48        47.97        96.36        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        12.30        21.30        31.30        11.77 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       10.36        32.98        21.57         5.75         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4153 
        4.64         0.36         0.23        16.80        27.16        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 
       24.66        17.19        25.55        25.91        23.01        23.74 
TCGA-B8-5162 TCGA-B8-5165 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
        1.18        24.23        16.60        14.27        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A54K 
       27.29        29.88        17.06         1.74        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4170 
      101.06        93.34        99.85         0.43        89.36        77.03 
TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       62.24        54.90        97.45        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4342 TCGA-BP-4344 
       37.25        21.21        15.16         0.07        74.17        54.77 
TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       49.08        12.23        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       48.07        61.68        10.82         5.33        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4801 
       56.91        60.95        48.95        36.53        36.39        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.71        47.97        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 
       61.51        58.98        48.89        49.38         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4988 
       53.65        14.93        36.07        33.34        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
        3.88        46.45        16.47         5.82        45.07        41.62 
TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       38.70        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 
       48.10        79.30        74.20        52.27        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       49.15        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       19.82        44.55         0.95        59.84        46.55        63.25 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4871 
       14.17        75.88        54.61        11.05        83.97        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4886 
       47.18        74.27        75.06        77.36        61.91        64.18 
TCGA-CJ-4887 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       30.64        68.55        26.93        50.01        24.66        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 
       50.24        56.35        47.67        49.97        49.18        50.33 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       79.89        84.66        18.87        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66        83.77 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6093 TCGA-CW-6097 
       66.31        78.18        74.66         1.35       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       25.45         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5454 
       63.39        93.04        61.41        63.42        58.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       18.44        56.28        56.94        55.33        47.01        10.85 
TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
       57.21         2.40        31.10        80.19        67.96        65.65 
TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       62.63        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U 
        7.96        10.29        70.13         2.01        19.96        15.25 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
       10.85         7.04        75.55        59.01       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
        8.48        16.31        15.75         8.28        12.46        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       76.64        13.55        30.35        25.08        44.61        49.25 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
        2.20        19.56        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       16.77         0.46         6.58        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       13.25         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-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.04         7.17         3.81        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A97G 
       34.19        19.00        24.89        10.68         2.40         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE 
       25.15        13.68        25.84         6.38        17.98        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       16.34        12.36        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       78.90        12.85        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       33.04        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM 
       41.62        26.47        48.30        43.76        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                       137.06                        194.79 
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                       31.890                        30.265 
[1] "0.1 - 137.1 (31.9)" "0.1 - 194.8 (30.3)"
[1] "hr=" "1.6"
D27V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 14(8P23.2) MUTATED        75       25        48       32
  DEL PEAK 14(8P23.2) WILD-TYPE     373       78       142       68
D27V3, multiclass
           clus
vv          DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  STAGE I                            75                           373
  STAGE II                           25                            78
  STAGE III                          48                           142
  STAGE IV                           32                            68
[1] 4 2
[1] 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(8P23.2) MUTATED    77  30  68   6
  DEL PEAK 14(8P23.2) WILD-TYPE 385  93 183   9
D27V4, multiclass
    clus
vv   DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  T1                          77                           385
  T2                          30                            93
  T3                          68                           183
  T4                           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                             N0  N1  N2
  DEL PEAK 14(8P23.2) MUTATED    73  11   0
  DEL PEAK 14(8P23.2) WILD-TYPE 244  32   6
D27V5, multiclass
    clus
vv   DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  N0                          73                           244
  N1                          11                            32
  N2                           0                             6
[1] 3 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 14(8P23.2) MUTATED   131  32
  DEL PEAK 14(8P23.2) WILD-TYPE 411  57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED    131   32
  DEL PEAK 14(8P23.2) WILD-TYPE  411   57
   clus
vv  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  0                         131                           411
  1                          32                            57
[1] 2 2
[1] FALSE
D27V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED    62 119
  DEL PEAK 14(8P23.2) WILD-TYPE 225 453
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED     62  119
  DEL PEAK 14(8P23.2) WILD-TYPE  225  453
        clus
vv       DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  FEMALE                          62                           225
  MALE                           119                           453
[1] 2 2
[1] FALSE
D27V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK 14(8P23.2) MUTATED                   12
  DEL PEAK 14(8P23.2) WILD-TYPE                 54
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 14(8P23.2) MUTATED                                 154
  DEL PEAK 14(8P23.2) WILD-TYPE                               370
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 14(8P23.2) MUTATED                                      15
  DEL PEAK 14(8P23.2) WILD-TYPE                                   254
D27V9, multiclass
                                       clus
vv                                      DEL PEAK 14(8P23.2) MUTATED
  KIDNEY CHROMOPHOBE                                             12
  KIDNEY CLEAR CELL RENAL CARCINOMA                             154
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          15
                                       clus
vv                                      DEL PEAK 14(8P23.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               54
  KIDNEY CLEAR CELL RENAL CARCINOMA                               370
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           254
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, continuous
D27V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(8P23.2) MUTATED                                  0     7
  DEL PEAK 14(8P23.2) WILD-TYPE                                2     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(8P23.2) MUTATED                          14   157
  DEL PEAK 14(8P23.2) WILD-TYPE                       102   545
D27V12, multiclass
                                  clus
vv                                 DEL PEAK 14(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    157
                                  clus
vv                                 DEL PEAK 14(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                  102
  WHITE                                                      545
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED    12 113
  DEL PEAK 14(8P23.2) WILD-TYPE  30 484
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED     12  113
  DEL PEAK 14(8P23.2) WILD-TYPE   30  484
                        clus
vv                       DEL PEAK 14(8P23.2) MUTATED
  HISPANIC OR LATINO                              12
  NOT HISPANIC OR LATINO                         113
                        clus
vv                       DEL PEAK 14(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                30
  NOT HISPANIC OR LATINO                           484
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK 15(9P23) MUTATION ANALYSIS
D28V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 15(9P23) MUTATED   108  85
  DEL PEAK 15(9P23) WILD-TYPE 524 126
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                        193                         650 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                         85                         126 
$`DEL PEAK 15(9P23) MUTATED`
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8332 TCGA-KL-8343 TCGA-KL-8346 TCGA-KN-8427 
      141.73        23.84        84.89        71.41        62.37         0.99 
TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8415 TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3316 
       42.35        10.68        57.17        36.82        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 
       49.02        37.15        24.69         4.50        52.93        18.44 
TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3436 TCGA-AK-3445 
       24.16        18.87       109.91        29.10        67.20        42.08 
TCGA-AK-3450 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4698 
       58.49        40.70         1.41         4.57         3.48         1.38 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4811 TCGA-B0-4815 TCGA-B0-4817 
       19.73         3.16        43.96        46.59        52.21        33.50 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4842 
        6.02        40.44        36.53        10.09        40.70        56.68 
TCGA-B0-4845 TCGA-B0-4848 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       65.29        29.03        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5107 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5402 
       52.08        62.89        30.48        11.80        21.60        14.76 
TCGA-B0-5694 TCGA-B0-5701 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5838 
       15.78        56.94        11.77        21.57         0.23         5.46 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5549 TCGA-B8-5551 TCGA-BP-4161 
       25.55        23.01        20.91         6.38         0.53        90.28 
TCGA-BP-4164 TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4351 
       32.61        89.36        64.27        74.17        62.86        31.89 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4781 
       11.31        12.33        41.75        48.07        13.15        68.38 
TCGA-BP-4782 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4962 
       11.64        36.39        10.98         6.71        71.41        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4973 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       60.30        61.22        45.50        46.45        31.30        25.81 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-5000 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5169 
       43.00        45.07        18.51        36.23        28.87         6.35 
TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5189 TCGA-BP-5191 
       30.64        62.86        74.40        42.44        27.02        31.79 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4871 
       33.47        19.82        31.27        46.55        14.17        79.66 
TCGA-CJ-4881 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4895 TCGA-CJ-4900 
       66.21        51.52        68.55        26.93        39.45        56.35 
TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 
       47.67        49.28        50.33        54.48        38.56         4.57 
TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 
       63.88        84.66        25.71        22.32        25.25        61.91 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 
       53.26        60.99        53.42        75.58        62.66         7.36 
TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6090 TCGA-CW-6097 
       64.57         5.39        66.31        74.66        83.90        18.77 
TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5461 
       46.16        47.08        69.21         6.77        56.28        10.85 
TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       10.22        47.54        22.52         1.94        31.10        12.69 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-G6-A5PC 
       67.96        65.65        14.63        23.90        66.02         7.96 
TCGA-G6-A8L7 TCGA-MM-A563 TCGA-MM-A84U TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       70.13        19.43        15.25        54.64        51.52        35.67 
TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-8516 TCGA-A4-A57E TCGA-A4-A5Y1 
       12.82        18.21        19.63         0.76         8.48        12.99 
TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A69E TCGA-BQ-5879 
        9.63        49.25        10.09        20.61        14.86        22.92 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-7048 TCGA-BQ-7056 TCGA-DZ-6131 TCGA-F9-A7Q0 
       13.25        10.88        93.34        20.12        79.86        13.08 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD 
        4.01        11.05        34.82        13.68        17.33        16.90 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
        2.04         0.13         6.61        16.01        18.02        86.27 
TCGA-Y8-A896 
       18.64 

$`DEL PEAK 15(9P23) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.22       137.06       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       98.96        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8344 
       86.56        28.11        66.54        24.79        73.91        28.80 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       54.74       151.96        23.28        44.91        28.80        47.24 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      115.00       100.87        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 
       61.58        63.95        12.66        12.16        47.21         0.53 
TCGA-A3-3313 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
       24.16        49.58        48.59        36.36        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 
       48.82        21.86        34.29        31.07        45.53        29.92 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.64        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 
        0.10         0.10        11.18        10.62        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 
       66.31        15.78        60.92        72.07        68.61        57.37 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        48.36        40.01        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4699 
        1.41         3.32         2.53        28.47        19.00         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 
       65.10         7.82         5.98         2.14         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 
       20.25        15.72         0.59         5.52        45.07        16.77 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 
       14.93        54.48        29.10        78.44        68.71        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 
       27.42        53.88         6.71        11.64        10.29        39.45 
TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       26.07         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 
       15.95        90.87        90.48        52.54        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       35.90        26.20        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       21.44        37.22        79.17       112.80        48.89       101.13 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 
       46.68        56.78        60.33        84.92        90.12        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR 
       12.30        21.30        31.30        10.36        32.98        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
        9.57         5.75         1.25         0.53         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       24.66        17.19        25.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 
        0.85        24.23        17.16        16.60        14.27        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        94.72       101.06        93.34        99.85         0.43 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 
       23.05        77.03        62.24        61.78        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 
       54.77        49.08        44.94        12.23        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       71.80        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       13.51        56.91        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       20.38        37.25        36.95        47.97         6.94        87.45 
TCGA-BP-4961 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       63.62        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       48.89        49.38         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       36.07        33.34        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 
       16.47         5.82        30.64        41.62        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 
       27.62        37.48        35.21        48.10        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 
       74.20        52.27         9.63        49.15        38.30        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
       24.62        44.55        34.95         0.95        59.84        63.25 
TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       73.22        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 
       11.05        21.24        83.97        49.25        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06        77.36        64.27        71.87        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4892 TCGA-CJ-4893 
       69.86        64.18        30.64        63.98        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       27.65        59.44        50.24        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 
       49.18        45.14         3.06        18.81        72.00        79.89 
TCGA-CJ-5678 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 
       18.87        18.15        62.10        73.35        67.00        83.77 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6087 
       92.02        81.83        85.78        73.18        78.18         1.35 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 
      105.93       103.43        25.45         0.59        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       60.59        63.39        93.04         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82         0.82        23.74        18.44        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5982 
       55.33        47.01        21.76        57.21         2.40        80.19 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       12.26        22.78        62.63        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
       12.16        11.67        37.15        66.28        56.84        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 
        3.91         6.77         4.18        10.29        35.87         2.01 
TCGA-MM-A564 TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       19.96        10.85         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
      100.27        56.91         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       56.81        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93Y TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       11.57        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        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-3467 
       16.96        16.31        15.75         8.28        12.46        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       76.64        13.55        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       16.77         0.46         6.58        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       12.46        10.16        50.50        28.18        26.40         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        6.81         0.16        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        63.72        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        26.04        25.35         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-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       44.84        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        40.77        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
       54.90        34.19        19.00        24.89        10.68         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        48.62        39.25        25.15 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.84         6.38        17.98        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25         5.49        16.80        19.99        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
       67.17        22.26        21.34        16.34        12.36        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.22        42.94        84.95        92.58        52.27 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
       50.60        78.90        12.85        17.75        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS 
       60.03        14.83        21.93         0.53        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       18.64        15.91        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                       0.13                        0.07 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                     141.73                      194.79 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                     31.270                      30.315 
[1] "0.1 - 141.7 (31.3)" "0.1 - 194.8 (30.3)"
[1] "hr=" "2.5"
D28V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 15(9P23) MUTATED        64       16        69       43
  DEL PEAK 15(9P23) WILD-TYPE     384       87       121       57
D28V3, multiclass
           clus
vv          DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  STAGE I                          64                         384
  STAGE II                         16                          87
  STAGE III                        69                         121
  STAGE IV                         43                          57
[1] 4 2
[1] 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(9P23) MUTATED    68  23  96   7
  DEL PEAK 15(9P23) WILD-TYPE 394 100 155   8
D28V4, multiclass
    clus
vv   DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  T1                        68                         394
  T2                        23                         100
  T3                        96                         155
  T4                         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                           N0  N1  N2
  DEL PEAK 15(9P23) MUTATED    71  19   2
  DEL PEAK 15(9P23) WILD-TYPE 246  24   4
D28V5, multiclass
    clus
vv   DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  N0                        71                         246
  N1                        19                          24
  N2                         2                           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 15(9P23) MUTATED   126  38
  DEL PEAK 15(9P23) WILD-TYPE 416  51
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED    126   38
  DEL PEAK 15(9P23) WILD-TYPE  416   51
   clus
vv  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  0                       126                         416
  1                        38                          51
[1] 2 2
[1] FALSE
D28V7, binary
                             cls
clus                            0   1
  DEL PEAK 15(9P23) MUTATED    59 137
  DEL PEAK 15(9P23) WILD-TYPE 228 435
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED     59  137
  DEL PEAK 15(9P23) WILD-TYPE  228  435
        clus
vv       DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  FEMALE                        59                         228
  MALE                         137                         435
[1] 2 2
[1] FALSE
D28V8, continuous
                             vv
clus                          KIDNEY CHROMOPHOBE
  DEL PEAK 15(9P23) MUTATED                   10
  DEL PEAK 15(9P23) WILD-TYPE                 56
                             vv
clus                          KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 15(9P23) MUTATED                                 151
  DEL PEAK 15(9P23) WILD-TYPE                               373
                             vv
clus                          KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 15(9P23) MUTATED                                      35
  DEL PEAK 15(9P23) WILD-TYPE                                   234
D28V9, multiclass
                                       clus
vv                                      DEL PEAK 15(9P23) MUTATED
  KIDNEY CHROMOPHOBE                                           10
  KIDNEY CLEAR CELL RENAL CARCINOMA                           151
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                        35
                                       clus
vv                                      DEL PEAK 15(9P23) WILD-TYPE
  KIDNEY CHROMOPHOBE                                             56
  KIDNEY CLEAR CELL RENAL CARCINOMA                             373
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                         234
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, continuous
D28V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(9P23) MUTATED                                  0     4
  DEL PEAK 15(9P23) WILD-TYPE                                2    11
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(9P23) MUTATED                          14   172
  DEL PEAK 15(9P23) WILD-TYPE                       102   530
D28V12, multiclass
                                  clus
vv                                 DEL PEAK 15(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               14
  WHITE                                                  172
                                  clus
vv                                 DEL PEAK 15(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                     11
  BLACK OR AFRICAN AMERICAN                                102
  WHITE                                                    530
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, binary
                             cls
clus                            0   1
  DEL PEAK 15(9P23) MUTATED     8 134
  DEL PEAK 15(9P23) WILD-TYPE  34 463
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED      8  134
  DEL PEAK 15(9P23) WILD-TYPE   34  463
                        clus
vv                       DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  HISPANIC OR LATINO                             8                          34
  NOT HISPANIC OR LATINO                       134                         463
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK 16(9P21.3) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(9P21.3) MUTATED   110  93
  DEL PEAK 16(9P21.3) WILD-TYPE 522 118
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          203                           640 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                           93                           118 
$`DEL PEAK 16(9P21.3) MUTATED`
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8332 TCGA-KL-8343 TCGA-KL-8346 TCGA-KN-8427 
      141.73        23.84        84.89        71.41        62.37         0.99 
TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8415 TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3316 
       42.35        10.68        57.17        36.82        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 
       49.02        37.15        24.69         4.50        52.93        18.44 
TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3436 TCGA-AK-3445 
       24.16        18.87       109.91        29.10        67.20        42.08 
TCGA-AK-3450 TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 
       58.49        40.70         3.32         1.41         4.57         3.48 
TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4811 
       28.47         1.38        19.73         3.16        43.96        46.59 
TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 
       52.21        33.50         6.02        40.44        36.53        10.09 
TCGA-B0-4836 TCGA-B0-4842 TCGA-B0-4845 TCGA-B0-4848 TCGA-B0-5094 TCGA-B0-5095 
       40.70        56.68        65.29        29.03        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5107 TCGA-B0-5109 
        2.24        21.86        52.08        62.89        30.48        19.30 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5121 TCGA-B0-5402 TCGA-B0-5694 TCGA-B0-5701 
       11.80        21.60        18.21        14.76        15.78        56.94 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4620 
       11.77        21.57         0.23         5.46        23.31        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-BP-4160 
       23.01        20.91         6.38        14.27         0.53        94.72 
TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4342 TCGA-BP-4343 
       90.28        32.61        89.36        64.27        74.17        62.86 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4766 
       31.89        11.31        12.33         5.98        41.75        48.07 
TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4798 
       13.15        68.38        11.64        15.78        36.39        10.98 
TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4973 
        6.71        71.41        58.68        60.30        61.22        45.50 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-5000 TCGA-BP-5009 
       31.30        25.81        43.00        45.07        18.51        36.23 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5183 
       28.87         6.35        30.64        62.86        74.40        42.44 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 
       27.02        31.79        33.47        19.82        31.27        46.55 
TCGA-CJ-4638 TCGA-CJ-4868 TCGA-CJ-4871 TCGA-CJ-4881 TCGA-CJ-4888 TCGA-CJ-4890 
       14.17        21.24        79.66        66.21        51.52        68.55 
TCGA-CJ-4891 TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4908 
       26.93        39.45        56.35        47.67        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5676 
       54.48        38.56         4.57        18.81        63.88        84.66 
TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5689 TCGA-CJ-6027 
       25.71        22.32        25.25        61.91        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5584 
       53.42        75.58        62.66         7.36        64.57         5.39 
TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 
       66.31        83.90        18.77        46.16        47.08        69.21 
TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 
        6.77        56.28        10.85        10.22        47.54        22.52 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-5576 
        1.94        31.10        67.96        65.65        14.63        23.90 
TCGA-DV-A4W0 TCGA-G6-A5PC TCGA-G6-A8L7 TCGA-MM-A563 TCGA-MM-A84U TCGA-2Z-A9JG 
       66.02         7.96        70.13        19.43        15.25        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-A57E 
       51.52        35.67        12.82        18.21        19.63         8.48 
TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A69E 
       12.99         9.63        49.25        10.09        20.61        14.86 
TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-7048 TCGA-BQ-7056 
        8.88        22.92        13.25        10.88        93.34        20.12 
TCGA-DZ-6131 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 
       79.86        13.08         4.01        11.05        34.82        13.68 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EA 
       17.33        16.90         3.68         2.04         0.13         6.61 
TCGA-P4-AAVL TCGA-SX-A71V TCGA-UN-AAZ9 TCGA-UZ-A9PQ TCGA-Y8-A896 
       16.01        28.80        18.02        86.27        18.64 

$`DEL PEAK 16(9P21.3) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.22       137.06       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       98.96        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8344 
       86.56        28.11        66.54        24.79        73.91        28.80 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       54.74       151.96        23.28        44.91        28.80        47.24 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      115.00       100.87        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 
       61.58        63.95        12.66        12.16        47.21         0.53 
TCGA-A3-3313 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
       24.16        49.58        48.59        36.36        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 
       48.82        21.86        34.29        31.07        45.53        29.92 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.64        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 
        0.10         0.10        11.18        10.62        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 
       66.31        15.78        60.92        72.07        68.61        57.37 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        48.36        40.01        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
        1.41         2.53        19.00         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        5.98         2.14         6.64         3.25        20.25        15.72 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4823 TCGA-B0-4824 
        0.59         5.52        45.07        16.77        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       29.10        78.44        68.71        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 
        6.71        11.64        10.29        39.45        26.07         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5099 TCGA-B0-5102 
        7.30        25.32        18.51        15.09        15.95        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 
       90.48        52.54        29.95        35.90        26.20        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 
        1.94        16.21        21.44        37.22        79.17       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
       48.89       101.13        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       90.12        52.77        39.55       120.59        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        31.30        10.36 
TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       32.98        16.67         9.57         5.75         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        4.64         0.36         0.23        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-5159 TCGA-B8-5162 
       25.05        24.66        17.19        25.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 
       27.02         0.85        24.23        17.16        16.60        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 
       85.51       101.06        93.34        99.85         0.43        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       77.03        62.24        61.78        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 
       15.16         0.07        93.99        18.48        52.24        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       49.08        44.94        12.23        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4769 
       72.59        77.98        77.62        44.15        71.80        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4801 
       60.95        48.95        36.53        20.38        37.25        36.95 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4965 TCGA-BP-4967 
       47.97         6.94        87.45        63.62        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 
       57.40        58.98        14.24        48.89        49.38         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       30.64        41.62        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       35.21        48.10        79.30         1.78        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        9.63        49.15        38.30        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 
       13.35        33.24        23.47        13.41        24.62        44.55 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4639 
       34.95         0.95        59.84        63.25        73.22        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4869 
       65.69        54.61        53.52        58.95        11.05        83.97 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       49.25        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       71.87        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4889 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 
       63.98        50.01        24.66        27.65        59.44        50.24 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4916 TCGA-CJ-4918 
       49.97        51.29        58.92        49.18        45.14         3.06 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 
       72.00        79.89        18.87        18.15        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 
       67.00        83.77        92.02        81.83        85.78        73.18 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35       105.93       103.43        25.45 
TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
        0.59        58.75        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 
       18.44        55.33        56.94        55.33        47.01        21.76 
TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 
       57.21         2.40        12.69        80.19        12.26        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       37.15        66.28        56.84        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC 
        4.18        10.29        35.87         2.01        19.96        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JK 
        4.57        67.30        75.42        34.85        56.81        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7288 
        5.29        16.18        22.49         0.13        11.57        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
       16.31        15.75         8.28        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       13.55        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        0.46         6.58        33.83        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
       10.16        50.50        28.18        26.40         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
        0.16        17.49        12.30        86.76        19.27        63.72 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       26.04        25.35         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       19.00        24.89        10.68         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM 
       51.78        48.62        39.25        25.15        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       17.98        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       16.34        12.36        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       84.95        92.58        52.27        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL 
       17.75        14.07        47.90        47.44        33.04        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       48.30        43.76        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 
       26.01        29.00        18.64        15.91        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                         0.13                          0.07 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                       141.73                        194.79 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                       28.870                        30.655 
[1] "0.1 - 141.7 (28.9)" "0.1 - 194.8 (30.7)"
[1] "hr=" "2.8"
D29V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 16(9P21.3) MUTATED        66       15        74       48
  DEL PEAK 16(9P21.3) WILD-TYPE     382       88       116       52
D29V3, multiclass
           clus
vv          DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  STAGE I                            66                           382
  STAGE II                           15                            88
  STAGE III                          74                           116
  STAGE IV                           48                            52
[1] 4 2
[1] 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(9P21.3) MUTATED    70  22 105   8
  DEL PEAK 16(9P21.3) WILD-TYPE 392 101 146   7
D29V4, multiclass
    clus
vv   DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  T1                          70                           392
  T2                          22                           101
  T3                         105                           146
  T4                           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                             N0  N1  N2
  DEL PEAK 16(9P21.3) MUTATED    77  24   2
  DEL PEAK 16(9P21.3) WILD-TYPE 240  19   4
D29V5, multiclass
    clus
vv   DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  N0                          77                           240
  N1                          24                            19
  N2                           2                             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"
D29V6, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P21.3) MUTATED   131  43
  DEL PEAK 16(9P21.3) WILD-TYPE 411  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED    131   43
  DEL PEAK 16(9P21.3) WILD-TYPE  411   46
   clus
vv  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  0                         131                           411
  1                          43                            46
[1] 2 2
[1] FALSE
D29V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P21.3) MUTATED    61 146
  DEL PEAK 16(9P21.3) WILD-TYPE 226 426
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED     61  146
  DEL PEAK 16(9P21.3) WILD-TYPE  226  426
        clus
vv       DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  FEMALE                          61                           226
  MALE                           146                           426
[1] 2 2
[1] FALSE
D29V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK 16(9P21.3) MUTATED                   10
  DEL PEAK 16(9P21.3) WILD-TYPE                 56
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 16(9P21.3) MUTATED                                 159
  DEL PEAK 16(9P21.3) WILD-TYPE                               365
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 16(9P21.3) MUTATED                                      38
  DEL PEAK 16(9P21.3) WILD-TYPE                                   231
D29V9, multiclass
                                       clus
vv                                      DEL PEAK 16(9P21.3) MUTATED
  KIDNEY CHROMOPHOBE                                             10
  KIDNEY CLEAR CELL RENAL CARCINOMA                             159
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          38
                                       clus
vv                                      DEL PEAK 16(9P21.3) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               56
  KIDNEY CLEAR CELL RENAL CARCINOMA                               365
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           231
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, continuous
D29V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(9P21.3) MUTATED                                  0     3
  DEL PEAK 16(9P21.3) WILD-TYPE                                2    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(9P21.3) MUTATED                          15   184
  DEL PEAK 16(9P21.3) WILD-TYPE                       101   518
D29V12, multiclass
                                  clus
vv                                 DEL PEAK 16(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                    184
                                  clus
vv                                 DEL PEAK 16(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                  101
  WHITE                                                      518
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P21.3) MUTATED     9 143
  DEL PEAK 16(9P21.3) WILD-TYPE  33 454
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED      9  143
  DEL PEAK 16(9P21.3) WILD-TYPE   33  454
                        clus
vv                       DEL PEAK 16(9P21.3) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         143
                        clus
vv                       DEL PEAK 16(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                33
  NOT HISPANIC OR LATINO                           454
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK 17(10Q23.31) MUTATION ANALYSIS
D30V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 17(10Q23.31) MUTATED   112  48
  DEL PEAK 17(10Q23.31) WILD-TYPE 520 163
  DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE 
                            160                             683 
  DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE 
                             48                             163 
$`DEL PEAK 17(10Q23.31) MUTATED`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       137.06       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       71.41        54.74        62.37        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       52.27        87.12         2.50        59.08       115.00        42.35 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       80.38       103.27        77.85        57.17        61.58        63.95 
TCGA-A3-3316 TCGA-A3-3331 TCGA-A3-3346 TCGA-A3-3352 TCGA-A3-3374 TCGA-A3-3380 
       49.08        48.82         4.50        18.44        43.20        18.64 
TCGA-A3-A6NN TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3458 
        0.10        15.78        72.07        57.37        46.78        38.40 
TCGA-AK-3461 TCGA-AK-3465 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 
       28.04        12.13         3.32         1.41         3.48        28.47 
TCGA-B0-4699 TCGA-B0-4712 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4819 TCGA-B0-4828 
        3.62        43.96        20.25        46.59         6.02        10.09 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-5099 
       40.70        45.30        11.64        10.29        65.29        15.95 
TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5703 TCGA-B0-5706 TCGA-B2-3923 TCGA-B2-5641 
       17.59        14.76        39.55        79.36        32.61        21.57 
TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-5158 TCGA-B8-5549 TCGA-B8-5550 
        0.53         5.46        23.31        20.91         6.38        14.27 
TCGA-B8-A7U6 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4329 
       16.27        90.28        32.61         0.43        89.36        27.78 
TCGA-BP-4334 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4766 TCGA-BP-4770 
       21.21        74.17        62.86        31.89        48.07        10.82 
TCGA-BP-4775 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4973 TCGA-BP-4985 
       60.59        36.39         6.71        71.41        45.50        31.30 
TCGA-BP-4994 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5173 TCGA-BP-5180 TCGA-BP-5185 
       43.00        28.87         6.35         1.78        74.40        37.22 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4642 TCGA-CJ-4644 
       33.47        19.82        31.27        46.55        53.52        11.05 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4882 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 
       47.18        75.06        61.91        24.66        59.44        47.67 
TCGA-CJ-4907 TCGA-CJ-4923 TCGA-CJ-5676 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-6090 
       49.28        18.81        84.66        83.77         7.36        83.90 
TCGA-CZ-4860 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 
        6.77        55.33        47.01        47.54         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-DV-5565 TCGA-DV-5566 TCGA-EU-5907 TCGA-G6-A8L8 
       12.69        80.19        43.69        45.96         4.18        35.87 
TCGA-2Z-A9J8 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5882 
       67.30        12.99         9.63         2.10        19.27        21.63 
TCGA-DZ-6131 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC 
       79.86         0.43         4.01        13.68        25.84        17.33 
TCGA-GL-7966 TCGA-J7-8537 TCGA-MH-A857 TCGA-Q2-A5QZ 
        3.68         0.13        21.44        14.07 

$`DEL PEAK 17(10Q23.31) WILD-TYPE`
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8344 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8441 
      141.73       109.22        28.80       151.96        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
       51.06        31.33        23.47        25.91         3.55         0.99 
TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z 
       19.33        11.21       100.87        87.78        86.10        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.16        36.82        47.21         0.53        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
       24.69        37.38        21.86        34.29        31.07        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       45.53        29.92        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
       10.49        28.70        74.63        74.76        24.16        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       55.76        20.71        18.87        28.31        65.52        20.28 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       15.39        22.65         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 
       29.10        84.36        73.08        66.31        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       67.20        48.36        42.08        40.01        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 TCGA-AS-3777 
       45.93        28.73        22.45        37.58        31.27        40.70 
TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 
        1.41         4.57         2.53        19.00         1.38        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4713 
        7.82         5.98         2.14        19.73         3.16         6.64 
TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
        3.25        15.72         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       29.10        78.44        68.71        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       56.68        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       21.86        52.08        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       21.60         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      120.59       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       97.41        35.90         1.68        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       11.77        10.36        32.98        16.67         9.57         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
        0.23         1.25         4.64         0.36         0.23        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       25.91        23.01        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       24.23        17.16        16.60         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       17.36        15.42        14.17       111.02        85.51        94.72 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
      101.06        93.34        99.85        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        80.68        37.25        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        54.77        49.08        44.94        12.23 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       11.31        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       13.15        61.68         5.33        61.97        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 
       20.38        10.98        37.25        36.95        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       87.45        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       46.45        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       16.47         5.82        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       48.10        79.30        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
       62.86        49.15        38.30        42.44        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
       24.62        44.55        34.95         0.95        59.84        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        54.61        58.95 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4875 
       21.24        83.97        49.25        79.66        74.27        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       64.27        71.87        66.21        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       27.65        39.45        50.24        56.35        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       58.92        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 
        3.06         4.57        63.88        72.00        79.89        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
       62.66        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 
       18.44        56.28        56.94        55.33        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5984 TCGA-CZ-5985 
       21.76        57.21        22.52         2.40        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5567 TCGA-DV-5568 
       12.26        14.63        22.78        62.63        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       11.67        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
       18.12         3.91         6.77         7.96        10.29        70.13 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE 
        2.01        19.43        19.96        15.25        10.85         7.04 
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-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       75.42        34.85        56.81        54.64        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       25.58         5.29        16.18        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       11.57        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       15.75         8.28        12.46        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       30.35        25.08        44.61        49.25         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-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 
        6.81         0.16        14.86        17.49        12.30        86.76 
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-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        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         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
       67.17        22.26        21.34        16.34        12.36        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       20.25         0.36        12.13        25.97        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.22        42.94         6.61        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
       16.01        50.60        78.90        12.85        17.75        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       18.02        60.03        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE 
                           0.10                            0.07 
  DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE 
                         137.06                          194.79 
  DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE 
                         40.125                          29.030 
[1] "0.1 - 137.1 (40.1)" "0.1 - 194.8 (29.0)"
[1] "hr=" "1.1"
D30V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 17(10Q23.31) MUTATED        52       32        53       25
  DEL PEAK 17(10Q23.31) WILD-TYPE     396       71       137       75
D30V3, multiclass
           clus
vv          DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE
  STAGE I                              52                             396
  STAGE II                             32                              71
  STAGE III                            53                             137
  STAGE IV                             25                              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"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 17(10Q23.31) MUTATED    53  33  69   7
  DEL PEAK 17(10Q23.31) WILD-TYPE 409  90 182   8
D30V4, multiclass
    clus
vv   DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE
  T1                            53                             409
  T2                            33                              90
  T3                            69                             182
  T4                             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                               N0  N1  N2
  DEL PEAK 17(10Q23.31) MUTATED    76  10   3
  DEL PEAK 17(10Q23.31) WILD-TYPE 241  33   3
D30V5, multiclass
    clus
vv   DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE
  N0                            76                             241
  N1                            10                              33
  N2                             3                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10Q23.31) MUTATED   111  19
  DEL PEAK 17(10Q23.31) WILD-TYPE 431  70
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10Q23.31) MUTATED    111   19
  DEL PEAK 17(10Q23.31) WILD-TYPE  431   70
   clus
vv  DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE
  0                           111                             431
  1                            19                              70
[1] 2 2
[1] FALSE
D30V7, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10Q23.31) MUTATED    52 110
  DEL PEAK 17(10Q23.31) WILD-TYPE 235 462
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10Q23.31) MUTATED     52  110
  DEL PEAK 17(10Q23.31) WILD-TYPE  235  462
        clus
vv       DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE
  FEMALE                            52                             235
  MALE                             110                             462
[1] 2 2
[1] FALSE
D30V8, continuous
                                 vv
clus                              KIDNEY CHROMOPHOBE
  DEL PEAK 17(10Q23.31) MUTATED                   49
  DEL PEAK 17(10Q23.31) WILD-TYPE                 17
                                 vv
clus                              KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 17(10Q23.31) MUTATED                                  96
  DEL PEAK 17(10Q23.31) WILD-TYPE                               428
                                 vv
clus                              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 17(10Q23.31) MUTATED                                      17
  DEL PEAK 17(10Q23.31) WILD-TYPE                                   252
D30V9, multiclass
                                       clus
vv                                      DEL PEAK 17(10Q23.31) MUTATED
  KIDNEY CHROMOPHOBE                                               49
  KIDNEY CLEAR CELL RENAL CARCINOMA                                96
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            17
                                       clus
vv                                      DEL PEAK 17(10Q23.31) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                 17
  KIDNEY CLEAR CELL RENAL CARCINOMA                                 428
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                             252
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, continuous
D30V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(10Q23.31) MUTATED                                  0     4
  DEL PEAK 17(10Q23.31) WILD-TYPE                                2    11
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(10Q23.31) MUTATED                          13   139
  DEL PEAK 17(10Q23.31) WILD-TYPE                       103   563
D30V12, multiclass
                                  clus
vv                                 DEL PEAK 17(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                      139
                                  clus
vv                                 DEL PEAK 17(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                         11
  BLACK OR AFRICAN AMERICAN                                    103
  WHITE                                                        563
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10Q23.31) MUTATED     9  95
  DEL PEAK 17(10Q23.31) WILD-TYPE  33 502
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10Q23.31) MUTATED      9   95
  DEL PEAK 17(10Q23.31) WILD-TYPE   33  502
                        clus
vv                       DEL PEAK 17(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                            95
                        clus
vv                       DEL PEAK 17(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  33
  NOT HISPANIC OR LATINO                             502
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK 18(11Q21) MUTATION ANALYSIS
D31V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 18(11Q21) MUTATED    37  22
  DEL PEAK 18(11Q21) WILD-TYPE 595 189
  DEL PEAK 18(11Q21) MUTATED DEL PEAK 18(11Q21) WILD-TYPE 
                          59                          784 
  DEL PEAK 18(11Q21) MUTATED DEL PEAK 18(11Q21) WILD-TYPE 
                          22                          189 
$`DEL PEAK 18(11Q21) MUTATED`
TCGA-KL-8328 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8345 TCGA-KM-8443 TCGA-KN-8427 
      102.81        98.96        28.11        54.74        49.97         0.99 
TCGA-KN-8428 TCGA-KN-8434 TCGA-KN-8436 TCGA-A3-3316 TCGA-A3-3346 TCGA-AK-3425 
       52.27        59.08        42.35        49.08         4.50       109.91 
TCGA-AK-3465 TCGA-B0-4696 TCGA-B0-4707 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-5084 
       12.13        28.47        19.73         6.02        36.53         7.30 
TCGA-B0-5094 TCGA-B0-5702 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4154 
       10.95        52.77        21.57         0.23         5.46        24.66 
TCGA-BP-4352 TCGA-BP-4768 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-5173 TCGA-BP-5201 
       11.31        13.15        31.30        25.81         1.78        31.27 
TCGA-CW-5588 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-2Z-A9JE TCGA-2Z-A9JG 
       66.31        47.54         1.94        31.10        56.81        54.64 
TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B9-A44B TCGA-BQ-5876 
       51.52        12.82        12.99         7.33         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        10.88         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         0.13 
TCGA-PJ-A5Z8 TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-Y8-A894 TCGA-Y8-A896 
       12.85        86.27        52.11        18.64        18.64 

$`DEL PEAK 18(11Q21) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       28.80        62.37       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       47.24       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8435 TCGA-KN-8437 
       87.12        19.33         2.50        11.21       115.00       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78       103.27        86.10        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       61.58        63.95        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        24.16        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
       48.59        36.36        38.99        24.69        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       21.86        34.29        31.07        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       10.62        29.10        84.36        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       60.92        72.07        68.61        67.20        57.37        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       48.36        42.08        40.01        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       40.70         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
        3.48        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        5.98         2.14         3.16        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       20.25        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4824 
       45.07        33.50        16.77        40.44        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 
       70.52        20.94        43.30        11.24        11.90        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       18.51        15.09         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       16.67         9.57         5.75         1.25         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       25.05        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       93.99        18.48        52.24        74.17        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4988 
       14.93        36.07        33.34        46.45        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
       79.30        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
       75.88        65.69        54.61        53.52        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15        61.91        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        57.21        22.52         2.40 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        43.69        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       11.67        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        15.25 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       10.85         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       56.91         4.57        67.30        75.42        34.85        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y 
       25.58         5.29        16.18        22.49         0.13        11.57 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-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        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       30.35        25.08        44.61        49.25         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        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         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 
        0.16        14.86        17.49        12.30        86.76        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.20        47.80        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       26.04        25.35        13.25         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
        2.76        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       54.90        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        2.40         1.18        51.78        48.62        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       25.15        13.68         6.38        17.98        17.33        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       21.93         0.53        38.86        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 
       12.99        26.01        29.00        15.91        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  DEL PEAK 18(11Q21) MUTATED DEL PEAK 18(11Q21) WILD-TYPE 
                        0.13                         0.07 
  DEL PEAK 18(11Q21) MUTATED DEL PEAK 18(11Q21) WILD-TYPE 
                      123.62                       194.79 
  DEL PEAK 18(11Q21) MUTATED DEL PEAK 18(11Q21) WILD-TYPE 
                      19.730                       31.135 
[1] "0.1 - 123.6 (19.7)" "0.1 - 194.8 (31.1)"
[1] "hr=" "2"  
D31V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 18(11Q21) MUTATED        16       11        20       12
  DEL PEAK 18(11Q21) WILD-TYPE     432       92       170       88
D31V3, multiclass
           clus
vv          DEL PEAK 18(11Q21) MUTATED DEL PEAK 18(11Q21) WILD-TYPE
  STAGE I                           16                          432
  STAGE II                          11                           92
  STAGE III                         20                          170
  STAGE IV                          12                           88
[1] 4 2
[1] 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(11Q21) MUTATED    17  12  29   1
  DEL PEAK 18(11Q21) WILD-TYPE 445 111 222  14
D31V4, multiclass
    clus
vv   DEL PEAK 18(11Q21) MUTATED DEL PEAK 18(11Q21) WILD-TYPE
  T1                         17                          445
  T2                         12                          111
  T3                         29                          222
  T4                          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                            N0  N1  N2
  DEL PEAK 18(11Q21) MUTATED    21  11   2
  DEL PEAK 18(11Q21) WILD-TYPE 296  32   4
D31V5, multiclass
    clus
vv   DEL PEAK 18(11Q21) MUTATED DEL PEAK 18(11Q21) WILD-TYPE
  N0                         21                          296
  N1                         11                           32
  N2                          2                            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 18(11Q21) MUTATED    30   9
  DEL PEAK 18(11Q21) WILD-TYPE 512  80
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 18(11Q21) MUTATED     30    9
  DEL PEAK 18(11Q21) WILD-TYPE  512   80
   clus
vv  DEL PEAK 18(11Q21) MUTATED DEL PEAK 18(11Q21) WILD-TYPE
  0                         30                          512
  1                          9                           80
[1] 2 2
[1] FALSE
D31V7, binary
                              cls
clus                             0   1
  DEL PEAK 18(11Q21) MUTATED    18  42
  DEL PEAK 18(11Q21) WILD-TYPE 269 530
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 18(11Q21) MUTATED     18   42
  DEL PEAK 18(11Q21) WILD-TYPE  269  530
        clus
vv       DEL PEAK 18(11Q21) MUTATED DEL PEAK 18(11Q21) WILD-TYPE
  FEMALE                         18                          269
  MALE                           42                          530
[1] 2 2
[1] FALSE
D31V8, continuous
                              vv
clus                           KIDNEY CHROMOPHOBE
  DEL PEAK 18(11Q21) MUTATED                    9
  DEL PEAK 18(11Q21) WILD-TYPE                 57
                              vv
clus                           KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 18(11Q21) MUTATED                                  25
  DEL PEAK 18(11Q21) WILD-TYPE                               499
                              vv
clus                           KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 18(11Q21) MUTATED                                      26
  DEL PEAK 18(11Q21) WILD-TYPE                                   243
D31V9, multiclass
                                       clus
vv                                      DEL PEAK 18(11Q21) MUTATED
  KIDNEY CHROMOPHOBE                                             9
  KIDNEY CLEAR CELL RENAL CARCINOMA                             25
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                         26
                                       clus
vv                                      DEL PEAK 18(11Q21) WILD-TYPE
  KIDNEY CHROMOPHOBE                                              57
  KIDNEY CLEAR CELL RENAL CARCINOMA                              499
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          243
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, continuous
D31V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(11Q21) MUTATED                                  0     2
  DEL PEAK 18(11Q21) WILD-TYPE                                2    13
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(11Q21) MUTATED                           6    49
  DEL PEAK 18(11Q21) WILD-TYPE                       110   653
D31V12, multiclass
                                  clus
vv                                 DEL PEAK 18(11Q21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 6
  WHITE                                                    49
                                  clus
vv                                 DEL PEAK 18(11Q21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                      13
  BLACK OR AFRICAN AMERICAN                                 110
  WHITE                                                     653
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, binary
                              cls
clus                             0   1
  DEL PEAK 18(11Q21) MUTATED     1  43
  DEL PEAK 18(11Q21) WILD-TYPE  41 554
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 18(11Q21) MUTATED      1   43
  DEL PEAK 18(11Q21) WILD-TYPE   41  554
                        clus
vv                       DEL PEAK 18(11Q21) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         43
                        clus
vv                       DEL PEAK 18(11Q21) WILD-TYPE
  HISPANIC OR LATINO                               41
  NOT HISPANIC OR LATINO                          554
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK 19(11Q23.1) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(11Q23.1) MUTATED    43  25
  DEL PEAK 19(11Q23.1) WILD-TYPE 589 186
  DEL PEAK 19(11Q23.1) MUTATED DEL PEAK 19(11Q23.1) WILD-TYPE 
                            68                            775 
  DEL PEAK 19(11Q23.1) MUTATED DEL PEAK 19(11Q23.1) WILD-TYPE 
                            25                            186 
$`DEL PEAK 19(11Q23.1) MUTATED`
TCGA-KL-8328 TCGA-KL-8331 TCGA-KL-8345 TCGA-KM-8443 TCGA-KN-8427 TCGA-KN-8428 
      102.81        98.96        54.74        49.97         0.99        52.27 
TCGA-KN-8434 TCGA-KN-8436 TCGA-KO-8404 TCGA-A3-3316 TCGA-A3-3346 TCGA-AK-3425 
       59.08        42.35        10.68        49.08         4.50       109.91 
TCGA-AK-3465 TCGA-B0-4690 TCGA-B0-4696 TCGA-B0-4707 TCGA-B0-4819 TCGA-B0-4822 
       12.13         1.41        28.47        19.73         6.02        36.53 
TCGA-B0-5084 TCGA-B0-5094 TCGA-B0-5702 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5838 
        7.30        10.95        52.77        21.57         0.23         5.46 
TCGA-BP-4352 TCGA-BP-4768 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-5173 
       11.31        13.15        46.45        31.30        25.81         1.78 
TCGA-BP-5201 TCGA-CW-5588 TCGA-CW-6088 TCGA-CZ-5458 TCGA-CZ-5465 TCGA-CZ-5468 
       31.27        66.31       105.93        56.94        47.54         1.94 
TCGA-CZ-5469 TCGA-CZ-5985 TCGA-G6-A8L7 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JG 
       31.10        65.65        70.13         4.57        56.81        54.64 
TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-4104 
       51.52        12.82        12.99        49.25         7.33        34.49 
TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5889 TCGA-BQ-5890 
        2.10        19.27         8.88        21.63        10.88         7.66 
TCGA-BQ-7044 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LD 
      123.62         0.43         4.01        11.05        25.84        16.90 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-PJ-A5Z8 TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-Y8-A894 
        2.04         0.13        12.85        86.27        52.11        18.64 
TCGA-Y8-A896 TCGA-Y8-A8S1 
       18.64        13.28 

$`DEL PEAK 19(11Q23.1) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       71.41        28.80        62.37       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       28.80        47.24       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19       104.52 
TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8435 
        3.55        87.12        19.33         2.50        11.21       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87        76.90        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78       103.27        86.10        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       61.58        63.95        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        24.16        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
       48.59        36.36        38.99        24.69        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       21.86        34.29        31.07        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       10.62        29.10        84.36        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       60.92        72.07        68.61        67.20        57.37        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       48.36        42.08        40.01        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         3.32         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        2.14         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       33.50        16.77        40.44        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.24        11.90        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       15.09         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 
       56.78        60.33        84.92        90.12        56.94        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR 
       21.30        31.30        11.77        10.36        32.98        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
        9.57         5.75         1.25         0.53         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       93.99        18.48        52.24        74.17        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       14.93        36.07        33.34        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 
       24.62        33.47        19.82        44.55        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       65.69        54.61        53.52        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       61.91        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        73.18        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       55.33        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
       57.21        22.52         2.40        12.69        80.19        67.96 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
        7.96        10.29        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.25        10.85         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
      100.27        56.91        67.30        75.42        34.85        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y 
       25.58         5.29        16.18        22.49         0.13        11.57 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-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        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       33.83        10.09        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-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       43.99        22.06        19.23         6.81         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       17.49        12.30        86.76        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-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 
       13.25         0.95        11.97         7.92         2.76        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.78        48.62        39.25        34.82        25.15        13.68 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
        6.38        17.98        17.33        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25         5.49        16.80        19.99        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
       67.17        22.26        21.34        16.34        12.36        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       52.27        16.01        50.60        78.90        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       38.86        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       29.00        15.91        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 
        6.02 

  DEL PEAK 19(11Q23.1) MUTATED DEL PEAK 19(11Q23.1) WILD-TYPE 
                          0.13                           0.07 
  DEL PEAK 19(11Q23.1) MUTATED DEL PEAK 19(11Q23.1) WILD-TYPE 
                        123.62                         194.79 
  DEL PEAK 19(11Q23.1) MUTATED DEL PEAK 19(11Q23.1) WILD-TYPE 
                         20.65                          30.67 
[1] "0.1 - 123.6 (20.6)" "0.1 - 194.8 (30.7)"
[1] "hr=" "1.8"
D32V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 19(11Q23.1) MUTATED        18       13        24       14
  DEL PEAK 19(11Q23.1) WILD-TYPE     430       90       166       86
D32V3, multiclass
           clus
vv          DEL PEAK 19(11Q23.1) MUTATED DEL PEAK 19(11Q23.1) WILD-TYPE
  STAGE I                             18                            430
  STAGE II                            13                             90
  STAGE III                           24                            166
  STAGE IV                            14                             86
[1] 4 2
[1] 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(11Q23.1) MUTATED    19  15  32   3
  DEL PEAK 19(11Q23.1) WILD-TYPE 443 108 219  12
D32V4, multiclass
    clus
vv   DEL PEAK 19(11Q23.1) MUTATED DEL PEAK 19(11Q23.1) WILD-TYPE
  T1                           19                            443
  T2                           15                            108
  T3                           32                            219
  T4                            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                              N0  N1  N2
  DEL PEAK 19(11Q23.1) MUTATED    24  11   2
  DEL PEAK 19(11Q23.1) WILD-TYPE 293  32   4
D32V5, multiclass
    clus
vv   DEL PEAK 19(11Q23.1) MUTATED DEL PEAK 19(11Q23.1) WILD-TYPE
  N0                           24                            293
  N1                           11                             32
  N2                            2                              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"
D32V6, binary
                                cls
clus                               0   1
  DEL PEAK 19(11Q23.1) MUTATED    34  10
  DEL PEAK 19(11Q23.1) WILD-TYPE 508  79
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q23.1) MUTATED     34   10
  DEL PEAK 19(11Q23.1) WILD-TYPE  508   79
   clus
vv  DEL PEAK 19(11Q23.1) MUTATED DEL PEAK 19(11Q23.1) WILD-TYPE
  0                           34                            508
  1                           10                             79
[1] 2 2
[1] FALSE
D32V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(11Q23.1) MUTATED    20  50
  DEL PEAK 19(11Q23.1) WILD-TYPE 267 522
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q23.1) MUTATED     20   50
  DEL PEAK 19(11Q23.1) WILD-TYPE  267  522
        clus
vv       DEL PEAK 19(11Q23.1) MUTATED DEL PEAK 19(11Q23.1) WILD-TYPE
  FEMALE                           20                            267
  MALE                             50                            522
[1] 2 2
[1] FALSE
D32V8, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  DEL PEAK 19(11Q23.1) MUTATED                    9
  DEL PEAK 19(11Q23.1) WILD-TYPE                 57
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 19(11Q23.1) MUTATED                                  30
  DEL PEAK 19(11Q23.1) WILD-TYPE                               494
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 19(11Q23.1) MUTATED                                      31
  DEL PEAK 19(11Q23.1) WILD-TYPE                                   238
D32V9, multiclass
                                       clus
vv                                      DEL PEAK 19(11Q23.1) MUTATED
  KIDNEY CHROMOPHOBE                                               9
  KIDNEY CLEAR CELL RENAL CARCINOMA                               30
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           31
                                       clus
vv                                      DEL PEAK 19(11Q23.1) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                57
  KIDNEY CLEAR CELL RENAL CARCINOMA                                494
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            238
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, continuous
D32V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(11Q23.1) MUTATED                                  0     3
  DEL PEAK 19(11Q23.1) WILD-TYPE                                2    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(11Q23.1) MUTATED                           7    57
  DEL PEAK 19(11Q23.1) WILD-TYPE                       109   645
D32V12, multiclass
                                  clus
vv                                 DEL PEAK 19(11Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      57
                                  clus
vv                                 DEL PEAK 19(11Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        12
  BLACK OR AFRICAN AMERICAN                                   109
  WHITE                                                       645
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, binary
                                cls
clus                               0   1
  DEL PEAK 19(11Q23.1) MUTATED     1  52
  DEL PEAK 19(11Q23.1) WILD-TYPE  41 545
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q23.1) MUTATED      1   52
  DEL PEAK 19(11Q23.1) WILD-TYPE   41  545
                        clus
vv                       DEL PEAK 19(11Q23.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           52
                        clus
vv                       DEL PEAK 19(11Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 41
  NOT HISPANIC OR LATINO                            545
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK 20(13Q12.13) MUTATION ANALYSIS
D33V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 20(13Q12.13) MUTATED    93  53
  DEL PEAK 20(13Q12.13) WILD-TYPE 539 158
  DEL PEAK 20(13Q12.13) MUTATED DEL PEAK 20(13Q12.13) WILD-TYPE 
                            146                             697 
  DEL PEAK 20(13Q12.13) MUTATED DEL PEAK 20(13Q12.13) WILD-TYPE 
                             53                             158 
$`DEL PEAK 20(13Q12.13) MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       141.73       137.06       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       98.96        84.89        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KM-8438 TCGA-KM-8440 
       86.56        28.11        66.54        24.79       151.96        44.91 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
       47.24        49.97       123.12       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       65.19       104.52         0.99        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
        2.50        59.08       115.00        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8416 
       79.04        92.71        16.67        80.38        77.85        61.58 
TCGA-KO-8417 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3370 TCGA-A3-3374 
       63.95        37.15         4.50        52.93        74.76        43.20 
TCGA-AK-3426 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3465 TCGA-AS-3777 
       29.10        72.07        57.37        42.08        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        1.41         4.57        28.47         1.38         3.62        65.10 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4815 TCGA-B0-4819 
       19.73         3.16        43.96         6.64        52.21         6.02 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5099 TCGA-B0-5113 TCGA-B0-5117 
       15.09        10.95         8.05        15.95        11.80        17.59 
TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-5163 TCGA-B8-5549 TCGA-BP-4167 
        0.23         0.53         5.46        27.02         6.38        89.36 
TCGA-BP-4334 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4761 
       21.21        62.86        31.89        11.31        33.99         5.98 
TCGA-BP-4765 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4964 
       71.80        13.15        10.82        15.78        36.39        61.22 
TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5175 
       57.40        45.50        31.30        43.00        37.02        30.64 
TCGA-BP-5184 TCGA-BP-5191 TCGA-BP-5196 TCGA-CJ-4639 TCGA-CJ-4868 TCGA-CJ-4881 
       37.25        31.79        33.47        75.88        21.24        66.21 
TCGA-CJ-4901 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-6090 
       47.67        25.71        22.32        53.42        66.31        83.90 
TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4863 TCGA-CZ-4864 
       18.77        46.16        47.08         6.77        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 
       61.41        18.44        55.33        47.54         1.94        31.10 
TCGA-CZ-5984 TCGA-DV-5568 TCGA-G6-A8L7 TCGA-2Z-A9JI TCGA-A4-7287 TCGA-A4-7915 
       67.96        12.16        70.13        51.52        19.63         0.23 
TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B3-A6W5 TCGA-BQ-5875 TCGA-BQ-5879 TCGA-BQ-5882 
       49.25        10.09        10.16        86.76        22.92        21.63 
TCGA-BQ-5894 TCGA-BQ-7061 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 
        2.76         7.17        10.68        13.08         4.01        11.05 
TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-J7-8537 TCGA-P4-A5E8 
       25.84        17.33        16.90         3.68         0.13        42.94 
TCGA-Q2-A5QZ TCGA-UN-AAZ9 
       14.07        18.02 

$`DEL PEAK 20(13Q12.13) WILD-TYPE`
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       23.84       109.22        98.33        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 
       54.74        62.37        23.28        28.80        51.06        31.33 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 TCGA-KN-8436 TCGA-KN-8437 
       23.47        25.91         3.55        11.21        42.35       100.87 
TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 TCGA-3Z-A93Z TCGA-6D-AA2E 
       87.78       103.27        86.10        57.17        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       49.02        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 
       37.38        48.82        21.86        34.29        31.07        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       29.92        18.44        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
       10.49        28.70        74.63        24.16        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91        84.36        73.08        66.31        15.78        60.92 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 
       68.61        67.20        46.78        48.36        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       48.69        45.93        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4693 TCGA-B0-4694 
       31.27        28.04         1.41         3.32         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4714 TCGA-B0-4718 
       19.00         7.82         5.98         2.14         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         0.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5102 
       18.51         2.24        21.86        52.08        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       26.20        21.60         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       37.22        14.76        79.17       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       56.94        52.77        39.55       120.59        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        12.30        21.30        31.30        11.77 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       10.36        32.98        21.57        16.67         9.57         5.75 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        1.25         4.64         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 
       25.91        23.01        20.91        23.74         1.18         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       24.23        17.16        16.60        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       99.85         0.43        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        80.68        37.25        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        74.17        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.23        12.33        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 
       77.62        44.15        41.75        48.07        61.68         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 
       60.95        48.95        36.53        20.38        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 
       63.62        58.68        60.30        61.51         6.74        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       14.24        48.89        49.38         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 
       30.64        41.62        18.51        38.70        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
        1.78        74.20        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       49.15        38.30        42.44        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 
       27.02        33.24        23.47        13.41        24.62        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       63.25        73.22        14.17        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       58.95        11.05        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 
       74.27        75.06        77.36        64.27        71.87        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       59.44        50.24        56.35        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       84.66        18.87        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        53.26        60.99        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       83.77         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       85.78        73.18        78.18        74.66         1.35       105.93 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
      103.43        25.45         0.59        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       60.59         5.46        63.42        58.82         0.82        23.74 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       56.28        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 
       21.76        57.21        22.52         2.40        12.69        80.19 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       45.96        65.88        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
        7.96        10.29        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.25        10.85         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
      100.27        56.91         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       56.81        54.64        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       24.33        31.20        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 
       22.49         0.13        12.82        11.57        18.21        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 
        0.10        35.18        19.13         0.89        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 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
        2.20        19.56         7.33        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 
        3.55        16.77         0.46         6.58        33.83        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-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23         6.81         0.16        14.86        17.49        12.30 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       19.27         8.88        63.72        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-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-7062 
       26.27        20.12        11.28         7.63         7.04         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
       24.89         2.40         1.18         0.43        51.78        48.62 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
       39.25        34.82        25.15        13.68         6.38        17.98 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65       194.79        12.92        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       16.34        12.36        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA 
       25.97        21.44        15.48        99.78        87.22         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       26.47        48.30        43.76        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  DEL PEAK 20(13Q12.13) MUTATED DEL PEAK 20(13Q12.13) WILD-TYPE 
                           0.13                            0.07 
  DEL PEAK 20(13Q12.13) MUTATED DEL PEAK 20(13Q12.13) WILD-TYPE 
                         151.96                          194.79 
  DEL PEAK 20(13Q12.13) MUTATED DEL PEAK 20(13Q12.13) WILD-TYPE 
                         36.705                          29.460 
[1] "0.1 - 152.0 (36.7)" "0.1 - 194.8 (29.5)"
[1] "hr=" "1.4"
D33V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 20(13Q12.13) MUTATED        46       24        50       28
  DEL PEAK 20(13Q12.13) WILD-TYPE     402       79       140       72
D33V3, multiclass
           clus
vv          DEL PEAK 20(13Q12.13) MUTATED DEL PEAK 20(13Q12.13) WILD-TYPE
  STAGE I                              46                             402
  STAGE II                             24                              79
  STAGE III                            50                             140
  STAGE IV                             28                              72
[1] 4 2
[1] 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(13Q12.13) MUTATED    48  26  65   9
  DEL PEAK 20(13Q12.13) WILD-TYPE 414  97 186   6
D33V4, multiclass
    clus
vv   DEL PEAK 20(13Q12.13) MUTATED DEL PEAK 20(13Q12.13) WILD-TYPE
  T1                            48                             414
  T2                            26                              97
  T3                            65                             186
  T4                             9                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 20(13Q12.13) MUTATED    68  14   4
  DEL PEAK 20(13Q12.13) WILD-TYPE 249  29   2
D33V5, multiclass
    clus
vv   DEL PEAK 20(13Q12.13) MUTATED DEL PEAK 20(13Q12.13) WILD-TYPE
  N0                            68                             249
  N1                            14                              29
  N2                             4                               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"
D33V6, binary
                                 cls
clus                                0   1
  DEL PEAK 20(13Q12.13) MUTATED    91  20
  DEL PEAK 20(13Q12.13) WILD-TYPE 451  69
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.13) MUTATED     91   20
  DEL PEAK 20(13Q12.13) WILD-TYPE  451   69
   clus
vv  DEL PEAK 20(13Q12.13) MUTATED DEL PEAK 20(13Q12.13) WILD-TYPE
  0                            91                             451
  1                            20                              69
[1] 2 2
[1] FALSE
D33V7, binary
                                 cls
clus                                0   1
  DEL PEAK 20(13Q12.13) MUTATED    62  86
  DEL PEAK 20(13Q12.13) WILD-TYPE 225 486
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.13) MUTATED     62   86
  DEL PEAK 20(13Q12.13) WILD-TYPE  225  486
        clus
vv       DEL PEAK 20(13Q12.13) MUTATED DEL PEAK 20(13Q12.13) WILD-TYPE
  FEMALE                            62                             225
  MALE                              86                             486
[1] 2 2
[1] FALSE
D33V8, continuous
                                 vv
clus                              KIDNEY CHROMOPHOBE
  DEL PEAK 20(13Q12.13) MUTATED                   44
  DEL PEAK 20(13Q12.13) WILD-TYPE                 22
                                 vv
clus                              KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 20(13Q12.13) MUTATED                                  81
  DEL PEAK 20(13Q12.13) WILD-TYPE                               443
                                 vv
clus                              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 20(13Q12.13) MUTATED                                      23
  DEL PEAK 20(13Q12.13) WILD-TYPE                                   246
D33V9, multiclass
                                       clus
vv                                      DEL PEAK 20(13Q12.13) MUTATED
  KIDNEY CHROMOPHOBE                                               44
  KIDNEY CLEAR CELL RENAL CARCINOMA                                81
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            23
                                       clus
vv                                      DEL PEAK 20(13Q12.13) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                 22
  KIDNEY CLEAR CELL RENAL CARCINOMA                                 443
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                             246
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, continuous
D33V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(13Q12.13) MUTATED                                  0     4
  DEL PEAK 20(13Q12.13) WILD-TYPE                                2    11
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(13Q12.13) MUTATED                          12   127
  DEL PEAK 20(13Q12.13) WILD-TYPE                       104   575
D33V12, multiclass
                                  clus
vv                                 DEL PEAK 20(13Q12.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                      127
                                  clus
vv                                 DEL PEAK 20(13Q12.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                         11
  BLACK OR AFRICAN AMERICAN                                    104
  WHITE                                                        575
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, binary
                                 cls
clus                                0   1
  DEL PEAK 20(13Q12.13) MUTATED     4  93
  DEL PEAK 20(13Q12.13) WILD-TYPE  38 504
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(13Q12.13) MUTATED      4   93
  DEL PEAK 20(13Q12.13) WILD-TYPE   38  504
                        clus
vv                       DEL PEAK 20(13Q12.13) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            93
                        clus
vv                       DEL PEAK 20(13Q12.13) WILD-TYPE
  HISPANIC OR LATINO                                  38
  NOT HISPANIC OR LATINO                             504
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 21(13Q14.2) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(13Q14.2) MUTATED    93  53
  DEL PEAK 21(13Q14.2) WILD-TYPE 539 158
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           146                            697 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                            53                            158 
$`DEL PEAK 21(13Q14.2) MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       141.73       137.06       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       98.96        84.89        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KM-8438 TCGA-KM-8440 
       86.56        28.11        66.54        24.79       151.96        44.91 
TCGA-KM-8442 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       47.24       123.12       129.37        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
      104.52         0.99        52.27        87.12        19.33         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       59.08       115.00        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
       92.71        16.67        80.38        77.85        61.58        63.95 
TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3370 TCGA-A3-3374 TCGA-AK-3426 
       37.15         4.50        52.93        74.76        43.20        29.10 
TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4688 
       72.07        57.37        42.08        12.13        40.70         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 
        1.41         4.57        28.47         1.38         3.62        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-5092 
        3.16        43.96         6.64        52.21         6.02        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5099 TCGA-B0-5113 TCGA-B0-5117 TCGA-B0-5696 
       10.95         8.05        15.95        11.80        17.59        56.78 
TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-5163 
        0.23         0.53         5.46        23.31        16.80        27.02 
TCGA-B8-5549 TCGA-BP-4167 TCGA-BP-4334 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 
        6.38        89.36        21.21        62.86        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4787 
       33.99         5.98        71.80        13.15        10.82        15.78 
TCGA-BP-4797 TCGA-BP-4964 TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4994 
       36.39        61.22        57.40        45.50        31.30        43.00 
TCGA-BP-5004 TCGA-BP-5175 TCGA-BP-5191 TCGA-BP-5196 TCGA-CJ-4639 TCGA-CJ-4868 
       37.02        30.64        31.79        33.47        75.88        21.24 
TCGA-CJ-4881 TCGA-CJ-4901 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6028 TCGA-CW-5588 
       66.21        47.67        25.71        22.32        53.42        66.31 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4863 
       83.90        18.77        46.16        47.08         6.77        63.39 
TCGA-CZ-4866 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 
       61.41        18.44        55.33        47.54         1.94        31.10 
TCGA-CZ-5984 TCGA-DV-5568 TCGA-G6-A8L7 TCGA-2Z-A9J8 TCGA-2Z-A9JI TCGA-A4-7287 
       67.96        12.16        70.13        67.30        51.52        19.63 
TCGA-A4-7915 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B3-A6W5 TCGA-BQ-5875 TCGA-BQ-5879 
        0.23        49.25        10.09        10.16        86.76        22.92 
TCGA-BQ-5882 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 
       21.63         2.76        10.68        13.08         4.01        11.05 
TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-J7-8537 TCGA-P4-A5E8 
       25.84        17.33        16.90         3.68         0.13        42.94 
TCGA-Q2-A5QZ TCGA-UN-AAZ9 
       14.07        18.02 

$`DEL PEAK 21(13Q14.2) WILD-TYPE`
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       23.84       109.22        98.33        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8443 TCGA-KM-8477 
       54.74        62.37        23.28        28.80        49.97        51.06 
TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 TCGA-KN-8436 
       31.33        23.47        25.91         3.55        11.21        42.35 
TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 TCGA-3Z-A93Z 
      100.87        87.78       103.27        86.10        57.17        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.16        36.82        47.21         0.53        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.08        49.02        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3372 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        24.16        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       10.62       109.91        84.36        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 
       60.92        68.61        67.20        46.78        48.36        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4694 
       38.40        31.27        28.04         1.41         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4714 
       19.00        65.10         7.82         5.98         2.14         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       20.25        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 
       25.32        18.51         2.24        21.86        52.08        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       35.90        26.20        21.60         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       21.44        37.22        14.76        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
      101.13        15.78        46.68        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       56.94        52.77        39.55       120.59        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        12.30        21.30        31.30        11.77 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       10.36        32.98        21.57        16.67         9.57         5.75 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4148 TCGA-B8-4151 
        1.25         4.64         0.36         0.23        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       20.91        23.74         1.18         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60        14.27         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       37.25        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 
       74.17        54.77        49.08        44.94        12.23        12.33 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 
       31.33        12.30        72.59        77.98        77.62        44.15 
TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       41.75        48.07        61.68         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
       13.51        56.91        68.38        11.64        60.95        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       36.53        20.38        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.51         6.74        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       49.38         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       18.51        38.70        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5199 
       33.24        23.47        13.41        24.62        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       73.22        14.17        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       11.05        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06        77.36        64.27        71.87        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       50.24        56.35        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        53.26        60.99        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 
       73.18        78.18        74.66         1.35       105.93       103.43 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
       25.45         0.59        69.21        58.75        14.66        60.59 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04         5.46        63.42        58.82         0.82        23.74 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       56.28        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 
       21.76        57.21        22.52         2.40        12.69        80.19 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       45.96        65.88        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
        7.96        10.29        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.25        10.85         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
      100.27        56.91         4.57        75.42        34.85        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       54.64        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 
        0.13        12.82        11.57        18.21        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       35.18        19.13         0.89        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       76.64        13.55        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       16.77         0.46         6.58        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 
        6.81         0.16        14.86        17.49        12.30        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
        8.88        63.72        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         7.92       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
       24.89         2.40         1.18         0.43        51.78        48.62 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
       39.25        34.82        25.15        13.68         6.38        17.98 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65       194.79        12.92        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       16.34        12.36        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA 
       25.97        21.44        15.48        99.78        87.22         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       26.47        48.30        43.76        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                          0.13                           0.07 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                        151.96                         194.79 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                         33.73                          29.92 
[1] "0.1 - 152.0 (33.7)" "0.1 - 194.8 (29.9)"
[1] "hr=" "1.4"
D34V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 21(13Q14.2) MUTATED        46       22        51       29
  DEL PEAK 21(13Q14.2) WILD-TYPE     402       81       139       71
D34V3, multiclass
           clus
vv          DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  STAGE I                             46                            402
  STAGE II                            22                             81
  STAGE III                           51                            139
  STAGE IV                            29                             71
[1] 4 2
[1] 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(13Q14.2) MUTATED    48  24  67   9
  DEL PEAK 21(13Q14.2) WILD-TYPE 414  99 184   6
D34V4, multiclass
    clus
vv   DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  T1                           48                            414
  T2                           24                             99
  T3                           67                            184
  T4                            9                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 21(13Q14.2) MUTATED    69  14   4
  DEL PEAK 21(13Q14.2) WILD-TYPE 248  29   2
D34V5, multiclass
    clus
vv   DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  N0                           69                            248
  N1                           14                             29
  N2                            4                              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"
D34V6, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED    90  21
  DEL PEAK 21(13Q14.2) WILD-TYPE 452  68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     90   21
  DEL PEAK 21(13Q14.2) WILD-TYPE  452   68
   clus
vv  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  0                           90                            452
  1                           21                             68
[1] 2 2
[1] FALSE
D34V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED    63  85
  DEL PEAK 21(13Q14.2) WILD-TYPE 224 487
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     63   85
  DEL PEAK 21(13Q14.2) WILD-TYPE  224  487
        clus
vv       DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  FEMALE                           63                            224
  MALE                             85                            487
[1] 2 2
[1] FALSE
D34V8, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  DEL PEAK 21(13Q14.2) MUTATED                   43
  DEL PEAK 21(13Q14.2) WILD-TYPE                 23
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 21(13Q14.2) MUTATED                                  82
  DEL PEAK 21(13Q14.2) WILD-TYPE                               442
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 21(13Q14.2) MUTATED                                      23
  DEL PEAK 21(13Q14.2) WILD-TYPE                                   246
D34V9, multiclass
                                       clus
vv                                      DEL PEAK 21(13Q14.2) MUTATED
  KIDNEY CHROMOPHOBE                                              43
  KIDNEY CLEAR CELL RENAL CARCINOMA                               82
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           23
                                       clus
vv                                      DEL PEAK 21(13Q14.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                23
  KIDNEY CLEAR CELL RENAL CARCINOMA                                442
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            246
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, continuous
D34V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(13Q14.2) MUTATED                                  0     4
  DEL PEAK 21(13Q14.2) WILD-TYPE                                2    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(13Q14.2) MUTATED                          12   127
  DEL PEAK 21(13Q14.2) WILD-TYPE                       104   575
D34V12, multiclass
                                  clus
vv                                 DEL PEAK 21(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                     127
                                  clus
vv                                 DEL PEAK 21(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                   104
  WHITE                                                       575
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED     5  93
  DEL PEAK 21(13Q14.2) WILD-TYPE  37 504
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED      5   93
  DEL PEAK 21(13Q14.2) WILD-TYPE   37  504
                        clus
vv                       DEL PEAK 21(13Q14.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           93
                        clus
vv                       DEL PEAK 21(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 37
  NOT HISPANIC OR LATINO                            504
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 22(14Q31.1) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(14Q31.1) MUTATED   170 103
  DEL PEAK 22(14Q31.1) WILD-TYPE 462 108
  DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE 
                           273                            570 
  DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE 
                           103                            108 
$`DEL PEAK 22(14Q31.1) MUTATED`
TCGA-KL-8344 TCGA-KN-8418 TCGA-KN-8427 TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3311 
       28.80       129.37         0.99        12.66        36.82        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3324 TCGA-A3-3335 
       49.08        49.02        37.15        49.58        38.99        21.86 
TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
       34.29         4.50        52.93        45.53        29.92        88.37 
TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3387 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3429 
       20.71        18.87        20.28        29.10        84.36        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       15.78        60.92        67.20        42.08        58.49        48.69 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3458 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4703 
       28.73        22.45        38.40         4.57         3.48         5.98 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4817 
       19.73        43.96         6.64         5.52        52.21        33.50 
TCGA-B0-4819 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 
        6.02        10.09        78.44        40.70        27.42        53.88 
TCGA-B0-4842 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       56.68        26.07        29.03        36.85        70.52        20.94 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 
       11.90         7.30        15.09        10.95         2.24        21.86 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5400 TCGA-B0-5692 
       52.54        30.48        35.90        11.80        37.22        48.89 
TCGA-B0-5694 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5710 TCGA-B0-5711 
       15.78        60.33        84.92        56.94        47.97        96.36 
TCGA-B0-5712 TCGA-B2-4098 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       89.49         1.68        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4143 
       21.57         0.23         4.64         5.46         0.36        23.31 
TCGA-B8-4619 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5550 
       17.19        20.91        23.74         1.18         0.85        14.27 
TCGA-B8-5551 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54G TCGA-B8-A54I TCGA-BP-4163 
        0.53        14.30        27.29         1.74         4.93        93.34 
TCGA-BP-4164 TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4331 
       32.61        89.36        62.24        61.78        64.27        80.68 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 
       62.86        49.08        44.94        11.31        12.33        33.99 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4777 TCGA-BP-4781 
        5.98        41.75        13.15         5.33        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4962 
       15.78        36.39        10.98         6.71        87.45        58.68 
TCGA-BP-4965 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4981 
       61.51        14.24        48.89        45.50        14.93        36.07 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5004 
       46.45        25.81         3.88        16.47        18.51        37.02 
TCGA-BP-5009 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       36.23         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5189 TCGA-BP-5190 
       62.86        74.40        42.44        37.22        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4636 
       31.79        24.62        33.47        19.82        31.27        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4644 
       73.22        14.17        65.69        54.61        53.52        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       21.24        83.97        79.66        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4888 TCGA-CJ-4891 TCGA-CJ-4893 
       64.27        66.21        57.83        51.52        26.93        24.66 
TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4900 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 
       27.65        59.44        56.35        51.29        58.92        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-4923 
       50.33        54.48        38.56        45.14         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       22.32        25.25        61.91        67.00        53.26        60.99 
TCGA-CJ-6030 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5588 
       75.58         7.36        64.57         5.39        73.18        66.31 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4860 
        1.35        83.90        18.77        46.16        69.21         6.77 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5455 
       14.66        63.39        93.04        61.41        58.82        18.44 
TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 
       56.28        10.85        10.22        21.76        47.54         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 
        1.94        31.10        12.69        67.96        65.65        14.63 
TCGA-CZ-5989 TCGA-DV-5573 TCGA-G6-A5PC TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MM-A84U 
       62.63        37.15         7.96        35.87        19.43        15.25 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       54.64        51.52        38.99        18.21        19.63         0.10 
TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       29.46        12.99         9.63        25.08        44.61        49.25 
TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-BQ-5876 
        7.33        16.77        10.09        20.61         6.81        19.27 
TCGA-BQ-5880 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-DZ-6131 
       43.20        30.28        13.25        10.88         2.76        79.86 
TCGA-DZ-6132 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 
       80.88        10.68        13.08         4.01        11.05        34.82 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-8500 TCGA-HE-A5NK 
       13.68        25.84        17.33        16.90        27.65        73.25 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-MH-A854 TCGA-P4-A5EA TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
       16.80         2.04         0.36         6.61        12.85        14.07 
TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-WN-A9G9 
       18.02        21.93        26.01 

$`DEL PEAK 22(14Q31.1) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       24.79        73.91        71.41        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       51.06        31.33        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       65.19       104.52         3.55        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        59.08       115.00        42.35       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78       103.27        86.10        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 
       61.58        63.95        12.16        47.21         0.53        24.16 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 
       48.59        36.36        24.69        37.38        48.82        31.07 
TCGA-A3-3352 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       18.44        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       18.64        28.31        65.52        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3433 
        0.10        11.18        10.62       109.91        73.08        72.07 
TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 
       68.61        57.37        46.78        48.36        40.01        45.93 
TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       37.58        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        3.32         1.41         2.53        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 
        3.62        65.10         7.82         2.14         3.16         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4818 
       20.25        15.72        46.59         0.59        45.07        16.77 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4834 
       40.44        36.53        14.93        54.48        29.10        68.71 
TCGA-B0-4837 TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
       45.30         6.71        11.64        10.29        65.29        39.45 
TCGA-B0-4849 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5095 
        2.27        43.30        11.24        25.32        18.51         8.05 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5108 
       52.08        15.95        62.89        90.87        90.48        29.95 
TCGA-B0-5109 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       19.30        26.20        21.60        17.59         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5693 
       18.21        21.44        14.76        79.17       112.80       101.13 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       46.68        56.78        90.12        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       79.36       102.48        61.32        97.41        32.61        35.90 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       12.30        21.30        16.67         9.57         5.75         1.25 
TCGA-B4-5835 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.53         0.23        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5163 TCGA-B8-5165 
       24.66        25.55        25.91        23.01        27.02        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5552 TCGA-B8-A54E TCGA-B8-A54F 
       17.16        16.60         6.38        34.39        29.88        17.06 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        8.42        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4166 
       85.51        94.72        90.28       101.06        99.85         0.43 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       23.05        77.03        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       27.78        62.07        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4349 
       93.99        18.48        52.24        74.17        54.77        12.23 
TCGA-BP-4351 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       31.89        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4774 
       44.15        71.80        48.07        61.68        10.82        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 
       60.59        13.51        11.64        60.95        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       20.38        37.25        36.95        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       63.62        60.30        61.22         6.74        57.40        58.98 
TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4985 
       49.38         7.23        47.11        53.65        33.34        31.30 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
       36.95        27.22        46.45         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       30.64        41.62        38.70        27.62        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 
       28.87        48.10        52.27         9.63        49.15        38.30 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5199 
       37.25        22.78        13.35        23.47        13.41        44.55 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4643 
       34.95         0.95        59.84        46.55        75.88        58.95 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 
       49.25        47.18        71.87        61.91        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4895 TCGA-CJ-4899 
       30.64        63.98        68.55        50.01        39.45        50.24 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4918 TCGA-CJ-5681 TCGA-CJ-5683 
       47.67        49.97        49.18         3.06        18.15        62.10 
TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
       73.35        53.42        62.66        83.77        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 
       85.78        78.18        74.66       105.93       103.43        25.45 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-CZ-5451 
        0.59        47.08        58.75        60.59         5.46        63.42 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
        0.82        23.74        55.33        56.94        55.33        47.01 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-DV-5565 
       57.21        22.52        80.19        12.26        22.78        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       45.96        65.88        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-2K-A9WE 
       10.29        70.13         2.01        19.96        10.85         7.04 
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-A9JJ TCGA-2Z-A9JL 
       67.30        75.42        34.85        56.81        35.67        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7288 
       16.18        22.49         0.13        12.82        11.57        61.05 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       15.75         8.28        12.46        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       30.35         2.20        19.56        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
        3.55         0.46         6.58        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       12.46        10.16        50.50        28.18        26.40         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 
        0.16        14.86        17.49        12.30        86.76         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        47.80        21.63        40.83        26.04 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       26.04        25.35         7.66         0.95        11.97         7.92 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        3.02        40.77        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       19.00        24.89         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE 
       48.62        39.25        25.15         6.38        17.98        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92         3.68         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       56.75         5.49        19.99        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
       20.25        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       87.22        42.94        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        17.75        47.90        47.44        33.04 
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        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM 
       41.62        26.47        48.30        43.76        60.03        14.83 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       27.39        12.99        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE 
                        129.37                         194.79 
  DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE 
                         30.48                          30.53 
[1] "0.1 - 129.4 (30.5)" "0.1 - 194.8 (30.5)"
[1] "hr=" "2.2"
D35V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 22(14Q31.1) MUTATED       103       31        83       54
  DEL PEAK 22(14Q31.1) WILD-TYPE     345       72       107       46
D35V3, multiclass
           clus
vv          DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE
  STAGE I                            103                            345
  STAGE II                            31                             72
  STAGE III                           83                            107
  STAGE IV                            54                             46
[1] 4 2
[1] 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(14Q31.1) MUTATED   110  40 119   5
  DEL PEAK 22(14Q31.1) WILD-TYPE 352  83 132  10
D35V4, multiclass
    clus
vv   DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE
  T1                          110                            352
  T2                           40                             83
  T3                          119                            132
  T4                            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                              N0  N1  N2
  DEL PEAK 22(14Q31.1) MUTATED   108  26   3
  DEL PEAK 22(14Q31.1) WILD-TYPE 209  17   3
D35V5, multiclass
    clus
vv   DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE
  N0                          108                            209
  N1                           26                             17
  N2                            3                              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"
D35V6, binary
                                cls
clus                               0   1
  DEL PEAK 22(14Q31.1) MUTATED   185  51
  DEL PEAK 22(14Q31.1) WILD-TYPE 357  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q31.1) MUTATED    185   51
  DEL PEAK 22(14Q31.1) WILD-TYPE  357   38
   clus
vv  DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE
  0                          185                            357
  1                           51                             38
[1] 2 2
[1] FALSE
D35V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(14Q31.1) MUTATED    94 180
  DEL PEAK 22(14Q31.1) WILD-TYPE 193 392
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q31.1) MUTATED     94  180
  DEL PEAK 22(14Q31.1) WILD-TYPE  193  392
        clus
vv       DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE
  FEMALE                           94                            193
  MALE                            180                            392
[1] 2 2
[1] FALSE
D35V8, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  DEL PEAK 22(14Q31.1) MUTATED                    3
  DEL PEAK 22(14Q31.1) WILD-TYPE                 63
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 22(14Q31.1) MUTATED                                 226
  DEL PEAK 22(14Q31.1) WILD-TYPE                               298
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 22(14Q31.1) MUTATED                                      45
  DEL PEAK 22(14Q31.1) WILD-TYPE                                   224
D35V9, multiclass
                                       clus
vv                                      DEL PEAK 22(14Q31.1) MUTATED
  KIDNEY CHROMOPHOBE                                               3
  KIDNEY CLEAR CELL RENAL CARCINOMA                              226
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           45
                                       clus
vv                                      DEL PEAK 22(14Q31.1) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                63
  KIDNEY CLEAR CELL RENAL CARCINOMA                                298
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, continuous
D35V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(14Q31.1) MUTATED                                  0     3
  DEL PEAK 22(14Q31.1) WILD-TYPE                                2    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(14Q31.1) MUTATED                          24   240
  DEL PEAK 22(14Q31.1) WILD-TYPE                        92   462
D35V12, multiclass
                                  clus
vv                                 DEL PEAK 22(14Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  24
  WHITE                                                     240
                                  clus
vv                                 DEL PEAK 22(14Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        12
  BLACK OR AFRICAN AMERICAN                                    92
  WHITE                                                       462
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, binary
                                cls
clus                               0   1
  DEL PEAK 22(14Q31.1) MUTATED    13 194
  DEL PEAK 22(14Q31.1) WILD-TYPE  29 403
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q31.1) MUTATED     13  194
  DEL PEAK 22(14Q31.1) WILD-TYPE   29  403
                        clus
vv                       DEL PEAK 22(14Q31.1) MUTATED
  HISPANIC OR LATINO                               13
  NOT HISPANIC OR LATINO                          194
                        clus
vv                       DEL PEAK 22(14Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 29
  NOT HISPANIC OR LATINO                            403
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 23(16Q23.3) MUTATION ANALYSIS
D36V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(16Q23.3) MUTATED    17  18
  DEL PEAK 23(16Q23.3) WILD-TYPE 615 193
  DEL PEAK 23(16Q23.3) MUTATED DEL PEAK 23(16Q23.3) WILD-TYPE 
                            35                            808 
  DEL PEAK 23(16Q23.3) MUTATED DEL PEAK 23(16Q23.3) WILD-TYPE 
                            18                            193 
$`DEL PEAK 23(16Q23.3) MUTATED`
TCGA-KL-8329 TCGA-KL-8336 TCGA-KL-8339 TCGA-KN-8427 TCGA-KN-8428 TCGA-KO-8408 
       90.48        30.25        28.11         0.99        52.27        16.67 
TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-A6NN TCGA-B0-4688 TCGA-B0-4822 TCGA-B0-4836 
       36.82        49.08         0.10         3.32        36.53        40.70 
TCGA-B0-4837 TCGA-B0-5097 TCGA-B0-5402 TCGA-B8-4151 TCGA-B8-5551 TCGA-BP-4354 
       45.30        21.86        14.76        27.55         0.53        33.99 
TCGA-BP-4770 TCGA-BP-4797 TCGA-BP-4985 TCGA-BP-5185 TCGA-CZ-5457 TCGA-CZ-5982 
       10.82        36.39        31.30        37.22        55.33        80.19 
TCGA-G6-A8L8 TCGA-MM-A564 TCGA-2Z-A9JI TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-B9-A8YI 
       35.87        19.96        51.52        19.63        12.99        12.30 
TCGA-BQ-5882 TCGA-BQ-5893 TCGA-G7-6793 TCGA-G7-A8LD TCGA-IA-A40X 
       21.63         7.92        11.05        16.90        19.99 

$`DEL PEAK 23(16Q23.3) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       28.80        54.74        62.37       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       28.80        47.24        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
      104.52         3.55        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87        76.90        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       74.93        79.04        92.71        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
       86.10        77.85        57.17        61.58        63.95        12.66 
TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       12.16        47.21         0.53        39.16        24.16        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       37.15        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        21.86        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       24.16        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       73.08        66.31        15.78        60.92        72.07        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       67.20        57.37        46.78        48.36        42.08        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        40.44        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4838 TCGA-B0-4839 
       29.10        10.09        78.44        68.71        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 
       15.09        10.95         8.05         2.24        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 
        1.94        16.21        18.21        21.44        37.22        79.17 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        11.77        10.36        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67         9.57         5.75         0.23         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.16        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 
       24.23        17.16        16.60         6.38        14.27        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       54.77        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       12.33        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       61.68         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       20.38        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.25        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       67.00        53.26        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       83.77         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       85.78        73.18        66.31        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
      105.93        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
        0.59        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       60.59        63.39        93.04         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 
       58.82         0.82        23.74        18.44        56.28        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        47.01        10.85        10.22        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       43.69        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       66.28        56.84        23.90        66.02        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 
        6.77         4.18         7.96        10.29        70.13         2.01 
TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.43        15.25        10.85         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       58.22       100.27        56.91         4.57        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       34.85        56.81        54.64        35.67        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 
       16.18        22.49         0.13        12.82        11.57        18.21 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
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-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        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         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 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        4.01        51.78        48.62        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       13.68        25.84         6.38        17.98        17.33        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y 
       11.84        56.75        73.25         5.49        16.80         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       78.90        12.85        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  DEL PEAK 23(16Q23.3) MUTATED DEL PEAK 23(16Q23.3) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 23(16Q23.3) MUTATED DEL PEAK 23(16Q23.3) WILD-TYPE 
                         90.48                         194.79 
  DEL PEAK 23(16Q23.3) MUTATED DEL PEAK 23(16Q23.3) WILD-TYPE 
                         27.55                          30.64 
[1] "0.1 - 90.5 (27.6)"  "0.1 - 194.8 (30.6)"
[1] "hr=" "2.9"
D36V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 23(16Q23.3) MUTATED        11        4        11       10
  DEL PEAK 23(16Q23.3) WILD-TYPE     437       99       179       90
D36V3, multiclass
           clus
vv          DEL PEAK 23(16Q23.3) MUTATED DEL PEAK 23(16Q23.3) WILD-TYPE
  STAGE I                             11                            437
  STAGE II                             4                             99
  STAGE III                           11                            179
  STAGE IV                            10                             90
[1] 4 2
[1] 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(16Q23.3) MUTATED    12   4  15   5
  DEL PEAK 23(16Q23.3) WILD-TYPE 450 119 236  10
D36V4, multiclass
    clus
vv   DEL PEAK 23(16Q23.3) MUTATED DEL PEAK 23(16Q23.3) WILD-TYPE
  T1                           12                            450
  T2                            4                            119
  T3                           15                            236
  T4                            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                              N0  N1  N2
  DEL PEAK 23(16Q23.3) MUTATED    12   7   2
  DEL PEAK 23(16Q23.3) WILD-TYPE 305  36   4
D36V5, multiclass
    clus
vv   DEL PEAK 23(16Q23.3) MUTATED DEL PEAK 23(16Q23.3) WILD-TYPE
  N0                           12                            305
  N1                            7                             36
  N2                            2                              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"
D36V6, binary
                                cls
clus                               0   1
  DEL PEAK 23(16Q23.3) MUTATED    18   5
  DEL PEAK 23(16Q23.3) WILD-TYPE 524  84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(16Q23.3) MUTATED     18    5
  DEL PEAK 23(16Q23.3) WILD-TYPE  524   84
   clus
vv  DEL PEAK 23(16Q23.3) MUTATED DEL PEAK 23(16Q23.3) WILD-TYPE
  0                           18                            524
  1                            5                             84
[1] 2 2
[1] FALSE
D36V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(16Q23.3) MUTATED    12  24
  DEL PEAK 23(16Q23.3) WILD-TYPE 275 548
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(16Q23.3) MUTATED     12   24
  DEL PEAK 23(16Q23.3) WILD-TYPE  275  548
        clus
vv       DEL PEAK 23(16Q23.3) MUTATED DEL PEAK 23(16Q23.3) WILD-TYPE
  FEMALE                           12                            275
  MALE                             24                            548
[1] 2 2
[1] FALSE
D36V8, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  DEL PEAK 23(16Q23.3) MUTATED                    6
  DEL PEAK 23(16Q23.3) WILD-TYPE                 60
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 23(16Q23.3) MUTATED                                  20
  DEL PEAK 23(16Q23.3) WILD-TYPE                               504
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 23(16Q23.3) MUTATED                                      10
  DEL PEAK 23(16Q23.3) WILD-TYPE                                   259
D36V9, multiclass
                                       clus
vv                                      DEL PEAK 23(16Q23.3) MUTATED
  KIDNEY CHROMOPHOBE                                               6
  KIDNEY CLEAR CELL RENAL CARCINOMA                               20
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           10
                                       clus
vv                                      DEL PEAK 23(16Q23.3) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                60
  KIDNEY CLEAR CELL RENAL CARCINOMA                                504
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            259
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, continuous
D36V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(16Q23.3) MUTATED                                  0     1
  DEL PEAK 23(16Q23.3) WILD-TYPE                                2    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(16Q23.3) MUTATED                           6    27
  DEL PEAK 23(16Q23.3) WILD-TYPE                       110   675
D36V12, multiclass
                                  clus
vv                                 DEL PEAK 23(16Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      27
                                  clus
vv                                 DEL PEAK 23(16Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        14
  BLACK OR AFRICAN AMERICAN                                   110
  WHITE                                                       675
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, binary
                                cls
clus                               0   1
  DEL PEAK 23(16Q23.3) MUTATED     1  23
  DEL PEAK 23(16Q23.3) WILD-TYPE  41 574
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(16Q23.3) MUTATED      1   23
  DEL PEAK 23(16Q23.3) WILD-TYPE   41  574
                        clus
vv                       DEL PEAK 23(16Q23.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           23
                        clus
vv                       DEL PEAK 23(16Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 41
  NOT HISPANIC OR LATINO                            574
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 24(18Q22.2) MUTATION ANALYSIS
D37V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(18Q22.2) MUTATED    90  59
  DEL PEAK 24(18Q22.2) WILD-TYPE 542 152
  DEL PEAK 24(18Q22.2) MUTATED DEL PEAK 24(18Q22.2) WILD-TYPE 
                           149                            694 
  DEL PEAK 24(18Q22.2) MUTATED DEL PEAK 24(18Q22.2) WILD-TYPE 
                            59                            152 
$`DEL PEAK 24(18Q22.2) MUTATED`
TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8336 TCGA-KN-8424 TCGA-KN-8427 
      102.81        90.48        98.96        30.25        65.19         0.99 
TCGA-KN-8429 TCGA-KO-8414 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3319 TCGA-A3-3346 
       87.12        77.85         0.53        24.16        37.15         4.50 
TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3372 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       52.93        88.37        24.16        65.52        20.28       109.91 
TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3465 TCGA-B0-4688 TCGA-B0-4690 
       15.78        67.20        57.37        12.13         3.32         1.41 
TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4712 
       28.47         1.38         3.62        65.10         5.98        43.96 
TCGA-B0-4713 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
        6.64         0.59        52.21         6.02        40.44        36.53 
TCGA-B0-4827 TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4848 TCGA-B0-4945 
       29.10        40.70        10.29        65.29        29.03        70.52 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5097 TCGA-B0-5121 TCGA-B2-4098 TCGA-B2-5641 
       15.09        10.95        21.86        18.21         1.68        21.57 
TCGA-B4-5832 TCGA-B4-5835 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-5163 TCGA-B8-5549 
        0.23         0.53        25.55        25.91        27.02         6.38 
TCGA-B8-5550 TCGA-BP-4164 TCGA-BP-4166 TCGA-BP-4338 TCGA-BP-4343 TCGA-BP-4352 
       14.27        32.61         0.43        93.99        62.86        11.31 
TCGA-BP-4353 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4803 
       12.33        12.30         5.98        68.38        36.39         6.71 
TCGA-BP-4962 TCGA-BP-4977 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 
       58.68        14.93        31.30        43.00        18.51         6.35 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 
       62.86        49.15        38.30        31.79        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4872 TCGA-CJ-4873 
       34.95        31.27        63.25        73.22        47.18        74.27 
TCGA-CJ-4881 TCGA-CJ-4888 TCGA-CJ-4891 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4920 
       66.21        51.52        26.93        47.67        49.28         4.57 
TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5588 
       25.71        22.32        60.99        53.42        83.77        66.31 
TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4863 TCGA-CZ-4866 
       46.16        47.08        69.21         6.77        63.39        61.41 
TCGA-CZ-5456 TCGA-CZ-5468 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5988 TCGA-MM-A84U 
       56.28         1.94        67.96        65.65        22.78        15.25 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JP TCGA-4A-A93X TCGA-A4-7286 
       54.64        51.52        35.67        29.36        12.82        18.21 
TCGA-A4-8310 TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A656 
       25.64         8.48        12.99        49.25         7.33         0.46 
TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A44B TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 
       10.09        20.61         2.10         8.88        22.92        21.63 
TCGA-BQ-5887 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7058 TCGA-BQ-7059 
       25.35         2.76       123.62        93.34        11.28         7.63 
TCGA-DW-7840 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 
        3.75        24.89        10.68        13.08         0.43         4.01 
TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EA 
       16.90        12.92         3.68         2.04         0.13         6.61 
TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO TCGA-UZ-A9PQ TCGA-Y8-A8S1 
       14.07        11.93        38.63        86.27        13.28 

$`DEL PEAK 24(18Q22.2) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8330 
       38.07       141.73        23.84       109.22       137.06       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 
       84.89        98.33        96.95        92.55        44.84        86.56 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       28.11        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       54.74        62.37       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       47.24        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
       23.47        87.91        25.48        25.91       104.52         3.55 
TCGA-KN-8428 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
       57.17        61.58        63.95        12.66        12.16        36.82 
TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 
       47.21        39.16        49.08        49.02        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        24.69        37.38        48.82        21.86 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3358 
       34.29        31.07        45.53        29.92        18.44        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       53.29        43.20        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       28.31        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 
       10.62        29.10        84.36        73.08        66.31        60.92 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       72.07        68.61        46.78        48.36        42.08        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4691 
       38.40        31.27        28.04        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4707 
        2.53         3.48        19.00         7.82         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 
        3.16         3.25        20.25        15.72        46.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 
       45.07        33.50        16.77        14.93        54.48        10.09 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        68.71        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 
       56.68        11.64        39.45        26.07         2.27        36.85 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
       18.51         8.05         2.24        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       16.21        21.44        37.22        14.76        79.17       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       97.41        32.61        35.90        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       11.77        10.36        32.98        16.67         9.57         5.75 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        1.25         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 
       23.01        20.91        23.74         1.18         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       17.16        16.60         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
       90.28       101.06        93.34        99.85        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       21.21        15.16         0.07        18.48        52.24        74.17 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 
       54.77        49.08        44.94        12.23        31.89        33.99 
TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 
       31.33        72.59        77.98        77.62        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       71.80        48.07        13.15        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
       61.97        60.59        13.51        56.91        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 
       15.78        48.95        36.53        20.38        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
       36.95        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
       53.65        36.07        33.34        46.45        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       30.64        41.62        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 
       35.21        36.23        28.87        48.10        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5183 
       74.20        30.64        52.27         9.63        74.40        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5202 TCGA-CJ-4634 
       23.47        13.41        24.62        44.55         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       46.55        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06        77.36        64.27        71.87        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       69.86        64.18        30.64        63.98        68.55        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        58.92        49.18        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       38.56        45.14         3.06        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       79.89        84.66        18.87        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CJ-6031 
       62.10        73.35        67.00        53.26        75.58        62.66 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       73.18        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 
      103.43        18.77        25.45         0.59        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       60.59        93.04         5.46        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        57.21        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5987 
        2.40        31.10        12.69        80.19        12.26        14.63 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-2K-A9WE 
       35.87         2.01        19.43        19.96        10.85         7.04 
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-A9JK TCGA-2Z-A9JL 
       67.30        75.42        34.85        56.81        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       30.71        24.33        31.20        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       22.49         0.13        11.57        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       29.46        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.73        14.33        12.46        16.96        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        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 
       24.56        16.87         3.55        16.77         6.58        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         6.81         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       86.76        19.27        63.72        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       26.04        30.28        26.04        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 
        0.95        11.97         7.92        48.26        96.92        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7060 
       61.28        50.40        49.84        26.27        20.12         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       37.55        24.46        13.78        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       19.00         2.40         1.18        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM 
       17.98        17.33        80.65       194.79        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       16.34        12.36        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       27.06        19.00        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       15.62        25.28         6.74         6.02 

  DEL PEAK 24(18Q22.2) MUTATED DEL PEAK 24(18Q22.2) WILD-TYPE 
                          0.13                           0.07 
  DEL PEAK 24(18Q22.2) MUTATED DEL PEAK 24(18Q22.2) WILD-TYPE 
                        123.62                         194.79 
  DEL PEAK 24(18Q22.2) MUTATED DEL PEAK 24(18Q22.2) WILD-TYPE 
                        25.550                         31.285 
[1] "0.1 - 123.6 (25.6)" "0.1 - 194.8 (31.3)"
[1] "hr=" "2.1"
D37V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 24(18Q22.2) MUTATED        51       12        55       31
  DEL PEAK 24(18Q22.2) WILD-TYPE     397       91       135       69
D37V3, multiclass
           clus
vv          DEL PEAK 24(18Q22.2) MUTATED DEL PEAK 24(18Q22.2) WILD-TYPE
  STAGE I                             51                            397
  STAGE II                            12                             91
  STAGE III                           55                            135
  STAGE IV                            31                             69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 24(18Q22.2) MUTATED    54  17  73   7
  DEL PEAK 24(18Q22.2) WILD-TYPE 408 106 178   8
D37V4, multiclass
    clus
vv   DEL PEAK 24(18Q22.2) MUTATED DEL PEAK 24(18Q22.2) WILD-TYPE
  T1                           54                            408
  T2                           17                            106
  T3                           73                            178
  T4                            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                              N0  N1  N2
  DEL PEAK 24(18Q22.2) MUTATED    64  15   3
  DEL PEAK 24(18Q22.2) WILD-TYPE 253  28   3
D37V5, multiclass
    clus
vv   DEL PEAK 24(18Q22.2) MUTATED DEL PEAK 24(18Q22.2) WILD-TYPE
  N0                           64                            253
  N1                           15                             28
  N2                            3                              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"
D37V6, binary
                                cls
clus                               0   1
  DEL PEAK 24(18Q22.2) MUTATED    97  27
  DEL PEAK 24(18Q22.2) WILD-TYPE 445  62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(18Q22.2) MUTATED     97   27
  DEL PEAK 24(18Q22.2) WILD-TYPE  445   62
   clus
vv  DEL PEAK 24(18Q22.2) MUTATED DEL PEAK 24(18Q22.2) WILD-TYPE
  0                           97                            445
  1                           27                             62
[1] 2 2
[1] FALSE
D37V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(18Q22.2) MUTATED    51 101
  DEL PEAK 24(18Q22.2) WILD-TYPE 236 471
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(18Q22.2) MUTATED     51  101
  DEL PEAK 24(18Q22.2) WILD-TYPE  236  471
        clus
vv       DEL PEAK 24(18Q22.2) MUTATED DEL PEAK 24(18Q22.2) WILD-TYPE
  FEMALE                           51                            236
  MALE                            101                            471
[1] 2 2
[1] FALSE
D37V8, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  DEL PEAK 24(18Q22.2) MUTATED                    9
  DEL PEAK 24(18Q22.2) WILD-TYPE                 57
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 24(18Q22.2) MUTATED                                 101
  DEL PEAK 24(18Q22.2) WILD-TYPE                               423
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 24(18Q22.2) MUTATED                                      42
  DEL PEAK 24(18Q22.2) WILD-TYPE                                   227
D37V9, multiclass
                                       clus
vv                                      DEL PEAK 24(18Q22.2) MUTATED
  KIDNEY CHROMOPHOBE                                               9
  KIDNEY CLEAR CELL RENAL CARCINOMA                              101
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           42
                                       clus
vv                                      DEL PEAK 24(18Q22.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                57
  KIDNEY CLEAR CELL RENAL CARCINOMA                                423
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            227
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, continuous
D37V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(18Q22.2) MUTATED                                  0     6
  DEL PEAK 24(18Q22.2) WILD-TYPE                                2     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(18Q22.2) MUTATED                          15   128
  DEL PEAK 24(18Q22.2) WILD-TYPE                       101   574
D37V12, multiclass
                                  clus
vv                                 DEL PEAK 24(18Q22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                     128
                                  clus
vv                                 DEL PEAK 24(18Q22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                   101
  WHITE                                                       574
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, binary
                                cls
clus                               0   1
  DEL PEAK 24(18Q22.2) MUTATED     3 106
  DEL PEAK 24(18Q22.2) WILD-TYPE  39 491
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(18Q22.2) MUTATED      3  106
  DEL PEAK 24(18Q22.2) WILD-TYPE   39  491
                        clus
vv                       DEL PEAK 24(18Q22.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          106
                        clus
vv                       DEL PEAK 24(18Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                 39
  NOT HISPANIC OR LATINO                            491
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 25(19P13.3) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(19P13.3) MUTATED    19  21
  DEL PEAK 25(19P13.3) WILD-TYPE 613 190
  DEL PEAK 25(19P13.3) MUTATED DEL PEAK 25(19P13.3) WILD-TYPE 
                            40                            803 
  DEL PEAK 25(19P13.3) MUTATED DEL PEAK 25(19P13.3) WILD-TYPE 
                            21                            190 
$`DEL PEAK 25(19P13.3) MUTATED`
TCGA-KL-8336 TCGA-KO-8404 TCGA-KO-8415 TCGA-A3-3319 TCGA-AK-3425 TCGA-B0-4690 
       30.25        10.68        57.17        37.15       109.91         1.41 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4707 TCGA-B0-4821 TCGA-B0-4828 TCGA-B0-5084 
        3.48        28.47        19.73        40.44        10.09         7.30 
TCGA-B0-5098 TCGA-B0-5109 TCGA-BP-4164 TCGA-BP-4352 TCGA-BP-4770 TCGA-BP-4985 
       52.08        19.30        32.61        11.31        10.82        31.30 
TCGA-CJ-5681 TCGA-CZ-4860 TCGA-2Z-A9JG TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-8517 
       18.15         6.77        54.64        18.21        25.64        19.63 
TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B1-7332 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5876 
       12.99         9.63         7.33         2.10        19.23        19.27 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y 
        7.66         0.95         4.01        25.84        16.90         2.04 
TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UZ-A9PN TCGA-UZ-A9PP 
        0.13        14.07        21.93         0.53 

$`DEL PEAK 25(19P13.3) WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       92.55        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       61.58        63.95        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 
        0.53        39.16        24.16        49.08        49.02        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
       48.59        36.36        38.99        24.69        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       21.86        34.29        31.07         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       29.92        18.44        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
       10.49        28.70        74.63        74.76        24.16        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
       43.20        55.76        20.71        18.64        18.87        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       65.52        20.28        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       11.18        10.62        29.10        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        60.92        72.07        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        42.08        40.01        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 
       28.04        12.13        40.70         1.41         3.32         4.57 
TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
        2.53        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        5.98         2.14         3.16        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       20.25        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 
       70.52        20.94        43.30        11.24        11.90        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       29.95        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       14.27         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        61.68         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       57.40        58.98        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       46.45        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
       75.88        65.69        54.61        53.52        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       61.91        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
       58.75        14.66        60.59        63.39        93.04         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        57.21        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        15.25        10.85         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       58.22       100.27        56.91         4.57        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       34.85        56.81        51.52        35.67        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 
       16.18        22.49         0.13        12.82        11.57        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 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        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
       19.56        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
        0.46         1.15        15.12        43.99        22.06         6.81 
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        10.88 
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 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-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        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 
       13.68         6.38        17.98        17.33        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       56.75        73.25         5.49        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PQ 
       48.30        43.76        18.02        60.03        14.83        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  DEL PEAK 25(19P13.3) MUTATED DEL PEAK 25(19P13.3) WILD-TYPE 
                          0.13                           0.07 
  DEL PEAK 25(19P13.3) MUTATED DEL PEAK 25(19P13.3) WILD-TYPE 
                        109.91                         194.79 
  DEL PEAK 25(19P13.3) MUTATED DEL PEAK 25(19P13.3) WILD-TYPE 
                        17.525                         31.300 
[1] "0.1 - 109.9 (17.5)" "0.1 - 194.8 (31.3)"
[1] "hr=" "4.3"
D38V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 25(19P13.3) MUTATED        10        1        17       11
  DEL PEAK 25(19P13.3) WILD-TYPE     438      102       173       89
D38V3, multiclass
           clus
vv          DEL PEAK 25(19P13.3) MUTATED DEL PEAK 25(19P13.3) WILD-TYPE
  STAGE I                             10                            438
  STAGE II                             1                            102
  STAGE III                           17                            173
  STAGE IV                            11                             89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 25(19P13.3) MUTATED    11   2  23   4
  DEL PEAK 25(19P13.3) WILD-TYPE 451 121 228  11
D38V4, multiclass
    clus
vv   DEL PEAK 25(19P13.3) MUTATED DEL PEAK 25(19P13.3) WILD-TYPE
  T1                           11                            451
  T2                            2                            121
  T3                           23                            228
  T4                            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                              N0  N1  N2
  DEL PEAK 25(19P13.3) MUTATED    10   7   2
  DEL PEAK 25(19P13.3) WILD-TYPE 307  36   4
D38V5, multiclass
    clus
vv   DEL PEAK 25(19P13.3) MUTATED DEL PEAK 25(19P13.3) WILD-TYPE
  N0                           10                            307
  N1                            7                             36
  N2                            2                              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"
D38V6, binary
                                cls
clus                               0   1
  DEL PEAK 25(19P13.3) MUTATED    17   7
  DEL PEAK 25(19P13.3) WILD-TYPE 525  82
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(19P13.3) MUTATED     17    7
  DEL PEAK 25(19P13.3) WILD-TYPE  525   82
   clus
vv  DEL PEAK 25(19P13.3) MUTATED DEL PEAK 25(19P13.3) WILD-TYPE
  0                           17                            525
  1                            7                             82
[1] 2 2
[1] FALSE
D38V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(19P13.3) MUTATED    14  26
  DEL PEAK 25(19P13.3) WILD-TYPE 273 546
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(19P13.3) MUTATED     14   26
  DEL PEAK 25(19P13.3) WILD-TYPE  273  546
        clus
vv       DEL PEAK 25(19P13.3) MUTATED DEL PEAK 25(19P13.3) WILD-TYPE
  FEMALE                           14                            273
  MALE                             26                            546
[1] 2 2
[1] FALSE
D38V8, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  DEL PEAK 25(19P13.3) MUTATED                    3
  DEL PEAK 25(19P13.3) WILD-TYPE                 63
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 25(19P13.3) MUTATED                                  17
  DEL PEAK 25(19P13.3) WILD-TYPE                               507
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 25(19P13.3) MUTATED                                      20
  DEL PEAK 25(19P13.3) WILD-TYPE                                   249
D38V9, multiclass
                                       clus
vv                                      DEL PEAK 25(19P13.3) MUTATED
  KIDNEY CHROMOPHOBE                                               3
  KIDNEY CLEAR CELL RENAL CARCINOMA                               17
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           20
                                       clus
vv                                      DEL PEAK 25(19P13.3) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                63
  KIDNEY CLEAR CELL RENAL CARCINOMA                                507
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            249
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, continuous
D38V11, continuous
[1] "Remove cluster labels:"       "DEL PEAK 25(19P13.3) MUTATED"
clus
  DEL PEAK 25(19P13.3) MUTATED DEL PEAK 25(19P13.3) WILD-TYPE 
                             2                             65 
                    TCGA-KL-8330                     TCGA-KL-8335 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-KL-8341                     TCGA-KL-8345 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-KM-8639                     TCGA-KN-8433 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-KO-8408                     TCGA-KO-8409 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-A3-A8OV                     TCGA-A3-A8OW 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-B2-A4SR                     TCGA-B8-5158 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-DV-A4W0                     TCGA-G6-A8L7 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-MM-A563                     TCGA-MM-A84U 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-2Z-A9J3                     TCGA-2Z-A9J7 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-2Z-A9J8                     TCGA-2Z-A9JD 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-2Z-A9JI                     TCGA-2Z-A9JN 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-2Z-A9JO                     TCGA-4A-A93W 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-4A-A93Y                     TCGA-A4-A48D 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-A4-A57E                     TCGA-A4-A5Y0 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-AL-3472                     TCGA-AL-7173 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-B1-A654                     TCGA-B9-4117 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-B9-A69E                     TCGA-DW-5561 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-DW-7963                     TCGA-F9-A97G 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-G7-7501                     TCGA-G7-A8LB 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-G7-A8LE                     TCGA-GL-7773 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-GL-A9DD                     TCGA-HE-A5NI 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-IA-A40U                     TCGA-MH-A854 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-MH-A856                     TCGA-P4-A5E6 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-P4-AAVK                     TCGA-PJ-A5Z9 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-SX-A71S                     TCGA-SX-A71U 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-SX-A7SL                     TCGA-SX-A7SM 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-SX-A7SR                     TCGA-SX-A7SS 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-UZ-A9PM                     TCGA-UZ-A9PO 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-UZ-A9PR                     TCGA-UZ-A9PS 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-UZ-A9PX                     TCGA-WN-A9G9 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-WN-AB4C                     TCGA-Y8-A894 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-Y8-A896                     TCGA-Y8-A8RY 
"DEL PEAK 25(19P13.3) WILD-TYPE" "DEL PEAK 25(19P13.3) WILD-TYPE" 
                    TCGA-Y8-A8RZ 
"DEL PEAK 25(19P13.3) WILD-TYPE" 
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(19P13.3) MUTATED                                  0     2
  DEL PEAK 25(19P13.3) WILD-TYPE                                2    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(19P13.3) MUTATED                           5    33
  DEL PEAK 25(19P13.3) WILD-TYPE                       111   669
D38V12, multiclass
                                  clus
vv                                 DEL PEAK 25(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      33
                                  clus
vv                                 DEL PEAK 25(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        13
  BLACK OR AFRICAN AMERICAN                                   111
  WHITE                                                       669
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, binary
                                cls
clus                               0   1
  DEL PEAK 25(19P13.3) MUTATED     1  32
  DEL PEAK 25(19P13.3) WILD-TYPE  41 565
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(19P13.3) MUTATED      1   32
  DEL PEAK 25(19P13.3) WILD-TYPE   41  565
                        clus
vv                       DEL PEAK 25(19P13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           32
                        clus
vv                       DEL PEAK 25(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 41
  NOT HISPANIC OR LATINO                            565
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 26(XP22.2) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 26(XP22.2) MUTATED    88  35
  DEL PEAK 26(XP22.2) WILD-TYPE 544 176
  DEL PEAK 26(XP22.2) MUTATED DEL PEAK 26(XP22.2) WILD-TYPE 
                          123                           720 
  DEL PEAK 26(XP22.2) MUTATED DEL PEAK 26(XP22.2) WILD-TYPE 
                           35                           176 
$`DEL PEAK 26(XP22.2) MUTATED`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07        23.84       102.81        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 
       86.56        28.11        66.54        73.91        71.41        54.74 
TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
       44.91        47.24       123.12       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
       65.19       104.52        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 
      115.00        76.90        79.04        92.71        16.67       103.27 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3306 TCGA-A3-3317 TCGA-A3-3319 
       57.17        61.58        63.95        36.82        49.02        37.15 
TCGA-A3-3322 TCGA-A3-3363 TCGA-A3-3383 TCGA-AK-3428 TCGA-AK-3440 TCGA-AK-3447 
       48.59        10.49        28.31        73.08        57.37        40.01 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4718 
       12.13        40.70         3.32        28.47         3.62        20.25 
TCGA-B0-4813 TCGA-B0-4827 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-4845 
        0.59        29.10        68.71        40.70        10.29        65.29 
TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5098 TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5705 
       11.24         7.30        52.08        17.59        14.76       120.59 
TCGA-B2-3923 TCGA-B8-5159 TCGA-B8-5549 TCGA-B8-A54D TCGA-BP-4164 TCGA-BP-4327 
       32.61        23.74         6.38        27.29        32.61         3.58 
TCGA-BP-4334 TCGA-BP-4761 TCGA-BP-4959 TCGA-BP-5004 TCGA-BP-5176 TCGA-BP-5180 
       21.21         5.98        87.45        37.02        52.27        74.40 
TCGA-BP-5183 TCGA-BP-5196 TCGA-CJ-4894 TCGA-CJ-5680 TCGA-CJ-6027 TCGA-CW-6090 
       42.44        33.47        27.65        25.25        60.99        83.90 
TCGA-CZ-5458 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       56.94        21.76        47.54        65.65        12.26        14.63 
TCGA-EU-5907 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MM-A84U TCGA-2Z-A9J2 TCGA-2Z-A9J8 
        4.18        35.87        19.43        15.25        59.01        67.30 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-A5Y1 
       54.64        51.52        12.82        18.21        19.63        12.99 
TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 
        7.33        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        13.68        16.90         0.13 
TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       14.07        18.02        86.27 

$`DEL PEAK 26(XP22.2) WILD-TYPE`
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8341 TCGA-KL-8344 TCGA-KL-8346 
      141.73       109.22       137.06        24.79        28.80        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 
      151.96        23.28        28.80        49.97        51.06        31.33 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 
       23.47        25.91         3.55         0.99        52.27        11.21 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 
       42.35       100.87        10.68        74.93        80.38        87.78 
TCGA-KO-8413 TCGA-KO-8414 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 
       86.10        77.85        12.66        12.16        47.21         0.53 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3324 
       39.16        24.16        49.08        49.58        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       42.97        82.32        51.25        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       24.16        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       18.87        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
       66.31        15.78        60.92        72.07        68.61        67.20 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       46.78        48.36        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        1.38        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 
        3.16        43.96         6.64         3.25        15.72        46.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 
       40.44        36.53        14.93        54.48        10.09        78.44 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       20.94        43.30        11.90        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05         2.24        21.86        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       35.90        11.80        26.20        21.60         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       18.21        21.44        37.22        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 
       90.12        56.94        52.77        39.55        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
       47.97        96.36        89.49        61.32        97.41        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67         9.57         5.75         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 
       17.19        25.55        25.91        23.01        20.91         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 
       27.02         0.85        24.23        17.16        16.60        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
        0.53        34.39        14.30        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
       61.78        64.27        54.90        97.45        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        80.68        37.25        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 
       44.94        12.23        31.89        11.31        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 
       31.33        12.30        72.59        77.98        77.62        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 
       41.75        71.80        48.07        13.15        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 
       45.07        30.64        41.62        18.51        38.70        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5178 
       79.30         1.78        74.20        30.64         9.63        62.86 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       49.15        38.30        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       54.61        53.52        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45        59.44        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        22.32        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        53.26        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        56.28        55.33        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.85        10.22        57.21        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5988 TCGA-CZ-5989 
       31.10        12.69        80.19        67.96        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       43.69        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       66.28        56.84        23.90        66.02        18.12         3.91 
TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A564 
        6.77         7.96        10.29        70.13         2.01        19.96 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
       10.85         7.04        75.55        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JK 
        4.57        75.42        34.85        56.81        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7288 
        5.29        16.18        22.49         0.13        11.57        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       49.25         2.20        19.56        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 
        3.55        16.77         0.46         6.58        33.83        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4117 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 
        6.81         0.16        14.86        17.49        12.30        86.76 
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-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-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        54.90        34.19        19.00        24.89         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        48.62        39.25        34.82 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 
       25.84         6.38        17.98        17.33        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       26.47        48.30        43.76        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
        0.53        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  DEL PEAK 26(XP22.2) MUTATED DEL PEAK 26(XP22.2) WILD-TYPE 
                         0.13                          0.07 
  DEL PEAK 26(XP22.2) MUTATED DEL PEAK 26(XP22.2) WILD-TYPE 
                       129.37                        194.79 
  DEL PEAK 26(XP22.2) MUTATED DEL PEAK 26(XP22.2) WILD-TYPE 
                       35.870                        30.315 
[1] "0.1 - 129.4 (35.9)" "0.1 - 194.8 (30.3)"
[1] "hr=" "1"  
D39V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 26(XP22.2) MUTATED        43       24        39       14
  DEL PEAK 26(XP22.2) WILD-TYPE     405       79       151       86
D39V3, multiclass
           clus
vv          DEL PEAK 26(XP22.2) MUTATED DEL PEAK 26(XP22.2) WILD-TYPE
  STAGE I                            43                           405
  STAGE II                           24                            79
  STAGE III                          39                           151
  STAGE IV                           14                            86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 26(XP22.2) MUTATED    44  26  49   3
  DEL PEAK 26(XP22.2) WILD-TYPE 418  97 202  12
D39V4, multiclass
    clus
vv   DEL PEAK 26(XP22.2) MUTATED DEL PEAK 26(XP22.2) WILD-TYPE
  T1                          44                           418
  T2                          26                            97
  T3                          49                           202
  T4                           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                             N0  N1  N2
  DEL PEAK 26(XP22.2) MUTATED    48  11   2
  DEL PEAK 26(XP22.2) WILD-TYPE 269  32   4
D39V5, multiclass
    clus
vv   DEL PEAK 26(XP22.2) MUTATED DEL PEAK 26(XP22.2) WILD-TYPE
  N0                          48                           269
  N1                          11                            32
  N2                           2                             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"
D39V6, binary
                               cls
clus                              0   1
  DEL PEAK 26(XP22.2) MUTATED    73  11
  DEL PEAK 26(XP22.2) WILD-TYPE 469  78
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 26(XP22.2) MUTATED     73   11
  DEL PEAK 26(XP22.2) WILD-TYPE  469   78
   clus
vv  DEL PEAK 26(XP22.2) MUTATED DEL PEAK 26(XP22.2) WILD-TYPE
  0                          73                           469
  1                          11                            78
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 26(XP22.2) MUTATED    44  79
  DEL PEAK 26(XP22.2) WILD-TYPE 243 493
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 26(XP22.2) MUTATED     44   79
  DEL PEAK 26(XP22.2) WILD-TYPE  243  493
        clus
vv       DEL PEAK 26(XP22.2) MUTATED DEL PEAK 26(XP22.2) WILD-TYPE
  FEMALE                          44                           243
  MALE                            79                           493
[1] 2 2
[1] FALSE
D39V8, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK 26(XP22.2) MUTATED                   39
  DEL PEAK 26(XP22.2) WILD-TYPE                 27
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 26(XP22.2) MUTATED                                  55
  DEL PEAK 26(XP22.2) WILD-TYPE                               469
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 26(XP22.2) MUTATED                                      29
  DEL PEAK 26(XP22.2) WILD-TYPE                                   240
D39V9, multiclass
                                       clus
vv                                      DEL PEAK 26(XP22.2) MUTATED
  KIDNEY CHROMOPHOBE                                             39
  KIDNEY CLEAR CELL RENAL CARCINOMA                              55
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          29
                                       clus
vv                                      DEL PEAK 26(XP22.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               27
  KIDNEY CLEAR CELL RENAL CARCINOMA                               469
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           240
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, continuous
D39V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(XP22.2) MUTATED                                  0     5
  DEL PEAK 26(XP22.2) WILD-TYPE                                2    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(XP22.2) MUTATED                          18    95
  DEL PEAK 26(XP22.2) WILD-TYPE                        98   607
D39V12, multiclass
                                  clus
vv                                 DEL PEAK 26(XP22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 18
  WHITE                                                     95
                                  clus
vv                                 DEL PEAK 26(XP22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   98
  WHITE                                                      607
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V13, binary
                               cls
clus                              0   1
  DEL PEAK 26(XP22.2) MUTATED     3  73
  DEL PEAK 26(XP22.2) WILD-TYPE  39 524
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 26(XP22.2) MUTATED      3   73
  DEL PEAK 26(XP22.2) WILD-TYPE   39  524
                        clus
vv                       DEL PEAK 26(XP22.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          73
                        clus
vv                       DEL PEAK 26(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                39
  NOT HISPANIC OR LATINO                           524
[1] 2 2
[1] FALSE
