[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/22506733/KIPAN-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIPAN-TP/22533781/transformed.cor.cli.txt"

nPatients in clinical file=941, in cluster file=882, common to both=882
[1]  32 882
[1] "AMP PEAK 1(1Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(1Q32.1) MUTATED AMP PEAK 1(1Q32.1) WILD-TYPE 
                          82                          800 
  AMP PEAK 1(1Q32.1) MUTATED AMP PEAK 1(1Q32.1) WILD-TYPE 
                          82                          800 
[1] "AMP PEAK 2(2Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                         136                          746 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                         136                          746 
[1] "AMP PEAK 3(3Q26.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(3Q26.32) MUTATED AMP PEAK 3(3Q26.32) WILD-TYPE 
                          193                           689 
  AMP PEAK 3(3Q26.32) MUTATED AMP PEAK 3(3Q26.32) WILD-TYPE 
                          193                           689 
[1] "AMP PEAK 4(5Q35.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(5Q35.1) MUTATED AMP PEAK 4(5Q35.1) WILD-TYPE 
                         376                          506 
  AMP PEAK 4(5Q35.1) MUTATED AMP PEAK 4(5Q35.1) WILD-TYPE 
                         376                          506 
[1] "AMP PEAK 5(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                         377                          505 
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                         377                          505 
[1] "AMP PEAK 6(8Q24.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 6(8Q24.22) MUTATED AMP PEAK 6(8Q24.22) WILD-TYPE 
                          125                           757 
  AMP PEAK 6(8Q24.22) MUTATED AMP PEAK 6(8Q24.22) WILD-TYPE 
                          125                           757 
[1] "AMP PEAK 7(10P14) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 7(10P14) MUTATED AMP PEAK 7(10P14) WILD-TYPE 
                         34                         848 
  AMP PEAK 7(10P14) MUTATED AMP PEAK 7(10P14) WILD-TYPE 
                         34                         848 
[1] "AMP PEAK 8(17Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 8(17Q24.3) MUTATED AMP PEAK 8(17Q24.3) WILD-TYPE 
                          243                           639 
  AMP PEAK 8(17Q24.3) MUTATED AMP PEAK 8(17Q24.3) WILD-TYPE 
                          243                           639 
[1] "AMP PEAK 9(XQ11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 9(XQ11.2) MUTATED AMP PEAK 9(XQ11.2) WILD-TYPE 
                         136                          746 
  AMP PEAK 9(XQ11.2) MUTATED AMP PEAK 9(XQ11.2) WILD-TYPE 
                         136                          746 
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           209                            673 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           209                            673 
[1] "DEL PEAK  2(1P31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                          166                           716 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                          166                           716 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                        116                         766 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                        116                         766 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           75                           807 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           75                           807 
[1] "DEL PEAK  5(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                          111                           771 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                          111                           771 
[1] "DEL PEAK  6(3P26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                          489                           393 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                          489                           393 
[1] "DEL PEAK  7(3P21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P21.2) MUTATED DEL PEAK  7(3P21.2) WILD-TYPE 
                          503                           379 
  DEL PEAK  7(3P21.2) MUTATED DEL PEAK  7(3P21.2) WILD-TYPE 
                          503                           379 
[1] "DEL PEAK  8(3P14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P14.1) MUTATED DEL PEAK  8(3P14.1) WILD-TYPE 
                          408                           474 
  DEL PEAK  8(3P14.1) MUTATED DEL PEAK  8(3P14.1) WILD-TYPE 
                          408                           474 
[1] "DEL PEAK  9(3P12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3P12.2) MUTATED DEL PEAK  9(3P12.2) WILD-TYPE 
                          336                           546 
  DEL PEAK  9(3P12.2) MUTATED DEL PEAK  9(3P12.2) WILD-TYPE 
                          336                           546 
[1] "DEL PEAK 10(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                          113                           769 
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                          113                           769 
[1] "DEL PEAK 11(5P15.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(5P15.33) MUTATED DEL PEAK 11(5P15.33) WILD-TYPE 
                            31                            851 
  DEL PEAK 11(5P15.33) MUTATED DEL PEAK 11(5P15.33) WILD-TYPE 
                            31                            851 
[1] "DEL PEAK 12(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        233                         649 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        233                         649 
[1] "DEL PEAK 13(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                        234                         648 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                        234                         648 
[1] "DEL PEAK 14(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                          184                           698 
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                          184                           698 
[1] "DEL PEAK 15(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                        198                         684 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                        198                         684 
[1] "DEL PEAK 16(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          209                           673 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          209                           673 
[1] "DEL PEAK 17(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE 
                            164                             718 
  DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE 
                            164                             718 
[1] "DEL PEAK 18(11Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(11Q23.1) MUTATED DEL PEAK 18(11Q23.1) WILD-TYPE 
                            71                            811 
  DEL PEAK 18(11Q23.1) MUTATED DEL PEAK 18(11Q23.1) WILD-TYPE 
                            71                            811 
[1] "DEL PEAK 19(13Q13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(13Q13.2) MUTATED DEL PEAK 19(13Q13.2) WILD-TYPE 
                           149                            733 
  DEL PEAK 19(13Q13.2) MUTATED DEL PEAK 19(13Q13.2) WILD-TYPE 
                           149                            733 
[1] "DEL PEAK 20(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(14Q31.1) MUTATED DEL PEAK 20(14Q31.1) WILD-TYPE 
                           279                            603 
  DEL PEAK 20(14Q31.1) MUTATED DEL PEAK 20(14Q31.1) WILD-TYPE 
                           279                            603 
[1] "DEL PEAK 21(16Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(16Q23.3) MUTATED DEL PEAK 21(16Q23.3) WILD-TYPE 
                            37                            845 
  DEL PEAK 21(16Q23.3) MUTATED DEL PEAK 21(16Q23.3) WILD-TYPE 
                            37                            845 
[1] "DEL PEAK 22(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                            43                            839 
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                            43                            839 
[1] "DEL PEAK 23(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(XP22.2) MUTATED DEL PEAK 23(XP22.2) WILD-TYPE 
                          125                           757 
  DEL PEAK 23(XP22.2) MUTATED DEL PEAK 23(XP22.2) WILD-TYPE 
                          125                           757 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 882 columns.

[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=213,	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=587,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=40,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 882 columns, 1 survival variables, and 13 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "KARNOFSKY_PERFORMANCE_SCORE"  
 [9] "HISTOLOGICAL_TYPE"             "NUMBER_PACK_YEARS_SMOKED"     
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RACE"                         
[13] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=63, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
480 127 258  15 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
480 127 258  15 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
480 127 258  15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
480 127 258  15 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
323  44   6 
[1] "table(vv)"
vv
 N0  N1  N2 
323  44   6 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
323  44   6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
323  44   6 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=10, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=44, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=40, 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  36
  AMP PEAK 1(1Q32.1) WILD-TYPE 602 192
  AMP PEAK 1(1Q32.1) MUTATED AMP PEAK 1(1Q32.1) WILD-TYPE 
                          82                          794 
  AMP PEAK 1(1Q32.1) MUTATED AMP PEAK 1(1Q32.1) WILD-TYPE 
                          36                          192 
$`AMP PEAK 1(1Q32.1) MUTATED`
TCGA-A3-3336 TCGA-A3-3343 TCGA-AK-3450 TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-4815 
       34.29        31.07        58.49        22.45        43.96        52.21 
TCGA-BP-4160 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4986 TCGA-CJ-6027 TCGA-CZ-4854 
       94.72        80.68        74.17        25.81       118.85        46.16 
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-KN-8427 TCGA-A3-3316 TCGA-A3-3372 TCGA-A3-3382 
       12.99        49.25         0.99        49.08        24.16        18.87 
TCGA-AK-3430 TCGA-B0-4713 TCGA-B0-4819 TCGA-B0-4838 TCGA-B0-4848 TCGA-B0-5092 
       15.78         6.64         6.02        27.42        29.03        15.09 
TCGA-B0-5096 TCGA-B0-5109 TCGA-B0-5115 TCGA-B0-5701 TCGA-B4-5843 TCGA-B8-4143 
        2.24        19.30        52.73        80.91         0.36        23.31 
TCGA-B8-5551 TCGA-BP-4161 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4329 TCGA-BP-4352 
        0.53        90.28        61.78        64.27        27.78        11.31 
TCGA-BP-4756 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4781 TCGA-BP-4963 TCGA-BP-4971 
       12.30        13.15         5.33        68.38        60.30        48.89 
TCGA-BP-4974 TCGA-BP-5173 TCGA-BP-5175 TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4873 
        6.94         2.04        30.64        46.55       114.41        74.27 
TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4895 TCGA-CJ-4916 TCGA-CJ-4923 TCGA-CJ-5675 
       64.27        66.21        39.45        45.14        18.81       129.40 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-6032 TCGA-CW-5587 TCGA-CW-6090 TCGA-CW-6097 
       18.87        22.32       119.64        73.18        83.90        18.77 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-5452 TCGA-G6-A5PC TCGA-MM-A564 TCGA-2Z-A9J2 
       69.21        58.75        58.82         7.96        19.96        59.01 
TCGA-5P-A9K9 TCGA-A4-7287 TCGA-AL-3466 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 
       19.36        19.63         9.63        30.28        25.35         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-A8LD TCGA-GL-7966 
        0.95         7.92        79.86         4.01        16.90         3.68 
TCGA-HE-7130 TCGA-IA-A40Y TCGA-Q2-A5QZ TCGA-WN-A9G9 
       58.19         2.04        14.07        26.01 

$`AMP PEAK 1(1Q32.1) WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3454 
       47.21        38.47        42.97        82.32       109.91        28.73 
TCGA-B0-4707 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       19.73        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4344 TCGA-BP-4353 
       15.42       111.02        32.61         3.58        54.77        12.33 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 
       77.62        44.15        60.59        11.64        20.38        37.25 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
        6.94        61.51        53.65        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 
       27.02        31.79        44.55        31.27        63.25       105.37 
TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CW-6093 
       26.93        27.65       108.56        53.26        75.58       103.43 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        0.59       107.54         5.46        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       81.21        70.13        23.01        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O 
       61.05        21.37         0.89        76.64        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       15.91        15.62         6.74        38.07       153.73        23.84 
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
      109.22       137.06        90.48       108.62        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       62.37       151.96        44.91        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-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 
      105.47        10.68       100.47       103.40        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
      104.55       103.10        99.88       105.60        96.62        90.48 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 
       92.55        12.66        11.90        36.82         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       20.71        18.64        28.31        65.52        20.28        33.47 
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-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3433 
       29.10       117.80       122.56       109.41        73.68       112.08 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       68.61       109.51        94.19        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       40.01        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       72.89        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-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.62        65.10         7.82         5.98         2.14        57.70 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77        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-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       45.30        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       65.29        39.45        26.07         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-B0-5094 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       90.87        90.48        52.54        30.48        58.59        66.05 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       38.63        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 
       46.39        56.98        42.41       111.52       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       86.47       126.28        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4146 
        1.25         0.53         4.64         5.46         0.23        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
       50.14        16.60         6.38        48.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         4.93        17.36 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       16.27        14.17        85.51       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4177 
        0.43        89.36        23.05        77.03        62.24        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       97.45        53.42        62.07        37.25        21.21        15.62 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
        0.07        93.99        18.48        52.24        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       44.94        12.23        31.89        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
       77.98         5.98        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4787 
       10.82        61.97        13.51        56.91        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 
       47.97        87.45        71.41        63.62        58.68        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        58.98        14.24        49.38        45.50 
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-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        6.35        79.30        74.20        52.27         9.63        74.40 
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-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       34.95         0.95       115.00        73.22        14.17       106.16 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4882 
       79.66        47.18        75.06       116.84        71.87        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
      115.69        50.01        24.66       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 
       54.48        38.56         3.06         4.57       131.08        72.00 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
      133.71        25.71        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 
       73.35        67.00        53.42        62.66         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4860 
       74.66         1.35       105.93        25.45        47.08         6.77 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5453 
       14.66        63.39        93.04       107.41        63.42        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       94.45        10.85        10.22        21.76        69.96        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       53.46        12.00        18.12         3.91         6.77         4.18 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MW-A4EC TCGA-T7-A92I 
       10.29        35.87         2.01        19.43        16.37        11.70 
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-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       15.48        71.80        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       27.09        67.43        18.21         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.46        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
       10.82         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       40.77        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       20.52        25.84        25.25        17.98        23.08        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
      194.79        12.92        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21        16.31        81.93        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25        25.22        16.80        19.99        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S 
       52.27        16.01        50.60        78.90        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      117.40       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       31.73        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        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 
                      129.40                       194.79 
  AMP PEAK 1(1Q32.1) MUTATED AMP PEAK 1(1Q32.1) WILD-TYPE 
                       27.60                        36.51 
[1] "0.4 - 129.4 (27.6)" "0.1 - 194.8 (36.5)"
[1] "hr=" "2"  
D1V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 1(1Q32.1) MUTATED        24       10        31       16
  AMP PEAK 1(1Q32.1) WILD-TYPE     430       93       159       88
D1V3, multiclass
           clus
vv          AMP PEAK 1(1Q32.1) MUTATED AMP PEAK 1(1Q32.1) WILD-TYPE
  STAGE I                           24                          430
  STAGE II                          10                           93
  STAGE III                         31                          159
  STAGE IV                          16                           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 1(1Q32.1) MUTATED    27  12  42   1
  AMP PEAK 1(1Q32.1) WILD-TYPE 453 115 216  14
D1V4, multiclass
    clus
vv   AMP PEAK 1(1Q32.1) MUTATED AMP PEAK 1(1Q32.1) WILD-TYPE
  T1                         27                          453
  T2                         12                          115
  T3                         42                          216
  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   2
  AMP PEAK 1(1Q32.1) WILD-TYPE 288  34   4
D1V5, multiclass
    clus
vv   AMP PEAK 1(1Q32.1) MUTATED AMP PEAK 1(1Q32.1) WILD-TYPE
  N0                         35                          288
  N1                         10                           34
  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"
D1V6, binary
                              cls
clus                             0   1
  AMP PEAK 1(1Q32.1) MUTATED    54  14
  AMP PEAK 1(1Q32.1) WILD-TYPE 492  75
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q32.1) MUTATED     54   14
  AMP PEAK 1(1Q32.1) WILD-TYPE  492   75
   clus
vv  AMP PEAK 1(1Q32.1) MUTATED AMP PEAK 1(1Q32.1) WILD-TYPE
  0                         54                          492
  1                         14                           75
[1] 2 2
[1] FALSE
D1V7, binary
                              cls
clus                             0   1
  AMP PEAK 1(1Q32.1) MUTATED    30  52
  AMP PEAK 1(1Q32.1) WILD-TYPE 262 538
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q32.1) MUTATED     30   52
  AMP PEAK 1(1Q32.1) WILD-TYPE  262  538
        clus
vv       AMP PEAK 1(1Q32.1) MUTATED AMP PEAK 1(1Q32.1) WILD-TYPE
  FEMALE                         30                          262
  MALE                           52                          538
[1] 2 2
[1] FALSE
D1V8, binary
                              cls
clus                             0   1
  AMP PEAK 1(1Q32.1) MUTATED    20   0
  AMP PEAK 1(1Q32.1) WILD-TYPE 388   3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q32.1) MUTATED     20    0
  AMP PEAK 1(1Q32.1) WILD-TYPE  388    3
     clus
vv    AMP PEAK 1(1Q32.1) MUTATED AMP PEAK 1(1Q32.1) WILD-TYPE
  NO                          20                          388
  YES                          0                            3
[1] 2 2
[1] FALSE
D1V9, 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                               466
                              vv
clus                           KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK 1(1Q32.1) MUTATED                                      19
  AMP PEAK 1(1Q32.1) WILD-TYPE                                   269
D1V10, multiclass
                                       clus
vv                                      AMP PEAK 1(1Q32.1) MUTATED
  KIDNEY CHROMOPHOBE                                             1
  KIDNEY CLEAR CELL RENAL CARCINOMA                             62
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                         19
                                       clus
vv                                      AMP PEAK 1(1Q32.1) WILD-TYPE
  KIDNEY CHROMOPHOBE                                              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                              466
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          269
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
D1V12, 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    15
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 1(1Q32.1) MUTATED                           5    75
  AMP PEAK 1(1Q32.1) WILD-TYPE                       116   644
D1V13, multiclass
                                  clus
vv                                 AMP PEAK 1(1Q32.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 5
  WHITE                                                    75
                                  clus
vv                                 AMP PEAK 1(1Q32.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                      15
  BLACK OR AFRICAN AMERICAN                                 116
  WHITE                                                     644
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                              cls
clus                             0   1
  AMP PEAK 1(1Q32.1) MUTATED     6  53
  AMP PEAK 1(1Q32.1) WILD-TYPE  36 569
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q32.1) MUTATED      6   53
  AMP PEAK 1(1Q32.1) WILD-TYPE   36  569
                        clus
vv                       AMP PEAK 1(1Q32.1) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                         53
                        clus
vv                       AMP PEAK 1(1Q32.1) WILD-TYPE
  HISPANIC OR LATINO                               36
  NOT HISPANIC OR LATINO                          569
[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  33
  AMP PEAK 2(2Q32.1) WILD-TYPE 545 195
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                         136                          740 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                          33                          195 
$`AMP PEAK 2(2Q32.1) MUTATED`
TCGA-AK-3450 TCGA-B0-4707 TCGA-BP-4342 TCGA-BP-4775 TCGA-BP-4799 TCGA-BP-5178 
       58.49        19.73        74.17        60.59        37.25        62.86 
TCGA-CZ-4854 TCGA-DV-A4W0 TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-A44B TCGA-BQ-5892 
       46.16        81.21        21.07        10.16        11.87        11.97 
TCGA-BQ-7046 TCGA-DW-5561 TCGA-GL-A59T TCGA-HE-A5NF TCGA-PJ-A5Z9 TCGA-KN-8427 
       96.92        13.61        17.95        84.89        17.75         0.99 
TCGA-KO-8410 TCGA-3Z-A93Z TCGA-A3-3372 TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3429 
      103.10        12.66        24.16        18.87         0.10       109.41 
TCGA-AK-3444 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4811 TCGA-B0-4821 TCGA-B0-5099 
       48.36         2.14        57.70        46.59        40.44        15.95 
TCGA-B0-5104 TCGA-B0-5113 TCGA-B0-5702 TCGA-B4-5832 TCGA-B4-5838 TCGA-B4-5843 
       90.48        38.63        71.41         5.10         5.46         0.36 
TCGA-B8-4620 TCGA-B8-5159 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4161 
       25.55        23.74        48.53         0.53         4.93        90.28 
TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 
      101.06         0.43        77.03        61.78         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4763 
       18.48        44.94        12.23        31.89        12.30        41.75 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4804 TCGA-BP-4969 TCGA-BP-4985 
       48.07        13.15        68.38        47.97        58.98        31.30 
TCGA-BP-4989 TCGA-BP-5001 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5185 
        3.88        38.70         2.04        74.20         9.63        37.22 
TCGA-BP-5196 TCGA-BP-5200 TCGA-CJ-4644 TCGA-CJ-4876 TCGA-CJ-4893 TCGA-CJ-4897 
       33.47        34.95        11.05        64.27        24.66       109.84 
TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 
       47.67        51.29        49.28       131.08        72.00       133.71 
TCGA-CJ-5682 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5587 TCGA-CW-5591 TCGA-CZ-4859 
      122.83        53.42       119.64        73.18        74.66        58.75 
TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5469 
        6.77        79.63        90.54        94.45        10.85        31.10 
TCGA-DV-A4VX TCGA-EU-5905 TCGA-2Z-A9J5 TCGA-2Z-A9JR TCGA-5P-A9K9 TCGA-A4-7585 
       53.46         3.91       100.27         5.29        19.36        35.18 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3466 
       16.96         8.48        16.31        15.75         8.28         9.63 
TCGA-AL-3471 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B9-4117 TCGA-B9-A69E 
       49.32        67.73         2.20        37.51         0.46        14.86 
TCGA-BQ-5878 TCGA-BQ-5885 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-DZ-6131 TCGA-DZ-6133 
       63.72        30.28         7.92         2.76        79.86        51.19 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A8LC 
        1.18         4.01        51.78        39.25        25.84        23.08 
TCGA-GL-7966 TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE 
        3.68        11.84        16.80         2.04        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A71V 
       11.41        34.29        42.94        99.12        14.07        28.80 
TCGA-SX-A7SQ TCGA-UZ-A9PK TCGA-UZ-A9PQ TCGA-V9-A7HT 
       41.62       117.40        86.27        31.73 

$`AMP PEAK 2(2Q32.1) WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 
      109.91        28.73        22.45        43.96        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
       24.82        25.91         1.18         8.42        15.42       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4353 
       94.72        32.61         3.58        80.68        54.77        12.33 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4965 
       77.62        44.15        11.64        20.38         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       27.62        35.90        48.10        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       44.55        31.27        63.25       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 
      108.56        53.26       118.85        75.58       103.43         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        43.69        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-G6-A8L7 
       11.67        37.15        66.28        56.84        23.90        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7049 TCGA-BQ-7055 
       21.86        19.23        26.04        13.25        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       20.12        11.28        48.85       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO 
       67.17        16.34        12.13        29.26        19.73        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
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-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 
      103.40        92.71        16.67       104.55        99.88       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 
       96.62        90.48        92.55        11.90        36.82         0.53 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
       39.16        24.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       48.59        36.36        38.99        37.38        48.82        62.01 
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-A3-3362 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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV 
       20.28        33.47        15.39        22.65         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 
       10.62        29.10       117.80       122.56        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
      112.08        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       40.01        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       72.89        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-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4713 TCGA-B0-4714 
        3.62        65.10         7.82         5.98         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       58.45        15.72         0.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        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        10.52        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-B0-5092 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-B0-5100 TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       62.89        90.87        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       66.05        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 
       85.78        86.47       126.28        80.91        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.66        32.98        21.57        16.67        12.00         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-B8-4622 
       49.97        42.71        25.05        45.37        17.19        50.14 
TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       40.04        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        6.38        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4163 
        1.74        17.36        16.27        14.17        85.51        93.34 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 
       99.85        89.36        23.05        62.24        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
       97.45        53.42        27.78        62.07        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4352 TCGA-BP-4354 
       15.62        52.24        62.86        49.08        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4769 
       31.33        72.59        77.98         5.98        71.80        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 
       10.82         5.33        61.97        13.51        56.91        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       46.45        36.95        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       18.51        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       79.30        30.64        52.27        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.25        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       24.62        19.82         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 
       14.17       106.16       114.41        54.61        58.95        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-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
      116.84        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 
       39.45        50.24        56.35        49.97        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 
      129.40        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 
       62.10        73.35        67.00        62.66         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        66.31        78.18 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
        1.35       105.93        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
       69.21        14.66        63.39        93.04       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 
       58.82        79.53        23.74        18.44        91.69        55.33 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
        1.94        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5906 
       14.63        22.78        62.63        12.00        18.12         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        4.18         7.96        10.29        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        16.37        11.70         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
       58.22        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
        0.10        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A6HP TCGA-AL-3467 
       19.63        19.73        14.33        12.46        12.46        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
       66.71        62.66        41.13        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       22.06        17.23         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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       40.83        26.04        25.35        10.82         7.66         0.95 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 
        7.63         7.04         7.17         3.81        40.77        80.88 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 
        2.40         0.43        90.90        11.05        71.44        25.15 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       20.52        25.25        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        81.93        58.19        26.01        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       25.22        19.99        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A55Z 
       21.34        12.36        12.76        10.55        10.09        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       99.78        87.09         6.61        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL 
       50.60        78.90        47.90        49.45        44.61        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       11.93        19.00        16.31        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       18.02        26.20       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
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 
                      133.71                       194.79 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                      33.880                       36.215 
[1] "0.1 - 133.7 (33.9)" "0.1 - 194.8 (36.2)"
[1] "hr=" "1"  
D2V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 2(2Q32.1) MUTATED        68       12        36       18
  AMP PEAK 2(2Q32.1) WILD-TYPE     386       91       154       86
D2V3, multiclass
           clus
vv          AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  STAGE I                           68                          386
  STAGE II                          12                           91
  STAGE III                         36                          154
  STAGE IV                          18                           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 2(2Q32.1) MUTATED    69  16  48   3
  AMP PEAK 2(2Q32.1) WILD-TYPE 411 111 210  12
D2V4, multiclass
    clus
vv   AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  T1                         69                          411
  T2                         16                          111
  T3                         48                          210
  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    48  11   3
  AMP PEAK 2(2Q32.1) WILD-TYPE 275  33   3
D2V5, multiclass
    clus
vv   AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  N0                         48                          275
  N1                         11                           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"
D2V6, binary
                              cls
clus                             0   1
  AMP PEAK 2(2Q32.1) MUTATED    85  13
  AMP PEAK 2(2Q32.1) WILD-TYPE 461  76
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(2Q32.1) MUTATED     85   13
  AMP PEAK 2(2Q32.1) WILD-TYPE  461   76
   clus
vv  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  0                         85                          461
  1                         13                           76
[1] 2 2
[1] FALSE
D2V7, binary
                              cls
clus                             0   1
  AMP PEAK 2(2Q32.1) MUTATED    51  85
  AMP PEAK 2(2Q32.1) WILD-TYPE 241 505
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(2Q32.1) MUTATED     51   85
  AMP PEAK 2(2Q32.1) WILD-TYPE  241  505
        clus
vv       AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  FEMALE                         51                          241
  MALE                           85                          505
[1] 2 2
[1] FALSE
D2V8, binary
                              cls
clus                             0   1
  AMP PEAK 2(2Q32.1) MUTATED    56   1
  AMP PEAK 2(2Q32.1) WILD-TYPE 352   2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(2Q32.1) MUTATED     56    1
  AMP PEAK 2(2Q32.1) WILD-TYPE  352    2
     clus
vv    AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  NO                          56                          352
  YES                          1                            2
[1] 2 2
[1] FALSE
D2V9, 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                                  81
  AMP PEAK 2(2Q32.1) WILD-TYPE                               447
                              vv
clus                           KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK 2(2Q32.1) MUTATED                                      53
  AMP PEAK 2(2Q32.1) WILD-TYPE                                   235
D2V10, multiclass
                                       clus
vv                                      AMP PEAK 2(2Q32.1) MUTATED
  KIDNEY CHROMOPHOBE                                             2
  KIDNEY CLEAR CELL RENAL CARCINOMA                             81
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                         53
                                       clus
vv                                      AMP PEAK 2(2Q32.1) WILD-TYPE
  KIDNEY CHROMOPHOBE                                              64
  KIDNEY CLEAR CELL RENAL CARCINOMA                              447
  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"
D2V11, continuous
D2V12, 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    13
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 2(2Q32.1) MUTATED                          15   115
  AMP PEAK 2(2Q32.1) WILD-TYPE                       106   604
D2V13, multiclass
                                  clus
vv                                 AMP PEAK 2(2Q32.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                15
  WHITE                                                   115
                                  clus
vv                                 AMP PEAK 2(2Q32.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                      13
  BLACK OR AFRICAN AMERICAN                                 106
  WHITE                                                     604
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                              cls
clus                             0   1
  AMP PEAK 2(2Q32.1) MUTATED     7  90
  AMP PEAK 2(2Q32.1) WILD-TYPE  35 532
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(2Q32.1) MUTATED      7   90
  AMP PEAK 2(2Q32.1) WILD-TYPE   35  532
                        clus
vv                       AMP PEAK 2(2Q32.1) MUTATED
  HISPANIC OR LATINO                              7
  NOT HISPANIC OR LATINO                         90
                        clus
vv                       AMP PEAK 2(2Q32.1) WILD-TYPE
  HISPANIC OR LATINO                               35
  NOT HISPANIC OR LATINO                          532
[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   135  54
  AMP PEAK 3(3Q26.32) WILD-TYPE 513 174
  AMP PEAK 3(3Q26.32) MUTATED AMP PEAK 3(3Q26.32) WILD-TYPE 
                          189                           687 
  AMP PEAK 3(3Q26.32) MUTATED AMP PEAK 3(3Q26.32) WILD-TYPE 
                           54                           174 
$`AMP PEAK 3(3Q26.32) MUTATED`
TCGA-KL-8339 TCGA-A3-3325 TCGA-B0-4712 TCGA-B8-4621 TCGA-BP-4762 TCGA-BP-5178 
       28.11        38.47        43.96        25.91        44.15        62.86 
TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       76.64        21.67        21.07        10.16        21.86        11.87 
TCGA-BQ-5886 TCGA-BQ-7046 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-GL-A59T 
       26.04        96.92        35.93        37.55        24.46        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-PJ-A5Z9 TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A8RZ 
       84.89        67.17        17.75        21.60        15.91         6.74 
TCGA-KL-8331 TCGA-KL-8346 TCGA-KM-8443 TCGA-KN-8427 TCGA-A3-3374 TCGA-A3-3387 
       98.96        62.37        49.97         0.99        43.20        20.28 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4690 TCGA-B0-4696 
       68.61       109.51        94.19        83.21         1.41        28.47 
TCGA-B0-4699 TCGA-B0-4713 TCGA-B0-4833 TCGA-B0-4845 TCGA-B0-5081 TCGA-B0-5084 
        3.62         6.64        78.44        65.29        11.90         7.30 
TCGA-B0-5094 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5102 TCGA-B0-5109 TCGA-B0-5116 
       10.95        21.86        52.08        90.87        19.30        41.88 
TCGA-B0-5690 TCGA-B0-5696 TCGA-B0-5710 TCGA-B0-5712 TCGA-B4-5835 TCGA-B4-5838 
      111.52        85.78        79.89        89.49         0.53         5.46 
TCGA-B8-4143 TCGA-B8-4620 TCGA-B8-5163 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-A54G 
       23.31        25.55        27.02         6.38         0.53         1.74 
TCGA-B8-A54I TCGA-BP-4163 TCGA-BP-4167 TCGA-BP-4329 TCGA-BP-4337 TCGA-BP-4338 
        4.93        93.34        89.36        27.78         0.07        93.99 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4960 
       31.89        11.31         5.98        13.15        68.38        71.41 
TCGA-BP-4964 TCGA-BP-4969 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5175 
       61.22        58.98        31.30        43.00         6.35        30.64 
TCGA-BP-5198 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4871 
       19.82        14.17       114.41        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       109.84        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        79.63        94.45 
TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 
       10.85        69.96        84.30         1.94        31.10        67.96 
TCGA-DV-A4VX TCGA-EU-5905 TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       53.46         3.91         7.04        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-5P-A9JY TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K9 TCGA-5P-A9KA 
       56.91        49.58        78.64        71.80        19.36        12.99 
TCGA-5P-A9KC TCGA-A4-7287 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
       12.39        19.63        30.48        23.97        23.31         0.76 
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-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B3-4103 TCGA-B9-4114 TCGA-B9-4117 
       49.32         2.20        37.51        30.58        28.18         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5890 
        1.15        43.99        22.06        17.49        47.80         7.66 
TCGA-BQ-7045 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
       48.26         7.04         3.81        40.77        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-A8LB 
       74.60        34.19        13.08         2.40        51.78        17.98 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NI 
       16.90       194.79        11.21        81.93        58.19        11.84 
TCGA-HE-A5NL TCGA-IA-A40Y TCGA-IA-A83S TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       25.22         2.04        85.78        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-P4-AAVM 
       34.29        99.78        87.09         6.61        16.01        50.60 
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        53.10 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      117.40       125.29        37.35        71.24        30.67        47.47 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
      110.73        51.35        31.73 

$`AMP PEAK 3(3Q26.32) WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 
       34.29        31.07        42.97        82.32       109.91        58.49 
TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 
       28.73        22.45        19.73        52.21        18.51       112.80 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 
      133.94        15.78        70.68       119.38       126.05        24.82 
TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 
        1.18         8.42        15.42       111.02        94.72        32.61 
TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 
        3.58        80.68        74.17        54.77        12.33        77.62 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       27.62        35.90        48.10        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       44.55        31.27        63.25       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
      108.56        53.26       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        0.59       107.54         5.46        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       81.21        70.13        23.01        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47O 
       61.05        21.37         0.89        12.99        49.25        27.68 
TCGA-B9-A5W7 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       19.23        13.25        11.97        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7840 
       11.28        48.85        13.61       129.86        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       14.63         3.02        61.02        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-Y8-A898 TCGA-KL-8323 
       19.73        41.33        62.83        86.37        15.62        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        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-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       54.74       151.96        44.91       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-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
      104.52         3.55        52.27        87.12        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
       11.21        59.08       115.00        42.35       100.87       105.47 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        99.88       105.60        96.62        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82         0.53        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
       28.70        74.63        74.76        24.16        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NI 
       20.71        18.64        18.87        28.31        65.52        33.47 
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-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
      112.08        46.78        48.36        78.64        40.01        94.29 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         3.32         4.57         2.53         3.48        19.00 
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        1.38        65.10         7.82         5.98         2.14        57.70 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
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-B0-4827 TCGA-B0-4828 TCGA-B0-4834 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        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        10.52 
TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       10.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5092 
       70.52        20.94        43.30        11.24        25.32        15.09 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 
        8.05         2.24        15.95        62.89        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5117 
       30.48        58.59        66.05        38.63        52.73        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
      129.67        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5711 TCGA-B0-5713 TCGA-B2-3923 
      149.16       105.37       130.65       131.15        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
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        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 
       42.71        25.05        45.37        17.19        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 
       23.74         0.85        24.23        50.14        16.60        48.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54J 
       34.39        14.30        27.29        29.88        17.06        17.36 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 
       16.27        14.17        85.51        90.28       101.06        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-4330 TCGA-BP-4332 TCGA-BP-4334 
       54.90        97.45        53.42        62.07        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 
       15.62        18.48        52.24        62.86        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.23        33.99        31.33        12.30        72.59        77.98 
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-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       61.97        13.51        56.91        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4968 
       87.45        63.62        58.68        60.30         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         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 
       14.93        36.07        33.34        46.45        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       46.45        16.47        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       37.48        35.21        28.87        79.30         2.04        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        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-5196 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       24.62        33.47        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4869 TCGA-CJ-4870 
       73.22       106.16        54.61        58.95        83.97        49.25 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4882 TCGA-CJ-4884 
       47.18        75.06       116.84        64.27        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 
       50.01        24.66        39.45        50.24        49.97        51.29 
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       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5580 
       62.10        73.35        67.00        62.66       119.64        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-6088 TCGA-CW-6090 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4863 
      105.93        83.90        25.45        47.08        58.75        63.39 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 
       18.44        90.54        91.69        55.33        10.22        21.76 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
       22.52         2.40        12.69        80.19        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5906 
       14.63        22.78        62.63        12.00        18.12         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        4.18         7.96        10.29        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2Z-A9J1 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       19.96        16.37        11.70        75.55         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
      106.55        90.21        22.26        15.48        62.93        43.04 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       27.09        67.43        18.21         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 
        7.82         0.23        16.64        29.46        25.64        23.28 
TCGA-A4-8517 TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       19.63         8.48         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 
       66.71        62.66        67.73        41.13        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 
       16.77        20.32        33.83        29.03        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       50.50        26.40        20.61        17.23         0.16        14.86 
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-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 
       10.82         0.95         7.92         2.76       123.62        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 
       61.28        50.40        49.84         7.63         7.17        79.86 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       19.00        24.89        10.68         1.18         0.43         4.01 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-7966 
       25.84        25.25        23.08        80.65        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NH 
       27.65         1.05        12.43        12.89        16.31        26.01 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83T TCGA-IA-A83V 
       56.75        73.25        16.80        19.99        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVO 
       15.48        42.94        99.12        92.58        52.27        78.90 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SR 
       47.90        49.45        44.61        27.06        11.93        26.47 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       43.76        18.02        26.20       103.63        98.96        86.27 
TCGA-UZ-A9PX TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       65.13        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       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                        153.73 
  AMP PEAK 3(3Q26.32) MUTATED AMP PEAK 3(3Q26.32) WILD-TYPE 
                        30.64                         36.82 
[1] "0.1 - 194.8 (30.6)" "0.1 - 153.7 (36.8)"
[1] "hr=" "1.2"
D3V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 3(3Q26.32) MUTATED        89       20        42       31
  AMP PEAK 3(3Q26.32) WILD-TYPE     365       83       148       73
D3V3, multiclass
           clus
vv          AMP PEAK 3(3Q26.32) MUTATED AMP PEAK 3(3Q26.32) WILD-TYPE
  STAGE I                            89                           365
  STAGE II                           20                            83
  STAGE III                          42                           148
  STAGE IV                           31                            73
[1] 4 2
[1] 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    97  26  63   6
  AMP PEAK 3(3Q26.32) WILD-TYPE 383 101 195   9
D3V4, multiclass
    clus
vv   AMP PEAK 3(3Q26.32) MUTATED AMP PEAK 3(3Q26.32) WILD-TYPE
  T1                          97                           383
  T2                          26                           101
  T3                          63                           195
  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    59  15   1
  AMP PEAK 3(3Q26.32) WILD-TYPE 264  29   5
D3V5, multiclass
    clus
vv   AMP PEAK 3(3Q26.32) MUTATED AMP PEAK 3(3Q26.32) WILD-TYPE
  N0                          59                           264
  N1                          15                            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"
D3V6, binary
                               cls
clus                              0   1
  AMP PEAK 3(3Q26.32) MUTATED    90  26
  AMP PEAK 3(3Q26.32) WILD-TYPE 456  63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(3Q26.32) MUTATED     90   26
  AMP PEAK 3(3Q26.32) WILD-TYPE  456   63
   clus
vv  AMP PEAK 3(3Q26.32) MUTATED AMP PEAK 3(3Q26.32) WILD-TYPE
  0                          90                           456
  1                          26                            63
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK 3(3Q26.32) MUTATED    56 137
  AMP PEAK 3(3Q26.32) WILD-TYPE 236 453
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(3Q26.32) MUTATED     56  137
  AMP PEAK 3(3Q26.32) WILD-TYPE  236  453
        clus
vv       AMP PEAK 3(3Q26.32) MUTATED AMP PEAK 3(3Q26.32) WILD-TYPE
  FEMALE                          56                           236
  MALE                           137                           453
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK 3(3Q26.32) MUTATED    98   0
  AMP PEAK 3(3Q26.32) WILD-TYPE 310   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(3Q26.32) MUTATED     98    0
  AMP PEAK 3(3Q26.32) WILD-TYPE  310    3
     clus
vv    AMP PEAK 3(3Q26.32) MUTATED AMP PEAK 3(3Q26.32) WILD-TYPE
  NO                           98                           310
  YES                           0                             3
[1] 2 2
[1] FALSE
D3V9, 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                                  87
  AMP PEAK 3(3Q26.32) WILD-TYPE                               441
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK 3(3Q26.32) MUTATED                                     100
  AMP PEAK 3(3Q26.32) WILD-TYPE                                   188
D3V10, multiclass
                                       clus
vv                                      AMP PEAK 3(3Q26.32) MUTATED
  KIDNEY CHROMOPHOBE                                              6
  KIDNEY CLEAR CELL RENAL CARCINOMA                              87
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                         100
                                       clus
vv                                      AMP PEAK 3(3Q26.32) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               60
  KIDNEY CLEAR CELL RENAL CARCINOMA                               441
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
D3V12, 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    15
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 3(3Q26.32) MUTATED                          26   155
  AMP PEAK 3(3Q26.32) WILD-TYPE                        95   564
D3V13, multiclass
                                  clus
vv                                 AMP PEAK 3(3Q26.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 26
  WHITE                                                    155
                                  clus
vv                                 AMP PEAK 3(3Q26.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       15
  BLACK OR AFRICAN AMERICAN                                   95
  WHITE                                                      564
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                               cls
clus                              0   1
  AMP PEAK 3(3Q26.32) MUTATED     8 142
  AMP PEAK 3(3Q26.32) WILD-TYPE  34 480
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(3Q26.32) MUTATED      8  142
  AMP PEAK 3(3Q26.32) WILD-TYPE   34  480
                        clus
vv                       AMP PEAK 3(3Q26.32) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         142
                        clus
vv                       AMP PEAK 3(3Q26.32) WILD-TYPE
  HISPANIC OR LATINO                                34
  NOT HISPANIC OR LATINO                           480
[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   263 112
  AMP PEAK 4(5Q35.1) WILD-TYPE 385 116
  AMP PEAK 4(5Q35.1) MUTATED AMP PEAK 4(5Q35.1) WILD-TYPE 
                         375                          501 
  AMP PEAK 4(5Q35.1) MUTATED AMP PEAK 4(5Q35.1) WILD-TYPE 
                         112                          116 
$`AMP PEAK 4(5Q35.1) MUTATED`
TCGA-KL-8339 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3358 TCGA-A3-3359 
       28.11        47.21        38.47        34.29        42.97        82.32 
TCGA-AK-3454 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       28.73        19.73        43.96        18.51       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-A54H TCGA-BP-4158 
       15.78       119.38       126.05        24.82         8.42       111.02 
TCGA-BP-4160 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4762 
       94.72        80.68        74.17        54.77        12.33        44.15 
TCGA-BP-4775 TCGA-BP-4799 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       60.59        37.25        61.51        53.65        25.81        27.22 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 
       45.07        41.62        27.62        35.90        48.10        62.86 
TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4904 
       49.15        27.02        31.79        31.27        63.25       108.56 
TCGA-CJ-6027 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
      118.85        46.16         0.59        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-A4W0 TCGA-BQ-5892 TCGA-DW-7838 TCGA-KL-8327 TCGA-KN-8426 
       66.28        81.21        11.97        24.46       137.06         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8414 TCGA-3Z-A93Z 
        0.99        52.27        42.35        10.68       105.60        12.66 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3326 
       49.08        49.02        49.58        48.59        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3347 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
       48.82        62.01        52.93        29.92        18.44        88.37 
TCGA-A3-3362 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       51.25        74.76        24.16        43.20        55.76        18.64 
TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8OW TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3440 
        0.10        10.62       109.41        15.78       109.51        94.19 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3458 TCGA-AK-3460 
       48.36        78.64        94.29        83.21        38.40        82.45 
TCGA-AK-3461 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       72.89         4.57         2.53        65.10         7.82         5.98 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4817 
       57.70         6.64         3.25        46.59         5.52        33.50 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4828 TCGA-B0-4833 
        6.02        40.44        36.53        14.93        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4844 
       40.70        27.42        53.88         6.71        56.68        10.29 
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-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       43.30        11.90        25.32        15.09        10.95         8.05 
TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       15.95        90.87        52.54        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5400 
       38.63        52.73        51.02        38.43        48.82        56.98 
TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5702 
       42.41       129.67        85.78        86.47        80.91        71.41 
TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      149.16       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
       35.90        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4146 
       21.57         5.10         1.25         5.46        23.31        16.80 
TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5549 
       25.55        40.04        23.74        27.02        24.23         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54G TCGA-B8-A54I 
       48.53         0.53        34.39        14.30         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4166 
       17.36        16.27        85.51       101.06        93.34         0.43 
TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4330 
       89.36        62.24        61.78        64.27        54.90        62.07 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4343 TCGA-BP-4347 TCGA-BP-4351 
       15.62         0.07        93.99        62.86        44.94        31.89 
TCGA-BP-4352 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4768 
       11.31        31.33        72.59        77.98        41.75        13.15 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       13.51        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
       36.39        36.95        47.97        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       58.68        60.30        61.22         6.74        57.40        58.98 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-4991 
       36.07        33.34        46.45        31.30         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 
       16.47        43.00        37.02        37.48        35.21        79.30 
TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5187 
        2.04        30.64         9.63        42.44        37.22        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4635 
       33.24        23.47        19.82        34.95         0.95        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4644 TCGA-CJ-4869 
       73.22        14.17       106.16        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       116.84        64.27        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
      113.46        64.18        30.64       115.69        50.01        24.66 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 
       49.28        50.33        54.48        45.14         3.06        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 
      131.08        72.00       129.40       133.71        18.87        22.32 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        7.36        92.02        81.83        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       78.18        74.66        25.45        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        6.77        14.66        63.39        93.04       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
       91.69        10.85        10.22        21.76        69.96        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40         1.94        31.10        12.69        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       12.26        62.63        53.46        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC 
        4.18         7.96        10.29         2.01        19.96        16.37 
TCGA-2K-A9WE TCGA-2Z-A9JK TCGA-2Z-A9JR TCGA-4A-A93X TCGA-5P-A9K3 TCGA-5P-A9K9 
        7.04        38.99         5.29        12.82        15.48        19.36 
TCGA-A4-8098 TCGA-A4-8516 TCGA-A4-A48D TCGA-A4-A57E TCGA-AL-3466 TCGA-AL-3473 
       29.46         0.76        12.46         8.48         9.63        62.66 
TCGA-B1-5398 TCGA-B1-A656 TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5887 TCGA-BQ-5890 
       41.13        20.32         0.46         0.16        25.35         7.66 
TCGA-BQ-5891 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-A8LC 
        0.95        19.00        13.08         0.43         4.01        23.08 
TCGA-GL-A4EM TCGA-HE-A5NK TCGA-IA-A40X TCGA-IA-A40Y TCGA-KV-A6GD TCGA-P4-A5E6 
        1.05        73.25        19.99         2.04        18.41        99.78 
TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SQ 
       99.12        14.07        41.62 

$`AMP PEAK 4(5Q35.1) WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3343 
      102.81        23.28        28.80        47.24       130.13        31.07 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3455 TCGA-B0-4815 TCGA-B0-5695 TCGA-B8-4621 
      109.91        58.49        22.45        52.21        70.68        25.91 
TCGA-B8-5162 TCGA-B8-A54K TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4760 TCGA-BP-4782 
        1.18        15.42        32.61         3.58        77.62        11.64 
TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4993 TCGA-BP-5199 TCGA-CJ-4642 TCGA-CJ-4891 
       20.38         6.94         5.82        44.55       105.37        26.93 
TCGA-CJ-4894 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4862 TCGA-CZ-4865 
       27.65        53.26        75.58       103.43       107.54         5.46 
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-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       13.25        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 
       48.85        13.61       129.86        35.93        37.55        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 
        6.74        38.07       153.73        23.84       109.22        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-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
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-8429 
       87.91        25.48        25.91        65.19       104.52        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 
       19.33         2.50        11.21        59.08       115.00       100.87 
TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
      105.47       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E 
      103.10        99.88        96.62        90.48        92.55        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3319 TCGA-A3-3323 
       36.82         0.53        39.16        24.16        37.15        36.36 
TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3373 
        4.50        45.53        10.49        28.70        74.63        53.29 
TCGA-A3-3378 TCGA-A3-3383 TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-AK-3426 TCGA-AK-3427 
       20.71        28.31         0.10        11.18        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3447 
      122.56        73.68       112.08        68.61        46.78        40.01 
TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       37.58        12.13        40.70         1.41         3.32         1.41 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4706 
        3.48        28.47        19.00         1.38         3.62         2.14 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4824 
       58.45        15.72         0.59        45.07        16.77        54.48 
TCGA-B0-4827 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 
       29.10        68.71        45.30        10.52        65.29        39.45 
TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 
       11.24         7.30         2.24        21.86        52.08        62.89 
TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5399 TCGA-B0-5690 
       90.48        30.48        41.88        52.87        46.39       111.52 
TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5706 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-A4SR 
      126.28        73.84       105.37        32.61         1.68        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
       12.00         5.75         0.53         4.64         0.36         0.23 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 
       49.97        42.71        25.05        45.37        17.19        50.14 
TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.85        50.14        16.60        27.29        29.88        17.06 
TCGA-B8-A8YJ TCGA-BP-4161 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4325 
       14.17        90.28        99.85        23.05        77.03        97.45 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4340 TCGA-BP-4341 
       53.42        27.78        37.25        21.21        18.48        52.24 
TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4765 
       49.08        12.23        33.99        12.30         5.98        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4784 
       48.07        61.68        10.82         5.33        61.97        60.95 
TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4970 TCGA-BP-4987 TCGA-BP-4998 TCGA-BP-5000 
       10.98         6.71        14.24        36.95        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5180 
       38.70        28.87         6.35        74.20        52.27        74.40 
TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       38.30        37.25        22.78        13.41        24.62        33.47 
TCGA-CJ-4634 TCGA-CJ-4640 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4872 
      115.00       114.41        58.95        21.24        49.25        47.18 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4895 
       71.87        66.21        61.91        51.52        63.98        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-6032 TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
      119.64        64.57         5.39         1.35       105.93        83.90 
TCGA-CW-6097 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5987 
       18.77        55.33        94.45        84.30        80.19        14.63 
TCGA-CZ-5988 TCGA-DV-A4VZ TCGA-G6-A8L8 TCGA-MM-A563 TCGA-T7-A92I TCGA-2Z-A9J1 
       22.78        12.00        35.87        19.43        11.70        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       56.81        54.64        51.52        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
       29.36         0.13        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        71.80        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         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-A6HP 
       14.33        16.96        16.31        15.75         8.28        12.46 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-7332 
       70.19        49.32        66.71        67.73         2.20        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       36.49        20.25        16.77        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH 
        1.15        43.99        22.06        17.23        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-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
       10.82         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 
       34.19        24.89        10.68         2.40         1.18        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.84        25.25        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92         3.68        27.65        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       25.22        16.80        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GE 
       21.34        12.36        12.76        10.55        10.09        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-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       17.62        31.13        15.48        87.09        42.94         6.61 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
       92.58        52.27        16.01        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       16.31        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      117.40       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         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 
                      149.16                       194.79 
  AMP PEAK 4(5Q35.1) MUTATED AMP PEAK 4(5Q35.1) WILD-TYPE 
                       38.99                        30.67 
[1] "0.1 - 149.2 (39.0)" "0.1 - 194.8 (30.7)"
[1] "hr=" "1.2"
D4V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 4(5Q35.1) MUTATED       173       42        91       66
  AMP PEAK 4(5Q35.1) WILD-TYPE     281       61        99       38
D4V3, multiclass
           clus
vv          AMP PEAK 4(5Q35.1) MUTATED AMP PEAK 4(5Q35.1) WILD-TYPE
  STAGE I                          173                          281
  STAGE II                          42                           61
  STAGE III                         91                           99
  STAGE IV                          66                           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   180  56 133   7
  AMP PEAK 4(5Q35.1) WILD-TYPE 300  71 125   8
D4V4, multiclass
    clus
vv   AMP PEAK 4(5Q35.1) MUTATED AMP PEAK 4(5Q35.1) WILD-TYPE
  T1                        180                          300
  T2                         56                           71
  T3                        133                          125
  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   163  14   2
  AMP PEAK 4(5Q35.1) WILD-TYPE 160  30   4
D4V5, multiclass
    clus
vv   AMP PEAK 4(5Q35.1) MUTATED AMP PEAK 4(5Q35.1) WILD-TYPE
  N0                        163                          160
  N1                         14                           30
  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"
D4V6, binary
                              cls
clus                             0   1
  AMP PEAK 4(5Q35.1) MUTATED   278  58
  AMP PEAK 4(5Q35.1) WILD-TYPE 268  31
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q35.1) MUTATED    278   58
  AMP PEAK 4(5Q35.1) WILD-TYPE  268   31
   clus
vv  AMP PEAK 4(5Q35.1) MUTATED AMP PEAK 4(5Q35.1) WILD-TYPE
  0                        278                          268
  1                         58                           31
[1] 2 2
[1] FALSE
D4V7, binary
                              cls
clus                             0   1
  AMP PEAK 4(5Q35.1) MUTATED   118 258
  AMP PEAK 4(5Q35.1) WILD-TYPE 174 332
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q35.1) MUTATED    118  258
  AMP PEAK 4(5Q35.1) WILD-TYPE  174  332
        clus
vv       AMP PEAK 4(5Q35.1) MUTATED AMP PEAK 4(5Q35.1) WILD-TYPE
  FEMALE                        118                          174
  MALE                          258                          332
[1] 2 2
[1] FALSE
D4V8, binary
                              cls
clus                             0   1
  AMP PEAK 4(5Q35.1) MUTATED   116   2
  AMP PEAK 4(5Q35.1) WILD-TYPE 292   1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q35.1) MUTATED    116    2
  AMP PEAK 4(5Q35.1) WILD-TYPE  292    1
     clus
vv    AMP PEAK 4(5Q35.1) MUTATED AMP PEAK 4(5Q35.1) WILD-TYPE
  NO                         116                          292
  YES                          2                            1
[1] 2 2
[1] FALSE
D4V9, 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                                 332
  AMP PEAK 4(5Q35.1) WILD-TYPE                               196
                              vv
clus                           KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK 4(5Q35.1) MUTATED                                      36
  AMP PEAK 4(5Q35.1) WILD-TYPE                                   252
D4V10, multiclass
                                       clus
vv                                      AMP PEAK 4(5Q35.1) MUTATED
  KIDNEY CHROMOPHOBE                                             8
  KIDNEY CLEAR CELL RENAL CARCINOMA                            332
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                         36
                                       clus
vv                                      AMP PEAK 4(5Q35.1) WILD-TYPE
  KIDNEY CHROMOPHOBE                                              58
  KIDNEY CLEAR CELL RENAL CARCINOMA                              196
  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"
D4V11, continuous
D4V12, 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    11
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 4(5Q35.1) MUTATED                          31   333
  AMP PEAK 4(5Q35.1) WILD-TYPE                        90   386
D4V13, multiclass
                                  clus
vv                                 AMP PEAK 4(5Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     5
  BLACK OR AFRICAN AMERICAN                                31
  WHITE                                                   333
                                  clus
vv                                 AMP PEAK 4(5Q35.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                      11
  BLACK OR AFRICAN AMERICAN                                  90
  WHITE                                                     386
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                              cls
clus                             0   1
  AMP PEAK 4(5Q35.1) MUTATED    17 256
  AMP PEAK 4(5Q35.1) WILD-TYPE  25 366
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q35.1) MUTATED     17  256
  AMP PEAK 4(5Q35.1) WILD-TYPE   25  366
                        clus
vv                       AMP PEAK 4(5Q35.1) MUTATED
  HISPANIC OR LATINO                             17
  NOT HISPANIC OR LATINO                        256
                        clus
vv                       AMP PEAK 4(5Q35.1) WILD-TYPE
  HISPANIC OR LATINO                               25
  NOT HISPANIC OR LATINO                          366
[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   280  93
  AMP PEAK 5(7Q31.2) WILD-TYPE 368 135
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                         373                          503 
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                          93                          135 
$`AMP PEAK 5(7Q31.2) MUTATED`
TCGA-KL-8339 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3358 TCGA-AK-3425 TCGA-B0-4707 
       28.11        38.47        34.29        42.97       109.91        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5694 TCGA-B0-5698 TCGA-B8-4621 TCGA-BP-4158 
       43.96        52.21        15.78       119.38        25.91       111.02 
TCGA-BP-4775 TCGA-BP-4799 TCGA-BP-5009 TCGA-BP-5178 TCGA-BP-5201 TCGA-CJ-4636 
       60.59        37.25        35.90        62.86        31.27        63.25 
TCGA-CW-6093 TCGA-CZ-4854 TCGA-DV-5565 TCGA-DV-5574 TCGA-G6-A8L7 TCGA-MM-A84U 
      103.43        46.16        43.69        66.28        70.13        23.01 
TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU 
       34.85        33.07        25.58        16.18        22.49        12.26 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       61.05        21.37         0.89        76.64        49.25        21.67 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5892 TCGA-BQ-7046 
       21.07        10.16        21.86        19.23        11.97        96.92 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IZ-A6M8 TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       16.34        17.75        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8343 
       15.62       153.73       137.06        98.96        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 
      100.47        16.67       104.55        99.88       105.60        96.62 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3347 
       24.16        49.08        49.02        48.59        38.99        52.93 
TCGA-A3-3363 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 
       10.49        24.16        43.20        18.87        65.52        20.28 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3433 
        0.10        11.18       117.80       109.41        15.78       112.08 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3444 TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 
      109.51        94.19        48.36        83.21         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4811 
        4.57         3.48        28.47        57.70         3.25        46.59 
TCGA-B0-4819 TCGA-B0-4828 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4852 
        6.02        10.09        27.42        53.88         6.71        36.85 
TCGA-B0-5077 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5102 TCGA-B0-5109 TCGA-B0-5113 
       43.30        10.95         2.24        90.87        19.30        38.63 
TCGA-B0-5116 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-5639 
       41.88        80.91        73.84        91.46        35.90        32.98 
TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-4146 
        5.10         0.53         5.46         0.36        23.31        16.80 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5550 TCGA-B8-A54E TCGA-B8-A54I 
       17.19        25.55        50.14        48.53        29.88         4.93 
TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4170 TCGA-BP-4173 
       85.51       101.06         0.43        89.36        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 
       61.78        64.27        97.45        37.25        15.62         0.07 
TCGA-BP-4338 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4759 
       93.99        62.86        31.89        11.31        33.99        77.98 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4790 
       48.07        13.15         5.33        68.38        15.78        36.53 
TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 
       10.98         6.71        47.97        71.41        58.68        60.30 
TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4983 
        6.74        58.98        48.89        45.50        14.93        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       31.30        36.95         3.88        16.47        43.00        30.64 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5177 TCGA-BP-5198 TCGA-BP-5200 
        6.35        79.30         2.04         9.63        19.82        34.95 
TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       46.55        14.17        11.05        79.66        47.18        74.27 
TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 
      116.84       113.46        30.64        63.98       109.84        47.67 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5677 
       51.29        49.28         4.57       131.08        72.00        25.71 
TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CW-5588 
       22.32       122.83        62.10        73.35        53.42        66.31 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 
       74.66         1.35        18.77        47.08        69.21         6.77 
TCGA-CZ-4866 TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 
      107.41        23.74        79.63        90.54        94.45        10.85 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5988 
       69.96        22.52         1.94        31.10        67.96        22.78 
TCGA-DV-A4VX TCGA-MM-A564 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       53.46        19.96         7.04        75.55        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JR 
       56.91         4.57        56.81        30.71        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
        0.13        12.82        49.58        90.21        22.26        78.64 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7732 
       71.80        62.93        19.36        12.39        27.09        19.13 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
       16.64        30.48        25.64        23.97        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.63        14.33        16.96         8.48        16.31        15.75 
TCGA-A4-A6HP TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-A47N 
       12.46        49.32        66.71        67.73         2.20        36.49 
TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 
       20.25        20.32        33.83        30.58        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 
       22.06        17.49        47.80        26.04        25.35        10.82 
TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7051 TCGA-BQ-7059 
        0.95         2.76       123.62        48.26        50.40         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
        7.04         7.17         3.81        40.77        80.88        51.19 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 
       34.19        24.89        13.08         2.40         1.18         4.01 
TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       51.78        11.05        39.25        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R 
       23.08        80.65       194.79         3.68        27.65        12.43 
TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NL TCGA-IA-A40Y TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8196 TCGA-IZ-A6M9 
       25.22         2.04        88.24        96.69        21.34        12.36 
TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVK TCGA-P4-AAVL TCGA-Q2-A5QZ 
       20.25        15.48        87.09        52.27        16.01        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        49.45        44.61        28.80        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ 
       16.31        41.62        26.47        53.10        43.76        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PU TCGA-UZ-A9PV 
      117.40       103.63       125.29        37.35        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-Y8-A896 TCGA-Y8-A8RY 
       65.13       110.73        51.35        31.73        18.64        25.28 
TCGA-Y8-A8S0 
        6.02 

$`AMP PEAK 5(7Q31.2) WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3343 TCGA-A3-3359 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-5088 
       31.07        82.32        58.49        28.73        22.45        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 
      112.80       133.94        70.68       126.05        24.82         1.18 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
        8.42        15.42        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 
       74.17        54.77        12.33        77.62        44.15        11.64 
TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       20.38         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5181 
        5.82        45.07        41.62        27.62        48.10        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       27.02        31.79        44.55       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CZ-4856 TCGA-CZ-4862 
      108.56        53.26       118.85        75.58         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        5.46        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-5P-A9JV 
       56.84        23.90        81.21        75.42        39.88        67.17 
TCGA-A4-A5Y1 TCGA-B1-A47O TCGA-B9-A44B TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7049 
       12.99        27.68        11.87        26.04        13.25        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-7839 TCGA-IA-A83W TCGA-MH-A855 
       26.27        20.12        11.28        13.78        67.17        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 
       29.26        19.73        41.33         6.74        38.07        23.84 
TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
      109.22        90.48       108.62        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 
       92.55        30.25        44.84        86.56        66.54        73.91 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8440 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       28.80        54.74        44.91       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       105.47       103.40 
TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       92.71       103.10        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 
       36.82         0.53        39.16        37.15        49.58        36.36 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 
       37.38        48.82        62.01         4.50        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       18.44        88.37        51.25        28.70        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-A6NI 
       53.29        55.76        20.71        18.64        28.31        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 
       15.39        22.65         0.10        10.62        29.10       122.56 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
       73.68        68.61        46.78        78.64        40.01        94.29 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        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        58.45        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        10.52        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-B0-5092 TCGA-B0-5095 
       11.24        11.90         7.30        25.32        15.09         8.05 
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-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
       30.48        58.59        66.05        52.73        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5705 
      129.67        85.78        86.47       126.28        71.41       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-3923 
      105.37       130.65        79.89       131.15        89.49        32.61 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5641 
        1.68        31.96        21.30        31.30        31.66        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5844 
       16.67        12.00         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 
       49.97        42.71        25.05        45.37        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
        0.53        34.39        14.30        27.29        17.06         1.74 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 
       17.36        16.27        14.17        90.28        93.34        99.85 
TCGA-BP-4169 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4334 
       23.05        54.90        53.42        27.78        62.07        21.21 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4355 
       18.48        52.24        49.08        44.94        12.23        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4769 
       12.30        72.59         5.98        41.75        71.80        61.68 
TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 
       10.82        61.97        13.51        56.91        60.95        48.95 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4968 
       36.39        36.95        87.45        63.62        61.22        57.40 
TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4981 TCGA-BP-4982 
       14.24        49.38         6.94        47.11        36.07        33.34 
TCGA-BP-4991 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       46.45        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5182 
       28.87        74.20        30.64        52.27        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4634 
       23.47        13.41        24.62        33.47         0.95       115.00 
TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 
       73.22       106.16       114.41        54.61        58.95        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       83.97        49.25        75.06        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4892 
       61.91        57.83        64.18        51.52       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4905 
       24.66        39.45        50.24        56.35        49.97        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 
       50.33        54.48        38.56        45.14         3.06        18.81 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5686 
      129.40       133.71        18.87        25.25        18.15        67.00 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        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-CZ-4853 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
       25.45        58.75        14.66        63.39        93.04        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 
       58.82        79.53        18.44        91.69        55.33        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 
       21.76        84.30         2.40        12.69        80.19        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       12.26        14.63        62.63        12.00        18.12         3.91 
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-MW-A4EC TCGA-T7-A92I TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9JG 
       19.43        16.37        11.70        59.01        91.73        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-5P-A9JW 
       51.52        38.99        24.33        31.20        11.57       106.55 
TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       15.48        43.04        12.99        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 
        0.10        35.18         7.82         0.23        29.46        23.28 
TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 
       19.73        12.46         8.28         9.63        70.19        62.66 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-A5W8 
       41.13        37.51        16.77        29.03        34.49        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        0.16        14.86        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5885 
       63.72        22.92        43.20        21.63        40.83        30.28 
TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-DZ-6131 
        7.66         7.92        93.34        61.28        49.84        79.86 
TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6796 
       74.60        19.00        10.68         0.43        90.90        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-A4EM TCGA-GL-A9DC 
       25.15        20.52        16.90        12.92         1.05        12.89 
TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IZ-8195 
       16.31        73.25        16.80        19.99        85.78        22.26 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A856 
       10.55        10.09        30.38        27.65        17.62        31.13 
TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVM 
       99.78        42.94         6.61        99.12        92.58        50.60 
TCGA-P4-AAVO TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
       78.90        27.06        18.02        98.96        86.27        71.24 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8S1 
       26.01        39.06        18.64        18.05        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                       149.16 
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                       31.27                        37.51 
[1] "0.1 - 194.8 (31.3)" "0.1 - 149.2 (37.5)"
[1] "hr=" "1"  
D5V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 5(7Q31.2) MUTATED       193       38        69       57
  AMP PEAK 5(7Q31.2) WILD-TYPE     261       65       121       47
D5V3, multiclass
           clus
vv          AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  STAGE I                          193                          261
  STAGE II                          38                           65
  STAGE III                         69                          121
  STAGE IV                          57                           47
[1] 4 2
[1] 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   206  52 110   8
  AMP PEAK 5(7Q31.2) WILD-TYPE 274  75 148   7
D5V4, multiclass
    clus
vv   AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  T1                        206                          274
  T2                         52                           75
  T3                        110                          148
  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   121  21   5
  AMP PEAK 5(7Q31.2) WILD-TYPE 202  23   1
D5V5, multiclass
    clus
vv   AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  N0                        121                          202
  N1                         21                           23
  N2                          5                            1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                              cls
clus                             0   1
  AMP PEAK 5(7Q31.2) MUTATED   191  47
  AMP PEAK 5(7Q31.2) WILD-TYPE 355  42
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(7Q31.2) MUTATED    191   47
  AMP PEAK 5(7Q31.2) WILD-TYPE  355   42
   clus
vv  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  0                        191                          355
  1                         47                           42
[1] 2 2
[1] FALSE
D5V7, binary
                              cls
clus                             0   1
  AMP PEAK 5(7Q31.2) MUTATED    94 283
  AMP PEAK 5(7Q31.2) WILD-TYPE 198 307
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(7Q31.2) MUTATED     94  283
  AMP PEAK 5(7Q31.2) WILD-TYPE  198  307
        clus
vv       AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  FEMALE                         94                          198
  MALE                          283                          307
[1] 2 2
[1] FALSE
D5V8, binary
                              cls
clus                             0   1
  AMP PEAK 5(7Q31.2) MUTATED   189   3
  AMP PEAK 5(7Q31.2) WILD-TYPE 219   0
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(7Q31.2) MUTATED    189    3
  AMP PEAK 5(7Q31.2) WILD-TYPE  219    0
     clus
vv    AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  NO                         189                          219
  YES                          3                            0
[1] 2 2
[1] FALSE
D5V9, 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                                 175
  AMP PEAK 5(7Q31.2) WILD-TYPE                               353
                              vv
clus                           KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK 5(7Q31.2) MUTATED                                     177
  AMP PEAK 5(7Q31.2) WILD-TYPE                                   111
D5V10, multiclass
                                       clus
vv                                      AMP PEAK 5(7Q31.2) MUTATED
  KIDNEY CHROMOPHOBE                                            25
  KIDNEY CLEAR CELL RENAL CARCINOMA                            175
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                        177
                                       clus
vv                                      AMP PEAK 5(7Q31.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                              41
  KIDNEY CLEAR CELL RENAL CARCINOMA                              353
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
D5V12, 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     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 5(7Q31.2) MUTATED                          45   309
  AMP PEAK 5(7Q31.2) WILD-TYPE                        76   410
D5V13, multiclass
                                  clus
vv                                 AMP PEAK 5(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          2
  ASIAN                                                     8
  BLACK OR AFRICAN AMERICAN                                45
  WHITE                                                   309
                                  clus
vv                                 AMP PEAK 5(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  76
  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"
D5V14, binary
                              cls
clus                             0   1
  AMP PEAK 5(7Q31.2) MUTATED    14 275
  AMP PEAK 5(7Q31.2) WILD-TYPE  28 347
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(7Q31.2) MUTATED     14  275
  AMP PEAK 5(7Q31.2) WILD-TYPE   28  347
                        clus
vv                       AMP PEAK 5(7Q31.2) MUTATED
  HISPANIC OR LATINO                             14
  NOT HISPANIC OR LATINO                        275
                        clus
vv                       AMP PEAK 5(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                               28
  NOT HISPANIC OR LATINO                          347
[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    79  45
  AMP PEAK 6(8Q24.22) WILD-TYPE 569 183
  AMP PEAK 6(8Q24.22) MUTATED AMP PEAK 6(8Q24.22) WILD-TYPE 
                          124                           752 
  AMP PEAK 6(8Q24.22) MUTATED AMP PEAK 6(8Q24.22) WILD-TYPE 
                           45                           183 
$`AMP PEAK 6(8Q24.22) MUTATED`
TCGA-KL-8339 TCGA-A3-3325 TCGA-A3-3336 TCGA-AK-3425 TCGA-AK-3454 TCGA-B0-4707 
       28.11        38.47        34.29       109.91        28.73        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-BP-4342 TCGA-BP-4799 TCGA-BP-5191 TCGA-CZ-4854 
       43.96        52.21        74.17        37.25        31.79        46.16 
TCGA-5P-A9JU TCGA-BQ-7056 TCGA-KL-8324 TCGA-KL-8331 TCGA-KL-8346 TCGA-KM-8438 
       12.26        20.12       153.73        98.96        62.37       151.96 
TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       49.97        23.47        25.91         3.55         0.99        52.27 
TCGA-KN-8433 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 
       11.21       100.47       104.55       103.10        99.88        96.62 
TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-AK-3433 TCGA-AK-3434 
        0.53        24.16        49.08        37.15       112.08        68.61 
TCGA-AK-3445 TCGA-B0-4688 TCGA-B0-4698 TCGA-B0-4703 TCGA-B0-4713 TCGA-B0-4813 
       78.64         3.32         1.38         5.98         6.64         0.59 
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        58.59 
TCGA-B0-5109 TCGA-B0-5701 TCGA-B0-5703 TCGA-B4-5832 TCGA-B8-5158 TCGA-B8-5163 
       19.30        80.91        73.84         5.10        40.04        27.02 
TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4174 TCGA-BP-4338 TCGA-BP-4352 TCGA-BP-4759 
        0.53         4.93        61.78        93.99        11.31        77.98 
TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4962 TCGA-BP-4983 
        5.98        13.15        15.78        10.98        58.68        46.45 
TCGA-BP-4985 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5177 
       31.30        18.51         6.35         2.04        30.64         9.63 
TCGA-BP-5185 TCGA-BP-5198 TCGA-CJ-4871 TCGA-CJ-4881 TCGA-CJ-4890 TCGA-CJ-4901 
       37.22        19.82        79.66        66.21       115.69        47.67 
TCGA-CJ-4912 TCGA-CJ-4923 TCGA-CJ-5677 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5588 
       54.48        18.81        25.71        62.66         7.36        66.31 
TCGA-CW-5591 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5462 TCGA-CZ-5464 
       74.66        69.21       107.41        79.63        10.22        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5987 
       84.30        22.52         1.94        31.10        12.69        14.63 
TCGA-DV-A4VX TCGA-MM-A564 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9JP TCGA-4A-A93X 
       53.46        19.96        59.01        58.22        29.36        12.82 
TCGA-5P-A9K9 TCGA-A4-8630 TCGA-AL-3466 TCGA-AL-3471 TCGA-B9-A5W9 TCGA-BQ-5880 
       19.36        14.33         9.63        49.32         0.16        43.20 
TCGA-BQ-5887 TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-A8LD 
       25.35         1.18         0.43         4.01        11.05        16.90 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A40Y TCGA-IZ-8195 TCGA-P4-A5EA TCGA-P4-AAVL 
        3.68         1.05         2.04        22.26         6.61        16.01 
TCGA-Q2-A5QZ TCGA-SX-A71U TCGA-SX-A7SR TCGA-V9-A7HT 
       14.07        44.61        26.47        31.73 

$`AMP PEAK 6(8Q24.22) WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3450 TCGA-AK-3455 TCGA-B0-5088 
       31.07        42.97        82.32        58.49        22.45        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
       24.82        25.91         1.18         8.42        15.42       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4353 
       94.72        32.61         3.58        80.68        54.77        12.33 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4807 
       77.62        44.15        60.59        11.64        20.38         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 
       27.02        44.55        31.27        63.25       105.37        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 
       27.65       108.56        53.26       118.85        75.58       103.43 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        0.59       107.54         5.46        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       81.21        70.13        23.01        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JV TCGA-A4-7288 
       33.07        25.58        16.18        22.49        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 
       15.91        15.62         6.74        38.07        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
      137.06        90.48       108.62        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-KM-8440 TCGA-KM-8476 
       73.91        71.41        28.80        54.74        44.91       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-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
      104.52        87.12        19.33         2.50        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       105.47        10.68       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       16.67       105.60        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       36.82        39.16        49.02        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        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       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       15.78        73.68       109.51        94.19        46.78        48.36 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       40.01        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       72.89        12.13        40.70         1.41         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4699 TCGA-B0-4700 
        2.53         3.48        28.47        19.00         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        7.82         2.14        57.70         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
       46.59         5.52        45.07        33.50        16.77         6.02 
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-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.52        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-B0-5084 
       36.85        70.52        20.94        43.30        11.24         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 
       25.32        15.09        10.95         8.05         2.24        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-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5705 
      129.67        85.78        86.47       126.28        71.41       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.66        32.98        21.57        16.67        12.00         5.75 
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        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 
       17.19        25.55        50.14        23.74         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
       50.14        16.60         6.38        48.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 
       27.29        29.88        17.06         1.74        17.36        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.17        85.51        90.28       101.06        93.34        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-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       21.21        15.62         0.07        18.48        52.24        62.86 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 
       49.08        44.94        12.23        31.89        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
       12.30        72.59        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-4781 
       10.82         5.33        61.97        13.51        56.91        68.38 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 
       60.95        48.95        36.53        36.39        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 
       47.97        87.45        71.41        63.62        60.30        61.22 
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-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 
       38.70        37.02        37.48        35.21        28.87        79.30 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       74.20        52.27        74.40        38.30        42.44        37.25 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       33.47        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       21.24        83.97        49.25        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
      116.84        64.27        71.87        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4892 TCGA-CJ-4893 
       64.18        30.64        51.52        63.98        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45       109.84        50.24        56.35        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        49.28        50.33        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 
        4.57       131.08        72.00       129.40       133.71        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       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       67.00        53.42       119.64        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 
        5.39        85.78        73.18        78.18         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4860 
       83.90        18.77        25.45        47.08        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       14.66        63.39        93.04        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5467 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
       10.85        21.76         2.40        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       12.26        22.78        62.63        12.00        18.12         3.91 
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-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J5 
       19.43        16.37        11.70         7.04        75.55       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JR TCGA-4A-A93W 
       38.99        30.71        24.33        31.20         5.29         0.13 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       15.48        71.80        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.73        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        8.28        12.46        70.19        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       43.99        22.06        17.23        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 
       86.76        19.27         8.88        63.72        22.92        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 
       21.63        40.83        26.04        30.28        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.78        90.90        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 
       25.84        25.25        17.98        23.08        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       12.92        27.65        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO 
       42.94        99.12        92.58        52.27        50.60        78.90 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        49.45        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       16.31        41.62        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      117.40       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        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 
                       153.73                        194.79 
  AMP PEAK 6(8Q24.22) MUTATED AMP PEAK 6(8Q24.22) WILD-TYPE 
                       27.565                        36.835 
[1] "0.2 - 153.7 (27.6)" "0.1 - 194.8 (36.8)"
[1] "hr=" "1.7"
D6V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 6(8Q24.22) MUTATED        35       23        38       27
  AMP PEAK 6(8Q24.22) WILD-TYPE     419       80       152       77
D6V3, multiclass
           clus
vv          AMP PEAK 6(8Q24.22) MUTATED AMP PEAK 6(8Q24.22) WILD-TYPE
  STAGE I                            35                           419
  STAGE II                           23                            80
  STAGE III                          38                           152
  STAGE IV                           27                            77
[1] 4 2
[1] 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  24  61   4
  AMP PEAK 6(8Q24.22) WILD-TYPE 444 103 197  11
D6V4, multiclass
    clus
vv   AMP PEAK 6(8Q24.22) MUTATED AMP PEAK 6(8Q24.22) WILD-TYPE
  T1                          36                           444
  T2                          24                           103
  T3                          61                           197
  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    53  13   3
  AMP PEAK 6(8Q24.22) WILD-TYPE 270  31   3
D6V5, multiclass
    clus
vv   AMP PEAK 6(8Q24.22) MUTATED AMP PEAK 6(8Q24.22) WILD-TYPE
  N0                          53                           270
  N1                          13                            31
  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"
D6V6, binary
                               cls
clus                              0   1
  AMP PEAK 6(8Q24.22) MUTATED    74  22
  AMP PEAK 6(8Q24.22) WILD-TYPE 472  67
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(8Q24.22) MUTATED     74   22
  AMP PEAK 6(8Q24.22) WILD-TYPE  472   67
   clus
vv  AMP PEAK 6(8Q24.22) MUTATED AMP PEAK 6(8Q24.22) WILD-TYPE
  0                          74                           472
  1                          22                            67
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK 6(8Q24.22) MUTATED    38  87
  AMP PEAK 6(8Q24.22) WILD-TYPE 254 503
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(8Q24.22) MUTATED     38   87
  AMP PEAK 6(8Q24.22) WILD-TYPE  254  503
        clus
vv       AMP PEAK 6(8Q24.22) MUTATED AMP PEAK 6(8Q24.22) WILD-TYPE
  FEMALE                          38                           254
  MALE                            87                           503
[1] 2 2
[1] FALSE
D6V8, binary
                               cls
clus                              0   1
  AMP PEAK 6(8Q24.22) MUTATED    49   0
  AMP PEAK 6(8Q24.22) WILD-TYPE 359   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(8Q24.22) MUTATED     49    0
  AMP PEAK 6(8Q24.22) WILD-TYPE  359    3
     clus
vv    AMP PEAK 6(8Q24.22) MUTATED AMP PEAK 6(8Q24.22) WILD-TYPE
  NO                           49                           359
  YES                           0                             3
[1] 2 2
[1] FALSE
D6V9, 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                                  79
  AMP PEAK 6(8Q24.22) WILD-TYPE                               449
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK 6(8Q24.22) MUTATED                                      28
  AMP PEAK 6(8Q24.22) WILD-TYPE                                   260
D6V10, multiclass
                                       clus
vv                                      AMP PEAK 6(8Q24.22) MUTATED
  KIDNEY CHROMOPHOBE                                             18
  KIDNEY CLEAR CELL RENAL CARCINOMA                              79
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          28
                                       clus
vv                                      AMP PEAK 6(8Q24.22) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               48
  KIDNEY CLEAR CELL RENAL CARCINOMA                               449
  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"
D6V11, continuous
D6V12, 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    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 6(8Q24.22) MUTATED                           8   110
  AMP PEAK 6(8Q24.22) WILD-TYPE                       113   609
D6V13, multiclass
                                  clus
vv                                 AMP PEAK 6(8Q24.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                    110
                                  clus
vv                                 AMP PEAK 6(8Q24.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                  113
  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"
D6V14, binary
                               cls
clus                              0   1
  AMP PEAK 6(8Q24.22) MUTATED     5  84
  AMP PEAK 6(8Q24.22) WILD-TYPE  37 538
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(8Q24.22) MUTATED      5   84
  AMP PEAK 6(8Q24.22) WILD-TYPE   37  538
                        clus
vv                       AMP PEAK 6(8Q24.22) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          84
                        clus
vv                       AMP PEAK 6(8Q24.22) WILD-TYPE
  HISPANIC OR LATINO                                37
  NOT HISPANIC OR LATINO                           538
[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  11
  AMP PEAK 7(10P14) WILD-TYPE 625 217
  AMP PEAK 7(10P14) MUTATED AMP PEAK 7(10P14) WILD-TYPE 
                         34                         842 
  AMP PEAK 7(10P14) MUTATED AMP PEAK 7(10P14) WILD-TYPE 
                         11                         217 
$`AMP PEAK 7(10P14) MUTATED`
TCGA-BP-4342 TCGA-BP-4986 TCGA-CZ-4854 TCGA-AL-3468 TCGA-KL-8324 TCGA-KN-8427 
       74.17        25.81        46.16        76.64       153.73         0.99 
TCGA-KN-8433 TCGA-KN-8436 TCGA-A3-3316 TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 
       11.21        42.35        49.08        83.21         3.32         1.41 
TCGA-B0-5109 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4143 TCGA-BP-4338 TCGA-BP-4768 
       19.30         5.10         5.46        23.31        93.99        13.15 
TCGA-BP-4781 TCGA-BP-5175 TCGA-CJ-5675 TCGA-CW-5588 TCGA-CZ-4866 TCGA-CZ-5454 
       68.38        30.64       129.40        66.31       107.41        23.74 
TCGA-EU-5905 TCGA-5P-A9K9 TCGA-A4-8098 TCGA-B9-4617 TCGA-BQ-5882 TCGA-F9-A7Q0 
        3.91        19.36        29.46         1.15        21.63        13.08 
TCGA-F9-A8NY TCGA-HE-7130 TCGA-SX-A7SS TCGA-UZ-A9PQ 
        1.18        58.19        53.10        86.27 

$`AMP PEAK 7(10P14) WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       54.77        12.33        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4988 
       20.38        37.25         6.94        61.51        53.65        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 
       62.86        49.15        27.02        31.79        44.55        31.27 
TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       63.25       105.37        26.93        27.65       108.56        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
      118.85        75.58       103.43         0.59       107.54         5.46 
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-G6-A8L7 TCGA-MM-A84U 
       66.28        56.84        23.90        81.21        70.13        23.01 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
        6.74        38.07        23.84       109.22       137.06        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-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
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-8434 TCGA-KN-8435 
       52.27        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       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67       104.55       103.10        99.88       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 
       90.48        92.55        12.66        11.90        36.82         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-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 
       36.36        38.99        37.38        48.82        62.01         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 
       52.93        45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
        0.10        11.18        10.62        29.10       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
      109.41        15.78        73.68       112.08        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
       94.19        46.78        48.36        78.64        40.01        94.29 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        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        10.52        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-B0-5092 
       43.30        11.24        11.90         7.30        25.32        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        58.59 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       21.30        31.30        31.66        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
       12.00         5.75         1.25         0.53         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       17.19        25.55        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
        1.74         4.93        17.36        16.27        14.17        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
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-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
       97.45        53.42        27.78        62.07        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
       15.62         0.07        18.48        52.24        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        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-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        60.95        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 
       10.98        36.95         6.71        47.97        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        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         6.94 
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-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 
        6.35        79.30         2.04        74.20        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        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       116.84        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       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        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-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       18.81       131.08        72.00       133.71        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       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         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-6097 TCGA-CZ-4853 
       74.66         1.35       105.93        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 
       47.08        69.21        58.75         6.77        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5456 
       93.04        63.42        58.82        79.53        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       14.63        22.78        62.63        53.46        12.00        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-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 
       19.43        19.96        16.37        11.70         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
        7.82         0.23        16.64        30.48        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46         9.63        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         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-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        47.80        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        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        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        81.93        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       16.31        41.62        26.47        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  AMP PEAK 7(10P14) MUTATED AMP PEAK 7(10P14) WILD-TYPE 
                       0.99                        0.07 
  AMP PEAK 7(10P14) MUTATED AMP PEAK 7(10P14) WILD-TYPE 
                     153.73                      194.79 
  AMP PEAK 7(10P14) MUTATED AMP PEAK 7(10P14) WILD-TYPE 
                     27.635                      36.000 
[1] "1.0 - 153.7 (27.6)" "0.1 - 194.8 (36.0)"
[1] "hr=" "1.3"
D7V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 7(10P14) MUTATED        12        7         6        7
  AMP PEAK 7(10P14) WILD-TYPE     442       96       184       97
D7V3, multiclass
           clus
vv          AMP PEAK 7(10P14) MUTATED AMP PEAK 7(10P14) WILD-TYPE
  STAGE I                          12                         442
  STAGE II                          7                          96
  STAGE III                         6                         184
  STAGE IV                          7                          97
[1] 4 2
[1] 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   8   4
  AMP PEAK 7(10P14) WILD-TYPE 467 118 250  11
D7V4, multiclass
    clus
vv   AMP PEAK 7(10P14) MUTATED AMP PEAK 7(10P14) WILD-TYPE
  T1                        13                         467
  T2                         9                         118
  T3                         8                         250
  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   1
  AMP PEAK 7(10P14) WILD-TYPE 311  39   5
D7V5, multiclass
    clus
vv   AMP PEAK 7(10P14) MUTATED AMP PEAK 7(10P14) WILD-TYPE
  N0                        12                         311
  N1                         5                          39
  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"
D7V6, binary
                             cls
clus                            0   1
  AMP PEAK 7(10P14) MUTATED    23   5
  AMP PEAK 7(10P14) WILD-TYPE 523  84
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 7(10P14) MUTATED     23    5
  AMP PEAK 7(10P14) WILD-TYPE  523   84
   clus
vv  AMP PEAK 7(10P14) MUTATED AMP PEAK 7(10P14) WILD-TYPE
  0                        23                         523
  1                         5                          84
[1] 2 2
[1] FALSE
D7V7, binary
                             cls
clus                            0   1
  AMP PEAK 7(10P14) MUTATED    12  22
  AMP PEAK 7(10P14) WILD-TYPE 280 568
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 7(10P14) MUTATED     12   22
  AMP PEAK 7(10P14) WILD-TYPE  280  568
        clus
vv       AMP PEAK 7(10P14) MUTATED AMP PEAK 7(10P14) WILD-TYPE
  FEMALE                        12                         280
  MALE                          22                         568
[1] 2 2
[1] FALSE
D7V8, binary
                             cls
clus                            0   1
  AMP PEAK 7(10P14) MUTATED    14   0
  AMP PEAK 7(10P14) WILD-TYPE 394   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 7(10P14) MUTATED     14    0
  AMP PEAK 7(10P14) WILD-TYPE  394    3
     clus
vv    AMP PEAK 7(10P14) MUTATED AMP PEAK 7(10P14) WILD-TYPE
  NO                         14                         394
  YES                         0                           3
[1] 2 2
[1] FALSE
D7V9, 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                               508
                             vv
clus                          KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK 7(10P14) MUTATED                                      10
  AMP PEAK 7(10P14) WILD-TYPE                                   278
D7V10, multiclass
                                       clus
vv                                      AMP PEAK 7(10P14) MUTATED
  KIDNEY CHROMOPHOBE                                            4
  KIDNEY CLEAR CELL RENAL CARCINOMA                            20
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                        10
                                       clus
vv                                      AMP PEAK 7(10P14) WILD-TYPE
  KIDNEY CHROMOPHOBE                                             62
  KIDNEY CLEAR CELL RENAL CARCINOMA                             508
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                         278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
D7V12, continuous
[1] "Remove cluster labels:"    "AMP PEAK 7(10P14) MUTATED"
clus
  AMP PEAK 7(10P14) MUTATED AMP PEAK 7(10P14) WILD-TYPE 
                          2                          72 
                 TCGA-DV-A4W0                  TCGA-G6-A8L7 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-MM-A84U                  TCGA-2Z-A9JD 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-DW-5561                  TCGA-PJ-A5Z9 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-UZ-A9PO                  TCGA-UZ-A9PR 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-Y8-A8RZ                  TCGA-KL-8330 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-KL-8335                  TCGA-KL-8341 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-KL-8345                  TCGA-KM-8639 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-KO-8408                  TCGA-KO-8409 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-A3-A8OV                  TCGA-A3-A8OW 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-AK-3445                  TCGA-AK-3451 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-B2-A4SR                  TCGA-B8-5158 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-B8-5550                  TCGA-MM-A563 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-T7-A92I                  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-A9JI                  TCGA-2Z-A9JN 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-2Z-A9JO                  TCGA-4A-A93W 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-4A-A93Y                  TCGA-A4-A48D 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-A4-A57E                  TCGA-A4-A5Y0 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-AL-3472                  TCGA-AL-7173 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-B1-A654                  TCGA-B9-4114 
"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-7963                  TCGA-F9-A97G 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-G7-6793                  TCGA-G7-6795 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-G7-7501                  TCGA-G7-A8LB 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-G7-A8LD                  TCGA-G7-A8LE 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-GL-7773                  TCGA-GL-A9DD 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-HE-A5NI                  TCGA-IA-A40U 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-MH-A854                  TCGA-MH-A856 
"AMP PEAK 7(10P14) WILD-TYPE" "AMP PEAK 7(10P14) WILD-TYPE" 
                 TCGA-P4-A5E6                  TCGA-P4-AAVK 
"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-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" 
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 7(10P14) MUTATED                                  0     2
  AMP PEAK 7(10P14) WILD-TYPE                                2    14
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 7(10P14) MUTATED                           3    27
  AMP PEAK 7(10P14) WILD-TYPE                       118   692
D7V13, multiclass
                                  clus
vv                                 AMP PEAK 7(10P14) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                                3
  WHITE                                                   27
                                  clus
vv                                 AMP PEAK 7(10P14) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                     14
  BLACK OR AFRICAN AMERICAN                                118
  WHITE                                                    692
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
                             cls
clus                            0   1
  AMP PEAK 7(10P14) MUTATED     1  22
  AMP PEAK 7(10P14) WILD-TYPE  41 600
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 7(10P14) MUTATED      1   22
  AMP PEAK 7(10P14) WILD-TYPE   41  600
                        clus
vv                       AMP PEAK 7(10P14) MUTATED AMP PEAK 7(10P14) WILD-TYPE
  HISPANIC OR LATINO                             1                          41
  NOT HISPANIC OR LATINO                        22                         600
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK 8(17Q24.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 8(17Q24.3) MUTATED   191  49
  AMP PEAK 8(17Q24.3) WILD-TYPE 457 179
  AMP PEAK 8(17Q24.3) MUTATED AMP PEAK 8(17Q24.3) WILD-TYPE 
                          240                           636 
  AMP PEAK 8(17Q24.3) MUTATED AMP PEAK 8(17Q24.3) WILD-TYPE 
                           49                           179 
$`AMP PEAK 8(17Q24.3) MUTATED`
TCGA-KL-8339 TCGA-A3-3325 TCGA-B0-4707 TCGA-B8-4621 TCGA-CJ-6027 TCGA-G6-A8L7 
       28.11        38.47        19.73        25.91       118.85        70.13 
TCGA-2Z-A9JD TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7288 TCGA-A4-7584 
       34.85        25.58        16.18        22.49        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       13.25        11.97        96.92        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IZ-A6M8 
       14.63         3.02        61.02        17.95        84.89        16.34 
TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       17.75        62.83        86.37        21.60        15.91        15.62 
TCGA-A3-3313 TCGA-A3-3363 TCGA-AK-3453 TCGA-B0-4698 TCGA-B0-4848 TCGA-B0-5099 
       24.16        10.49        83.21         1.38        29.03        15.95 
TCGA-B0-5102 TCGA-B0-5109 TCGA-B0-5696 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 
       90.87        19.30        85.78         0.53         5.46        23.31 
TCGA-B8-5551 TCGA-BP-4166 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4337 TCGA-BP-4756 
        0.53         0.43        64.27        54.90         0.07        12.30 
TCGA-BP-4758 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4985 TCGA-BP-5173 TCGA-BP-5176 
       72.59        13.15        68.38        31.30         2.04        52.27 
TCGA-BP-5182 TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4873 TCGA-CJ-4901 TCGA-CJ-4907 
       38.30        37.22        34.95        74.27        47.67        49.28 
TCGA-CJ-4912 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-EU-5905 
       54.48         6.77       107.41         1.94        31.10         3.91 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JM TCGA-2Z-A9JP 
       56.91         4.57        56.81        51.52        30.71        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
        5.29         0.13        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KE TCGA-A4-7286 
       15.48        71.80        62.93        19.36        27.09        18.21 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 
       35.18        19.13         0.23        16.64        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N 
        9.63        49.32        66.71         2.20        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.25        16.77        33.83        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       50.50        28.18        26.40         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5880 
       22.06         0.16        17.49        86.76         8.88        43.20 
TCGA-BQ-5881 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7045 
       47.80        25.35         7.66         0.95         7.92        48.26 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
       50.40        49.84         7.04         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF 
       80.88        51.19        34.19        24.89        13.08         2.40 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        1.18         4.01        51.78        11.05        39.25        71.44 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
      194.79         3.68         1.05        12.43        12.89        11.21 
TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
       81.93        26.01        11.84        56.75        25.22        16.80 
TCGA-IA-A40Y TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
        2.04        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-O9-A75Z 
       34.29        27.78        30.38        27.65        20.25        15.48 
TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A71R 
       87.09         6.61        99.12        16.01        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP 
       49.45        44.61        28.80        27.06        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       41.62        26.47        53.10        43.76        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      103.63       125.29        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A8RY TCGA-Y8-A8S0 
       65.13       110.73        31.73        39.06        25.28         6.02 

$`AMP PEAK 8(17Q24.3) WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 
       34.29        31.07        42.97        82.32       109.91        58.49 
TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 
       28.73        22.45        43.96        52.21        18.51       112.80 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 
      133.94        15.78        70.68       119.38       126.05        24.82 
TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 
        1.18         8.42        15.42       111.02        94.72        32.61 
TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 
        3.58        80.68        74.17        54.77        12.33        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 
       27.02        31.79        44.55        31.27        63.25       105.37 
TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CW-6093 
       26.93        27.65       108.56        53.26        75.58       103.43 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 
       46.16         0.59       107.54         5.46        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-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       23.90        81.21        23.01        75.42        39.88        33.07 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-IA-A83W 
       12.26        67.17        44.84        26.27        20.12        67.17 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-Y8-A8RZ TCGA-KL-8323 
       12.13        29.26        19.73        41.33         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        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-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-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        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-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-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
      103.40        92.71        16.67       104.55       103.10        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
      105.60        96.62        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
       36.82         0.53        39.16        49.08        49.02        37.15 
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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       62.01         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       88.37        51.25        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 
        0.10         0.10        11.18        10.62        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
      122.56       109.41        15.78        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
      109.51        94.19        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       94.29        37.58        38.40        82.45        72.89        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-B0-4699 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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14        57.70         6.64         3.25        58.45 
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-B0-4819 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-B0-4834 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        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       65.29        39.45        26.07         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-B0-5092 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-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       62.89        90.48        52.54        30.48        58.59        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.66        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
        5.10         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 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
       50.14        16.60         6.38        48.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         4.93        17.36 
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-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-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
       97.45        53.42        27.78        62.07        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
       15.62        93.99        18.48        52.24        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
       77.98         5.98        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-4784 
       10.82         5.33        61.97        13.51        56.91        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         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-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       36.07        33.34        46.45        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
       37.48        35.21        28.87         6.35        79.30        74.20 
TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
       30.64         9.63        74.40        42.44        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       19.82         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      106.16       114.41        54.61        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       116.84 
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       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 
       24.66        39.45       109.84        50.24        56.35        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       51.29        49.18        50.33        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       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
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       119.64 
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-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       14.66        63.39        93.04        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       94.45        10.85        10.22        21.76        69.96        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
       22.52         2.40        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ 
       12.26        14.63        22.78        62.63        53.46        12.00 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
       18.12         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-2Z-A9J8 TCGA-2Z-A9JG 
        2.01        19.43        19.96        16.37        91.73        54.64 
TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       38.99        24.33        31.20        12.82        11.57       106.55 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 
       43.04        12.99        12.39        67.43        19.63         0.10 
TCGA-A4-7828 TCGA-A4-7997 TCGA-A4-8312 TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3473 
        7.82        30.48        23.28        12.46        70.19        62.66 
TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A656 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A5W8 
       67.73        41.13        20.32        29.03        20.61        17.23 
TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5882 
       14.86        12.30        19.27        63.72        22.92        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7044 
       40.83        26.04        30.28        10.82         2.76       123.62 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6135 TCGA-EV-5902 
       93.34        61.28         7.63         7.17        74.60        19.00 
TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-7773 
       10.68         0.43        90.90        25.15        20.52        12.92 
TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-7130 TCGA-HE-A5NK TCGA-IA-A40X TCGA-IA-A83S 
       27.65        16.31        58.19        73.25        19.99        85.78 
TCGA-MH-A854 TCGA-MH-A856 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5ED TCGA-P4-AAVK 
       17.62        31.13        99.78        42.94        92.58        52.27 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A7SM TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ 
       50.60        78.90        11.93        18.02        37.35        86.27 
TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8S1 
       51.35        26.01        18.64        18.64        18.05        13.28 

  AMP PEAK 8(17Q24.3) MUTATED AMP PEAK 8(17Q24.3) WILD-TYPE 
                         0.07                          0.10 
  AMP PEAK 8(17Q24.3) MUTATED AMP PEAK 8(17Q24.3) WILD-TYPE 
                       194.79                        153.73 
  AMP PEAK 8(17Q24.3) MUTATED AMP PEAK 8(17Q24.3) WILD-TYPE 
                       25.315                        40.700 
[1] "0.1 - 194.8 (25.3)" "0.1 - 153.7 (40.7)"
[1] "hr=" "1"  
D8V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 8(17Q24.3) MUTATED       145       22        41       16
  AMP PEAK 8(17Q24.3) WILD-TYPE     309       81       149       88
D8V3, multiclass
           clus
vv          AMP PEAK 8(17Q24.3) MUTATED AMP PEAK 8(17Q24.3) WILD-TYPE
  STAGE I                           145                           309
  STAGE II                           22                            81
  STAGE III                          41                           149
  STAGE IV                           16                            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 8(17Q24.3) MUTATED   156  31  51   4
  AMP PEAK 8(17Q24.3) WILD-TYPE 324  96 207  11
D8V4, multiclass
    clus
vv   AMP PEAK 8(17Q24.3) MUTATED AMP PEAK 8(17Q24.3) WILD-TYPE
  T1                         156                           324
  T2                          31                            96
  T3                          51                           207
  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(17Q24.3) MUTATED    48  16   3
  AMP PEAK 8(17Q24.3) WILD-TYPE 275  28   3
D8V5, multiclass
    clus
vv   AMP PEAK 8(17Q24.3) MUTATED AMP PEAK 8(17Q24.3) WILD-TYPE
  N0                          48                           275
  N1                          16                            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"
D8V6, binary
                               cls
clus                              0   1
  AMP PEAK 8(17Q24.3) MUTATED    93  10
  AMP PEAK 8(17Q24.3) WILD-TYPE 453  79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 8(17Q24.3) MUTATED     93   10
  AMP PEAK 8(17Q24.3) WILD-TYPE  453   79
   clus
vv  AMP PEAK 8(17Q24.3) MUTATED AMP PEAK 8(17Q24.3) WILD-TYPE
  0                          93                           453
  1                          10                            79
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK 8(17Q24.3) MUTATED    60 183
  AMP PEAK 8(17Q24.3) WILD-TYPE 232 407
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 8(17Q24.3) MUTATED     60  183
  AMP PEAK 8(17Q24.3) WILD-TYPE  232  407
        clus
vv       AMP PEAK 8(17Q24.3) MUTATED AMP PEAK 8(17Q24.3) WILD-TYPE
  FEMALE                          60                           232
  MALE                           183                           407
[1] 2 2
[1] FALSE
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK 8(17Q24.3) MUTATED   151   1
  AMP PEAK 8(17Q24.3) WILD-TYPE 257   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 8(17Q24.3) MUTATED    151    1
  AMP PEAK 8(17Q24.3) WILD-TYPE  257    2
     clus
vv    AMP PEAK 8(17Q24.3) MUTATED AMP PEAK 8(17Q24.3) WILD-TYPE
  NO                          151                           257
  YES                           1                             2
[1] 2 2
[1] FALSE
D8V9, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  AMP PEAK 8(17Q24.3) MUTATED                    1
  AMP PEAK 8(17Q24.3) WILD-TYPE                 65
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  AMP PEAK 8(17Q24.3) MUTATED                                  42
  AMP PEAK 8(17Q24.3) WILD-TYPE                               486
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK 8(17Q24.3) MUTATED                                     200
  AMP PEAK 8(17Q24.3) WILD-TYPE                                    88
D8V10, multiclass
                                       clus
vv                                      AMP PEAK 8(17Q24.3) MUTATED
  KIDNEY CHROMOPHOBE                                              1
  KIDNEY CLEAR CELL RENAL CARCINOMA                              42
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                         200
                                       clus
vv                                      AMP PEAK 8(17Q24.3) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               65
  KIDNEY CLEAR CELL RENAL CARCINOMA                               486
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
D8V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 8(17Q24.3) MUTATED                                  2     7
  AMP PEAK 8(17Q24.3) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 8(17Q24.3) MUTATED                          40   184
  AMP PEAK 8(17Q24.3) WILD-TYPE                        81   535
D8V13, multiclass
                                  clus
vv                                 AMP PEAK 8(17Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 40
  WHITE                                                    184
                                  clus
vv                                 AMP PEAK 8(17Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   81
  WHITE                                                      535
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
                               cls
clus                              0   1
  AMP PEAK 8(17Q24.3) MUTATED     8 196
  AMP PEAK 8(17Q24.3) WILD-TYPE  34 426
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 8(17Q24.3) MUTATED      8  196
  AMP PEAK 8(17Q24.3) WILD-TYPE   34  426
                        clus
vv                       AMP PEAK 8(17Q24.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         196
                        clus
vv                       AMP PEAK 8(17Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                34
  NOT HISPANIC OR LATINO                           426
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK 9(XQ11.2) MUTATION ANALYSIS
D9V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 9(XQ11.2) MUTATED   111  23
  AMP PEAK 9(XQ11.2) WILD-TYPE 537 205
  AMP PEAK 9(XQ11.2) MUTATED AMP PEAK 9(XQ11.2) WILD-TYPE 
                         134                          742 
  AMP PEAK 9(XQ11.2) MUTATED AMP PEAK 9(XQ11.2) WILD-TYPE 
                          23                          205 
$`AMP PEAK 9(XQ11.2) MUTATED`
TCGA-BP-4762 TCGA-BP-4799 TCGA-CZ-4854 TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-AL-3468 
       44.15        37.25        46.16        25.58        16.18        76.64 
TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-BQ-7046 
       21.67        21.07        10.16        21.86        11.87        96.92 
TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7841 TCGA-GL-A59T TCGA-HE-A5NF TCGA-PJ-A5Z9 
       13.61        35.93        14.63        17.95        84.89        17.75 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-KL-8346 TCGA-KN-8419 
       62.83        86.37        21.60        15.91        62.37        23.47 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       25.91         3.55        11.21       103.10        99.88       105.60 
TCGA-A3-3363 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3453 TCGA-B0-4696 TCGA-B0-5109 
       10.49       109.41       109.51        83.21        28.47        19.30 
TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4352 
        4.93       101.06        61.78         0.07        93.99        11.31 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4969 TCGA-BP-4989 TCGA-BP-5176 TCGA-CJ-4644 
       61.68        61.97        58.98         3.88        52.27        11.05 
TCGA-CJ-4885 TCGA-CJ-4899 TCGA-CW-5591 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5464 
      113.46        50.24        74.66        79.63        91.69        69.96 
TCGA-DV-A4VX TCGA-EU-5905 TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
       53.46         3.91        75.55        58.22       100.27        56.91 
TCGA-2Z-A9JR TCGA-5P-A9JY TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 
        5.29        49.58        22.26        78.64        71.80        62.93 
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-3471 TCGA-AT-A5NU TCGA-B1-A47N TCGA-B3-4103 TCGA-B9-4113 TCGA-B9-4114 
       49.32         2.20        36.49        30.58        50.50        28.18 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH 
        0.46         1.15        43.99        22.06         0.16        17.49 
TCGA-BQ-5881 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7051 
       47.80        25.35         0.95         7.92        48.26        50.40 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6133 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 
        3.81        40.77        51.19         2.40         1.18        51.78 
TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-GL-6846 TCGA-HE-7129 TCGA-HE-A5NI 
       39.25        25.25        17.98       194.79        81.93        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       56.75        25.22        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A562 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVL 
       27.78        20.25        87.09        99.12        52.27        16.01 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       44.61        28.80        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       53.10       117.40        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       51.35        31.73 

$`AMP PEAK 9(XQ11.2) WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4775 TCGA-BP-4782 
       74.17        54.77        12.33        77.62        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       20.38         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 
       62.86        49.15        27.02        31.79        44.55        31.27 
TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       63.25       105.37        26.93        27.65       108.56        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
      118.85        75.58       103.43         0.59       107.54         5.46 
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-G6-A8L7 TCGA-MM-A84U 
       66.28        56.84        23.90        81.21        70.13        23.01 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JT TCGA-5P-A9JU 
       75.42        34.85        39.88        33.07        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-A5DJ 
       67.17        61.05        21.37         0.89        12.99        49.25 
TCGA-B1-A47O TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7049 
       27.68        19.23        26.04        13.25        11.97        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7837 
       26.27        20.12        11.28        48.85       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-DZ-6134 TCGA-IA-A83W 
       24.46        13.78         3.75         3.02        61.02        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-Y8-A898 
       16.34        12.13        29.26        19.73        41.33        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-KM-8438 TCGA-KM-8440 
       73.91        71.41        28.80        54.74       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 
       49.97       123.12        51.06        31.33       129.37        87.91 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       25.48        65.19       104.52         0.99        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
       19.33         2.50        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 
      105.47        10.68       100.47       103.40        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
      104.55        96.62        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       36.82         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-A3-3326 
       37.15        49.58        48.59        36.36        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       48.82        62.01         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       18.44        88.37        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-A6NI TCGA-A3-A6NJ 
       18.87        28.31        65.52        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 
       22.65         0.10         0.10        11.18        10.62        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
      117.80       122.56        15.78        73.68       112.08        68.61 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
       94.19        46.78        48.36        78.64        40.01        94.29 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         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-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        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-B0-4819 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        10.52        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-B0-5092 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 
       58.59        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
      111.52       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 
       31.96        21.30        31.30        31.66        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67        12.00         5.75         5.10         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 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J 
       14.30        27.29        29.88        17.06         1.74        17.36 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 
       16.27        14.17        85.51        90.28        93.34        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-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
       21.21        15.62        18.48        52.24        62.86        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-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        13.51        56.91        68.38 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       60.95        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4991 
       36.07        33.34        46.45        31.30        36.95        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       74.20        30.64         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
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       116.84        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-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        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       131.08        72.00       129.40       133.71        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       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         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-6097 
       66.31        78.18         1.35       105.93        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
       25.45        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       107.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       23.74        18.44        90.54        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        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-A4VZ TCGA-EU-5904 TCGA-EU-5906 
       14.63        22.78        62.63        12.00        18.12         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        4.18         7.96        10.29        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J7 
       19.96        16.37        11.70         7.04        59.01         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       24.33        31.20        29.36         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
      106.55        90.21        15.48        43.04        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       35.18         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-AL-3467 
       25.64        23.28        19.73         8.48         8.28        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A654 
       66.71        62.66        67.73        41.13        37.51        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 
       16.77        20.32        33.83        29.03        34.49        12.46 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
       26.40        20.61        17.23        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-5889 TCGA-BQ-5890 TCGA-BQ-5894 
       40.83        26.04        30.28        10.82         7.66         2.76 
TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
      123.62        93.34        61.28        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        7.17        79.86        80.88        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 
       24.89        10.68        13.08         0.43         4.01        90.90 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC 
       11.05        71.44        25.15        20.52        25.84        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       16.90        80.65        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7130 TCGA-HE-A5NH 
       12.43        12.89        11.21        16.31        58.19        26.01 
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-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       10.09        30.38        27.65        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO 
       99.78        42.94         6.61        92.58        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SU 
       14.07        47.90        49.45        27.06        11.93        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       18.02        26.20       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       86.27        71.24        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  AMP PEAK 9(XQ11.2) MUTATED AMP PEAK 9(XQ11.2) WILD-TYPE 
                        0.07                         0.10 
  AMP PEAK 9(XQ11.2) MUTATED AMP PEAK 9(XQ11.2) WILD-TYPE 
                      194.79                       153.73 
  AMP PEAK 9(XQ11.2) MUTATED AMP PEAK 9(XQ11.2) WILD-TYPE 
                       29.84                        36.46 
[1] "0.1 - 194.8 (29.8)" "0.1 - 153.7 (36.5)"
[1] "hr=" "1.5"
D9V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 9(XQ11.2) MUTATED        79       17        16       13
  AMP PEAK 9(XQ11.2) WILD-TYPE     375       86       174       91
D9V3, multiclass
           clus
vv          AMP PEAK 9(XQ11.2) MUTATED AMP PEAK 9(XQ11.2) WILD-TYPE
  STAGE I                           79                          375
  STAGE II                          17                           86
  STAGE III                         16                          174
  STAGE IV                          13                           91
[1] 4 2
[1] 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(XQ11.2) MUTATED    86  23  25   2
  AMP PEAK 9(XQ11.2) WILD-TYPE 394 104 233  13
D9V4, multiclass
    clus
vv   AMP PEAK 9(XQ11.2) MUTATED AMP PEAK 9(XQ11.2) WILD-TYPE
  T1                         86                          394
  T2                         23                          104
  T3                         25                          233
  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 9(XQ11.2) MUTATED    36   6   0
  AMP PEAK 9(XQ11.2) WILD-TYPE 287  38   6
D9V5, multiclass
    clus
vv   AMP PEAK 9(XQ11.2) MUTATED AMP PEAK 9(XQ11.2) WILD-TYPE
  N0                         36                          287
  N1                          6                           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"
D9V6, binary
                              cls
clus                             0   1
  AMP PEAK 9(XQ11.2) MUTATED    52  10
  AMP PEAK 9(XQ11.2) WILD-TYPE 494  79
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 9(XQ11.2) MUTATED     52   10
  AMP PEAK 9(XQ11.2) WILD-TYPE  494   79
   clus
vv  AMP PEAK 9(XQ11.2) MUTATED AMP PEAK 9(XQ11.2) WILD-TYPE
  0                         52                          494
  1                         10                           79
[1] 2 2
[1] FALSE
D9V7, binary
                              cls
clus                             0   1
  AMP PEAK 9(XQ11.2) MUTATED    26 110
  AMP PEAK 9(XQ11.2) WILD-TYPE 266 480
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 9(XQ11.2) MUTATED     26  110
  AMP PEAK 9(XQ11.2) WILD-TYPE  266  480
        clus
vv       AMP PEAK 9(XQ11.2) MUTATED AMP PEAK 9(XQ11.2) WILD-TYPE
  FEMALE                         26                          266
  MALE                          110                          480
[1] 2 2
[1] FALSE
D9V8, binary
                              cls
clus                             0   1
  AMP PEAK 9(XQ11.2) MUTATED    86   0
  AMP PEAK 9(XQ11.2) WILD-TYPE 322   3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 9(XQ11.2) MUTATED     86    0
  AMP PEAK 9(XQ11.2) WILD-TYPE  322    3
     clus
vv    AMP PEAK 9(XQ11.2) MUTATED AMP PEAK 9(XQ11.2) WILD-TYPE
  NO                          86                          322
  YES                          0                            3
[1] 2 2
[1] FALSE
D9V9, continuous
                              vv
clus                           KIDNEY CHROMOPHOBE
  AMP PEAK 9(XQ11.2) MUTATED                    8
  AMP PEAK 9(XQ11.2) WILD-TYPE                 58
                              vv
clus                           KIDNEY CLEAR CELL RENAL CARCINOMA
  AMP PEAK 9(XQ11.2) MUTATED                                  29
  AMP PEAK 9(XQ11.2) WILD-TYPE                               499
                              vv
clus                           KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMP PEAK 9(XQ11.2) MUTATED                                      99
  AMP PEAK 9(XQ11.2) WILD-TYPE                                   189
D9V10, multiclass
                                       clus
vv                                      AMP PEAK 9(XQ11.2) MUTATED
  KIDNEY CHROMOPHOBE                                             8
  KIDNEY CLEAR CELL RENAL CARCINOMA                             29
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                         99
                                       clus
vv                                      AMP PEAK 9(XQ11.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                              58
  KIDNEY CLEAR CELL RENAL CARCINOMA                              499
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          189
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
D9V12, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 9(XQ11.2) MUTATED                                  1     3
  AMP PEAK 9(XQ11.2) WILD-TYPE                                1    13
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 9(XQ11.2) MUTATED                          23   103
  AMP PEAK 9(XQ11.2) WILD-TYPE                        98   616
D9V13, multiclass
                                  clus
vv                                 AMP PEAK 9(XQ11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                23
  WHITE                                                   103
                                  clus
vv                                 AMP PEAK 9(XQ11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      13
  BLACK OR AFRICAN AMERICAN                                  98
  WHITE                                                     616
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                              cls
clus                             0   1
  AMP PEAK 9(XQ11.2) MUTATED     5 104
  AMP PEAK 9(XQ11.2) WILD-TYPE  37 518
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 9(XQ11.2) MUTATED      5  104
  AMP PEAK 9(XQ11.2) WILD-TYPE   37  518
                        clus
vv                       AMP PEAK 9(XQ11.2) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                        104
                        clus
vv                       AMP PEAK 9(XQ11.2) WILD-TYPE
  HISPANIC OR LATINO                               37
  NOT HISPANIC OR LATINO                          518
[1] 2 2
[1] FALSE

Clustering(10) Variable = DEL PEAK  1(1P36.31) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.31) MUTATED   138  70
  DEL PEAK  1(1P36.31) WILD-TYPE 510 158
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           208                            668 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            70                            158 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-B8-5162 TCGA-BP-4342 
      102.81        28.11        47.24       130.13         1.18        74.17 
TCGA-BP-4353 TCGA-BP-4775 TCGA-BP-4965 TCGA-BP-4986 TCGA-BP-5201 TCGA-CJ-4894 
       12.33        60.59        61.51        25.81        31.27        27.65 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-BQ-5888 
      118.85        75.58        12.99        49.25        11.87        13.25 
TCGA-BQ-7055 TCGA-PJ-A5Z8 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       26.27        19.73         6.74        38.07       153.73        23.84 
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
      109.22       137.06        90.48       108.62        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 
       62.37       151.96        44.91        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       105.47 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 
      100.47       103.40        92.71        16.67       104.55       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3347 
       96.62        90.48        92.55        24.16        49.08        52.93 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3380 TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3436 
       53.29        43.20        18.64       117.80       112.08       109.51 
TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 
       94.19        40.01        83.21        12.13        40.70         1.41 
TCGA-B0-4691 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4718 TCGA-B0-4813 
        4.57         1.38         3.62        65.10        58.45         0.59 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4834 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4852 
       40.44        36.53        68.71        10.52        65.29        36.85 
TCGA-B0-4945 TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5098 TCGA-B0-5102 TCGA-B0-5117 
       70.52         7.30        15.09        52.08        90.87        52.87 
TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5709 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-5641 
       80.91        73.84       130.65        32.61         1.68        21.57 
TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4619 TCGA-B8-5164 
        5.10         0.53         5.46        23.31        17.19         0.85 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-BP-4176 TCGA-BP-4334 TCGA-BP-4338 
        6.38        48.53         0.53        64.27        21.21        93.99 
TCGA-BP-4340 TCGA-BP-4343 TCGA-BP-4352 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4781 
       18.48        62.86        11.31        13.15         5.33        68.38 
TCGA-BP-4968 TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5173 
       57.40        31.30         3.88        43.00        37.02         2.04 
TCGA-BP-5185 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4869 
       37.22        46.55        73.22       114.41        54.61        83.97 
TCGA-CJ-4876 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5678 
       64.27       109.84        47.67        51.29        49.28        18.87 
TCGA-CJ-5679 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 
       22.32         7.36        64.57        66.31        83.90        18.77 
TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5462 
       47.08         6.77        93.04       107.41        90.54        10.22 
TCGA-CZ-5469 TCGA-EU-5907 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-T7-A92I TCGA-2Z-A9J8 
       31.10         4.18        35.87         2.01        11.70        91.73 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9JY TCGA-5P-A9K3 TCGA-5P-A9K8 
       54.64        51.52        12.82        49.58        15.48        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-8098 TCGA-A4-A5XZ 
       19.36        67.43        18.21         0.10        29.46        15.75 
TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E 
        9.63        37.51        29.03        20.61        17.23        14.86 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5885 TCGA-BQ-5890 
       86.76         8.88        22.92        21.63        30.28         7.66 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6797 
        2.76       123.62        10.68        13.08         4.01        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-GL-8500 
       20.52        25.84        23.08        16.90         3.68        27.65 
TCGA-HE-A5NK TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EA TCGA-P4-AAVO TCGA-Q2-A5QZ 
       73.25         2.04        10.55         6.61        78.90        14.07 
TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-A9G9 
       18.02        37.35        86.27        26.01 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 
       23.28        28.80        47.21        38.47        34.29        31.07 
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       42.97        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       19.73        43.96        52.21        18.51       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 
       15.78        70.68       119.38       126.05        24.82        25.91 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 
        8.42        15.42       111.02        94.72        32.61         3.58 
TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4795 
       80.68        54.77        77.62        44.15        11.64        20.38 
TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       37.25         6.94        53.65        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 
       27.02        31.79        44.55        63.25       105.37        26.93 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      108.56        53.26       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
        0.89        76.64        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       21.86        19.23        26.04        11.97        96.92        44.84 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       29.26        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 
       15.91        15.62        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       103.10 
TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 
       99.88        12.66        11.90        36.82         0.53        39.16 
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-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 
       37.38        48.82        62.01         4.50        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3429 
        0.10        11.18        10.62        29.10       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       15.78        73.68        68.61        46.78        48.36        78.64 
TCGA-AK-3451 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 
       94.29        37.58        38.40        82.45        72.89         1.41 
TCGA-B0-4688 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4701 
        3.32         2.53         3.48        28.47        19.00         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 
        5.98         2.14        57.70         6.64         3.25        15.72 
TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
       46.59         5.52        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-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       11.24        11.90        25.32        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       21.86        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 
      111.52       129.67        85.78        86.47       126.28        71.41 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      149.16       105.37        79.89       131.15        89.49        91.46 
TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
       35.90        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 
       16.67        12.00         5.75         1.25         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5165 
       25.55        50.14        40.04        23.74        27.02        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       50.14        16.60        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
       17.06         1.74         4.93        17.36        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        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-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 
       97.45        53.42        27.78        62.07        37.25        15.62 
TCGA-BP-4337 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
        0.07        52.24        49.08        44.94        12.23        31.89 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
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-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-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 
       36.39        10.98        36.95         6.71        47.97        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
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         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 
       47.11        14.93        36.07        33.34        46.45        36.95 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5007 
       46.45        16.47        30.64        18.51        38.70        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
       35.21        28.87         6.35        79.30        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4638 
       33.47        19.82        34.95         0.95       115.00        14.17 
TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 
      106.16        58.95        11.05        21.24        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       116.84        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       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 
       63.98       115.69        50.01        24.66        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       56.35        49.97        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       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
      129.40       133.71        25.71        25.25        18.15       122.83 
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       119.64 
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-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 
       74.66         1.35       105.93        25.45        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       14.66        63.39        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       18.44        79.63        91.69        55.33        94.45        10.85 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        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-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       22.78        62.63        53.46        12.00        18.12         3.91 
TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC 
        6.77         7.96        10.29        19.43        19.96        16.37 
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-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
        4.57        56.81        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ 
       29.36         5.29         0.13        11.57       106.55        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9KA TCGA-5P-A9KC 
       22.26        78.64        71.80        62.93        12.99        12.39 
TCGA-5P-A9KE TCGA-A4-7287 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       27.09        19.63        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       16.64        30.48        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 
        8.48        16.31         8.28        12.46        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N 
       66.71        62.66        67.73         2.20        41.13        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       20.25        16.77        20.32        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
       12.46        50.50        28.18        26.40         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 
       43.99        22.06         0.16        17.49        12.30        19.27 
TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5887 
       63.72        43.20        47.80        40.83        26.04        25.35 
TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
       10.82         0.95         7.92        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        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-A4TM TCGA-G7-A8LB 
       90.90        11.05        39.25        71.44        25.25        17.98 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       80.65       194.79        12.92         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       56.75        25.22        16.80        19.99        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 
       96.69        22.26        21.34        12.36        12.76        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       87.09        42.94        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       50.60        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PP 
       43.76        26.20       117.40       103.63       125.29        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       31.73        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        153.73                         194.79 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        40.225                         34.290 
[1] "0.1 - 153.7 (40.2)" "0.1 - 194.8 (34.3)"
[1] "hr=" "1.3"
D10V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  1(1P36.31) MUTATED        73       38        59       31
  DEL PEAK  1(1P36.31) WILD-TYPE     381       65       131       73
D10V3, multiclass
           clus
vv          DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  STAGE I                             73                            381
  STAGE II                            38                             65
  STAGE III                           59                            131
  STAGE IV                            31                             73
[1] 4 2
[1] 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    80  47  76   6
  DEL PEAK  1(1P36.31) WILD-TYPE 400  80 182   9
D10V4, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T1                           80                            400
  T2                           47                             80
  T3                           76                            182
  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  20   4
  DEL PEAK  1(1P36.31) WILD-TYPE 231  24   2
D10V5, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  N0                           92                            231
  N1                           20                             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"
D10V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED   126  24
  DEL PEAK  1(1P36.31) WILD-TYPE 420  65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED    126   24
  DEL PEAK  1(1P36.31) WILD-TYPE  420   65
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                          126                            420
  1                           24                             65
[1] 2 2
[1] FALSE
D10V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    75 134
  DEL PEAK  1(1P36.31) WILD-TYPE 217 456
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     75  134
  DEL PEAK  1(1P36.31) WILD-TYPE  217  456
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                           75                            217
  MALE                            134                            456
[1] 2 2
[1] FALSE
D10V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED   113   0
  DEL PEAK  1(1P36.31) WILD-TYPE 295   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED    113    0
  DEL PEAK  1(1P36.31) WILD-TYPE  295    3
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  NO                           113                            295
  YES                            0                              3
[1] 2 2
[1] FALSE
D10V9, 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                                 102
  DEL PEAK  1(1P36.31) WILD-TYPE                               426
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  1(1P36.31) MUTATED                                      54
  DEL PEAK  1(1P36.31) WILD-TYPE                                   234
D10V10, multiclass
                                       clus
vv                                      DEL PEAK  1(1P36.31) MUTATED
  KIDNEY CHROMOPHOBE                                              53
  KIDNEY CLEAR CELL RENAL CARCINOMA                              102
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           54
                                       clus
vv                                      DEL PEAK  1(1P36.31) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                13
  KIDNEY CLEAR CELL RENAL CARCINOMA                                426
  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"
D10V11, continuous
D10V12, 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    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.31) MUTATED                          25   173
  DEL PEAK  1(1P36.31) WILD-TYPE                        96   546
D10V13, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     173
                                  clus
vv                                 DEL PEAK  1(1P36.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    96
  WHITE                                                       546
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    12 135
  DEL PEAK  1(1P36.31) WILD-TYPE  30 487
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     12  135
  DEL PEAK  1(1P36.31) WILD-TYPE   30  487
                        clus
vv                       DEL PEAK  1(1P36.31) MUTATED
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          135
                        clus
vv                       DEL PEAK  1(1P36.31) WILD-TYPE
  HISPANIC OR LATINO                                 30
  NOT HISPANIC OR LATINO                            487
[1] 2 2
[1] FALSE

Clustering(11) Variable = DEL PEAK  2(1P31.1) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P31.1) MUTATED   119  46
  DEL PEAK  2(1P31.1) WILD-TYPE 529 182
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                          165                           711 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                           46                           182 
$`DEL PEAK  2(1P31.1) MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-B0-4712 TCGA-BP-4342 
      102.81        28.11        47.24       130.13        43.96        74.17 
TCGA-BP-4353 TCGA-BP-4775 TCGA-BP-4986 TCGA-BP-5201 TCGA-CJ-4894 TCGA-A4-A5Y1 
       12.33        60.59        25.81        31.27        27.65        12.99 
TCGA-BQ-7055 TCGA-PJ-A5Z8 TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 
       26.27        19.73        38.07       153.73        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        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-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 
      151.96        44.91        49.97       123.12       129.37        87.91 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 
       25.48        65.19       104.52         0.99        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 
        2.50        59.08       115.00        42.35       105.47       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 
      103.40        92.71        16.67       104.55       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3373 
       90.48        92.55        24.16        49.08        37.15        53.29 
TCGA-A3-3374 TCGA-A3-3380 TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 
       43.20        18.64       117.80       112.08       109.51        94.19 
TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4718 
       40.01        12.13        40.70         1.38         3.62        58.45 
TCGA-B0-4814 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4834 TCGA-B0-4845 TCGA-B0-4852 
        5.52        40.44        36.53        68.71        65.29        36.85 
TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5098 TCGA-B0-5102 TCGA-B0-5109 
        7.30        15.09        10.95        52.08        90.87        19.30 
TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5703 TCGA-B2-3923 TCGA-B2-4098 TCGA-B4-5832 
       52.87        42.41        73.84        32.61         1.68         5.10 
TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4619 TCGA-B8-5549 TCGA-BP-4176 TCGA-BP-4334 
        0.53         5.46        17.19         6.38        64.27        21.21 
TCGA-BP-4340 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4968 TCGA-BP-4983 TCGA-BP-4985 
       18.48        13.15        68.38        57.40        46.45        31.30 
TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5173 TCGA-BP-5175 TCGA-CJ-4635 TCGA-CJ-4640 
       43.00        37.02         2.04        30.64        46.55       114.41 
TCGA-CJ-4869 TCGA-CJ-4876 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-5678 
       83.97        64.27       109.84        47.67        49.28        18.87 
TCGA-CJ-5679 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6090 TCGA-CZ-4860 TCGA-CZ-4866 
       22.32        66.31        74.66        83.90         6.77       107.41 
TCGA-CZ-5457 TCGA-CZ-5462 TCGA-CZ-5469 TCGA-EU-5907 TCGA-G6-A8L8 TCGA-T7-A92I 
       90.54        10.22        31.10         4.18        35.87        11.70 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9JY TCGA-5P-A9K3 TCGA-5P-A9K8 
       54.64        51.52        12.82        49.58        15.48        43.04 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-8098 TCGA-B1-7332 TCGA-B3-3926 
       67.43        18.21         0.10        29.46        37.51        29.03 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5894 
       17.23        14.86        86.76         8.88        21.63         2.76 
TCGA-BQ-7044 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6797 TCGA-G7-7502 
      123.62        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 
       23.08         3.68        27.65        73.25         2.04         6.61 
TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       14.07        18.02        86.27 

$`DEL PEAK  2(1P31.1) WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 
       23.28        28.80        47.21        38.47        34.29        31.07 
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       42.97        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-4707 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       19.73        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 
        8.42        15.42       111.02        94.72        32.61         3.58 
TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4795 
       80.68        54.77        77.62        44.15        11.64        20.38 
TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4993 
       37.25         6.94        61.51        53.65        27.22         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 
       45.07        41.62        27.62        35.90        48.10        62.86 
TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4642 
       49.15        27.02        31.79        44.55        63.25       105.37 
TCGA-CJ-4891 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 
       26.93       108.56        53.26       118.85        75.58       103.43 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 
       46.16         0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD 
       23.90        81.21        70.13        23.01        75.42        34.85 
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU 
       39.88        33.07        25.58        16.18        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ 
       67.17        61.05        21.37         0.89        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       29.26        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 
       15.91        15.62         6.74        51.06        31.33        23.47 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 
       25.91         3.55        52.27        11.21       100.87        10.68 
TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 
      103.10        99.88        12.66        11.90        36.82         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-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       37.38        48.82        62.01         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       29.92        18.44        88.37        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 
       74.63        74.76        24.16        55.76        20.71        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 
        0.10         0.10        11.18        10.62        29.10       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 
      109.41        15.78        73.68        68.61        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
        3.48        28.47        19.00        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 
        2.14        57.70         6.64         3.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 
        0.59        45.07        33.50        16.77         6.02        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-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
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-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5095 TCGA-B0-5096 
       43.30        11.24        11.90        25.32         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       21.86        15.95        62.89        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       58.59        66.05        38.63        52.73        41.88        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5692 
       38.43        48.82        46.39        56.98       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 
       85.78        86.47       126.28        80.91        71.41       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
       35.90        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 
       21.57        16.67        12.00         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        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       25.05        45.37        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 
       27.02         0.85        24.23        50.14        16.60        48.53 
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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
        1.74         4.93        17.36        16.27        14.17        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
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-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 
       53.42        27.78        62.07        37.25        15.62         0.07 
TCGA-BP-4338 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       93.99        52.24        62.86        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
       77.98         5.98        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-4784 
       10.82         5.33        61.97        13.51        56.91        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 
       33.34        36.95         3.88        46.45        16.47        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       18.51        38.70        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       79.30        74.20        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4641 
        0.95       115.00        73.22        14.17       106.16        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       58.95        11.05        21.24        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       74.27        75.06       116.84        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       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
      115.69        50.01        24.66        39.45        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       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
      129.40       133.71        25.71        25.25        18.15       122.83 
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       119.64 
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-6087 TCGA-CW-6088 TCGA-CW-6097 TCGA-CZ-4853 
       73.18        78.18         1.35       105.93        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       47.08        69.21        58.75        14.66        63.39        93.04 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
       91.69        55.33        94.45        10.85        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
       84.30        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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC 
       53.46        12.00        18.12         3.91         6.77         7.96 
TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-2K-A9WE 
       10.29         2.01        19.43        19.96        16.37         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-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       91.73        56.81        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ 
       29.36         5.29         0.13        11.57       106.55        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KA 
       22.26        78.64        71.80        62.93        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7287 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       12.39        27.09        19.63        35.18        19.13         7.82 
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-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-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
        2.20        41.13        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       33.83        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 
        0.16        17.49        12.30        19.27        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        47.80        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7048 
       10.82         7.66         0.95         7.92        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
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-G7-7501 
       51.78        90.90        11.05        39.25        71.44        20.52 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
       58.19        26.01        11.84        56.75        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         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 
                       153.73                        194.79 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                        43.00                         33.83 
[1] "0.1 - 153.7 (43.0)" "0.1 - 194.8 (33.8)"
[1] "hr=" "1.1"
D11V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  2(1P31.1) MUTATED        60       34        42       24
  DEL PEAK  2(1P31.1) WILD-TYPE     394       69       148       80
D11V3, multiclass
           clus
vv          DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  STAGE I                            60                           394
  STAGE II                           34                            69
  STAGE III                          42                           148
  STAGE IV                           24                            80
[1] 4 2
[1] 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    66  40  54   6
  DEL PEAK  2(1P31.1) WILD-TYPE 414  87 204   9
D11V4, multiclass
    clus
vv   DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  T1                          66                           414
  T2                          40                            87
  T3                          54                           204
  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  15   3
  DEL PEAK  2(1P31.1) WILD-TYPE 251  29   3
D11V5, multiclass
    clus
vv   DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  N0                          72                           251
  N1                          15                            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"
D11V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P31.1) MUTATED   104  16
  DEL PEAK  2(1P31.1) WILD-TYPE 442  73
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED    104   16
  DEL PEAK  2(1P31.1) WILD-TYPE  442   73
   clus
vv  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  0                         104                           442
  1                          16                            73
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P31.1) MUTATED    56 110
  DEL PEAK  2(1P31.1) WILD-TYPE 236 480
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED     56  110
  DEL PEAK  2(1P31.1) WILD-TYPE  236  480
        clus
vv       DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  FEMALE                          56                           236
  MALE                           110                           480
[1] 2 2
[1] FALSE
D11V8, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P31.1) MUTATED    95   0
  DEL PEAK  2(1P31.1) WILD-TYPE 313   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED     95    0
  DEL PEAK  2(1P31.1) WILD-TYPE  313    3
     clus
vv    DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  NO                           95                           313
  YES                           0                             3
[1] 2 2
[1] FALSE
D11V9, 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                                  77
  DEL PEAK  2(1P31.1) WILD-TYPE                               451
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  2(1P31.1) MUTATED                                      36
  DEL PEAK  2(1P31.1) WILD-TYPE                                   252
D11V10, multiclass
                                       clus
vv                                      DEL PEAK  2(1P31.1) MUTATED
  KIDNEY CHROMOPHOBE                                             53
  KIDNEY CLEAR CELL RENAL CARCINOMA                              77
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          36
                                       clus
vv                                      DEL PEAK  2(1P31.1) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               13
  KIDNEY CLEAR CELL RENAL CARCINOMA                               451
  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"
D11V11, continuous
D11V12, 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    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P31.1) MUTATED                          20   135
  DEL PEAK  2(1P31.1) WILD-TYPE                       101   584
D11V13, multiclass
                                  clus
vv                                 DEL PEAK  2(1P31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 20
  WHITE                                                    135
                                  clus
vv                                 DEL PEAK  2(1P31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                  101
  WHITE                                                      584
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V14, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P31.1) MUTATED    11  99
  DEL PEAK  2(1P31.1) WILD-TYPE  31 523
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED     11   99
  DEL PEAK  2(1P31.1) WILD-TYPE   31  523
                        clus
vv                       DEL PEAK  2(1P31.1) MUTATED
  HISPANIC OR LATINO                              11
  NOT HISPANIC OR LATINO                          99
                        clus
vv                       DEL PEAK  2(1P31.1) WILD-TYPE
  HISPANIC OR LATINO                                31
  NOT HISPANIC OR LATINO                           523
[1] 2 2
[1] FALSE

Clustering(12) Variable = DEL PEAK  3(1Q44) MUTATION ANALYSIS
D12V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  3(1Q44) MUTATED    86  29
  DEL PEAK  3(1Q44) WILD-TYPE 562 199
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                        115                         761 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         29                         199 
$`DEL PEAK  3(1Q44) MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-BP-4353 TCGA-BP-4775 
      102.81        28.11        47.24       130.13        12.33        60.59 
TCGA-PJ-A5Z8 TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8329 
       19.73        38.07       153.73        23.84       137.06        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-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       71.41        28.80        54.74       151.96        44.91        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-8431 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       52.27        87.12        19.33        59.08       115.00        42.35 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      105.47        10.68       100.47       103.40        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3370 
      104.55       105.60        96.62        90.48        92.55        74.76 
TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-A8OV TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 
       43.20        18.64        11.18       117.80       112.08        94.19 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4821 
       12.13        40.70        28.47         1.38         3.62        40.44 
TCGA-B0-4834 TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5102 TCGA-B0-5117 
       68.71        65.29        36.85        70.52        90.87        52.87 
TCGA-B0-5703 TCGA-B2-3923 TCGA-B4-5838 TCGA-B8-4619 TCGA-B8-5549 TCGA-BP-4329 
       73.84        32.61         5.46        17.19         6.38        27.78 
TCGA-BP-4334 TCGA-BP-4352 TCGA-BP-4768 TCGA-BP-4968 TCGA-BP-4994 TCGA-CJ-4878 
       21.21        11.31        13.15        57.40        43.00        71.87 
TCGA-CJ-4888 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CW-5585 TCGA-CW-5588 
       51.52       109.84        47.67        49.28        85.78        66.31 
TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5469 TCGA-G6-A8L8 TCGA-2Z-A9JG 
        6.77       107.41        90.54        31.10        35.87        54.64 
TCGA-4A-A93X TCGA-5P-A9JY TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-B1-7332 
       12.82        49.58        67.43        18.21         0.10        37.51 
TCGA-B1-A655 TCGA-B3-3926 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5894 TCGA-F9-A7Q0 
       16.77        29.03        17.23         0.16         2.76        13.08 
TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-8500 TCGA-HE-A5NK TCGA-P4-A5EA TCGA-P4-AAVL 
       25.84        23.08        27.65        73.25         6.61        16.01 
TCGA-UN-AAZ9 
       18.02 

$`DEL PEAK  3(1Q44) WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 
       23.28        28.80        47.21        38.47        34.29        31.07 
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       42.97        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       19.73        43.96        52.21        18.51       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 
       15.78        70.68       119.38       126.05        24.82        25.91 
TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 
        1.18         8.42        15.42       111.02        94.72        32.61 
TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 
        3.58        80.68        74.17        54.77        77.62        44.15 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       35.90        48.10        62.86        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       44.55        31.27        63.25       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
      108.56        53.26       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        0.59       107.54         5.46        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       81.21        70.13        23.01        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       12.13        29.26        17.75        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8326 TCGA-KL-8346 
       21.60        15.91        15.62         6.74       109.22        62.37 
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-8432 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z 
        2.50        11.21       100.87       103.10        99.88        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       11.90        36.82         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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       37.38        48.82        62.01         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       29.92        18.44        88.37        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 
       74.63        24.16        53.29        55.76        20.71        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3429 
        0.10         0.10        10.62        29.10       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
       15.78        73.68        68.61       109.51        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       78.64        40.01        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
        2.53         3.48        19.00        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        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-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       56.68        10.52        10.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
        2.27        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
      111.52       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       71.41       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       89.49        91.46        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
        5.75         5.10         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        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       45.37        25.55        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 
        0.85        24.23        50.14        16.60        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        4.93        17.36        16.27        14.17        85.51        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-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       53.42        62.07        37.25        15.62         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        62.86        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-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
        5.98        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       16.47        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        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       116.84        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       113.46        64.18        30.64 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 
       63.98       115.69        50.01        24.66        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       56.35        49.97        51.29        49.18        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       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        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       122.83        62.10        73.35        67.00 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83         5.39        73.18        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
      105.93        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39        93.04        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        79.63        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       94.45        10.85        10.22        21.76        69.96        84.30 
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-A4VX 
       65.65        12.26        14.63        22.78        62.63        53.46 
TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       12.00        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       10.29         2.01        19.43        19.96        16.37        11.70 
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-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
        4.57        91.73        56.81        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y 
       24.33        31.20        29.36         5.29         0.13        11.57 
TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
      106.55        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       62.93        43.04        19.36        12.99        12.39        27.09 
TCGA-A4-7287 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
       19.63        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
       41.13        36.49        20.25        20.32        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-B9-5156 TCGA-B9-7268 TCGA-B9-A69E TCGA-B9-A8YH 
        0.46         1.15        43.99        22.06        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-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 
       25.35        10.82         7.66         0.95         7.92       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
       11.05        39.25        71.44        25.15        20.52        25.25 
TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.98        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
       58.19        26.01        11.84        56.75        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO 
       42.94        99.12        92.58        52.27        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       43.76        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                       0.10                        0.07 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                     153.73                      194.79 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                      49.97                       33.47 
[1] "0.1 - 153.7 (50.0)" "0.1 - 194.8 (33.5)"
[1] "hr=" "1.4"
D12V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  3(1Q44) MUTATED        47       28        23       14
  DEL PEAK  3(1Q44) WILD-TYPE     407       75       167       90
D12V3, multiclass
           clus
vv          DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  STAGE I                          47                         407
  STAGE II                         28                          75
  STAGE III                        23                         167
  STAGE IV                         14                          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  3(1Q44) MUTATED    49  29  34   4
  DEL PEAK  3(1Q44) WILD-TYPE 431  98 224  11
D12V4, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  T1                        49                         431
  T2                        29                          98
  T3                        34                         224
  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(1Q44) MUTATED    60   6   2
  DEL PEAK  3(1Q44) WILD-TYPE 263  38   4
D12V5, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  N0                        60                         263
  N1                         6                          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"
D12V6, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    73   8
  DEL PEAK  3(1Q44) WILD-TYPE 473  81
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     73    8
  DEL PEAK  3(1Q44) WILD-TYPE  473   81
   clus
vv  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  0                        73                         473
  1                         8                          81
[1] 2 2
[1] FALSE
D12V7, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    45  71
  DEL PEAK  3(1Q44) WILD-TYPE 247 519
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     45   71
  DEL PEAK  3(1Q44) WILD-TYPE  247  519
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                        45                         247
  MALE                          71                         519
[1] 2 2
[1] FALSE
D12V8, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    82   0
  DEL PEAK  3(1Q44) WILD-TYPE 326   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     82    0
  DEL PEAK  3(1Q44) WILD-TYPE  326    3
     clus
vv    DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  NO                         82                         326
  YES                         0                           3
[1] 2 2
[1] FALSE
D12V9, continuous
                             vv
clus                          KIDNEY CHROMOPHOBE
  DEL PEAK  3(1Q44) MUTATED                   51
  DEL PEAK  3(1Q44) WILD-TYPE                 15
                             vv
clus                          KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK  3(1Q44) MUTATED                                  44
  DEL PEAK  3(1Q44) WILD-TYPE                               484
                             vv
clus                          KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  3(1Q44) MUTATED                                      21
  DEL PEAK  3(1Q44) WILD-TYPE                                   267
D12V10, multiclass
                                       clus
vv                                      DEL PEAK  3(1Q44) MUTATED
  KIDNEY CHROMOPHOBE                                           51
  KIDNEY CLEAR CELL RENAL CARCINOMA                            44
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                        21
                                       clus
vv                                      DEL PEAK  3(1Q44) WILD-TYPE
  KIDNEY CHROMOPHOBE                                             15
  KIDNEY CLEAR CELL RENAL CARCINOMA                             484
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                         267
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
D12V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(1Q44) MUTATED                                  0     4
  DEL PEAK  3(1Q44) WILD-TYPE                                2    12
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q44) MUTATED                          11    96
  DEL PEAK  3(1Q44) WILD-TYPE                       110   623
D12V13, multiclass
                                  clus
vv                                 DEL PEAK  3(1Q44) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               11
  WHITE                                                   96
                                  clus
vv                                 DEL PEAK  3(1Q44) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                     12
  BLACK OR AFRICAN AMERICAN                                110
  WHITE                                                    623
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED     8  74
  DEL PEAK  3(1Q44) WILD-TYPE  34 548
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      8   74
  DEL PEAK  3(1Q44) WILD-TYPE   34  548
                        clus
vv                       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             8                          34
  NOT HISPANIC OR LATINO                        74                         548
[1] 2 2
[1] FALSE

Clustering(13) Variable = DEL PEAK  4(2Q22.1) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q22.1) MUTATED    57  17
  DEL PEAK  4(2Q22.1) WILD-TYPE 591 211
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           74                           802 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           17                           211 
$`DEL PEAK  4(2Q22.1) MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-BP-5199 TCGA-A4-A5Y1 
      102.81        28.11        47.24       130.13        44.55        12.99 
TCGA-BQ-5888 TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8329 
       13.25        38.07       153.73        23.84       137.06        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-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 
       44.84        86.56        66.54        24.79        73.91        54.74 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8424 
      151.96        44.91        49.97       123.12       129.37        65.19 
TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
      104.52        52.27        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      115.00        42.35       105.47       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       16.67       104.55       105.60        96.62        90.48        92.55 
TCGA-A3-3374 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 
       43.20       112.08        94.19        40.01        12.13        40.70 
TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-5094 TCGA-B0-5098 TCGA-B0-5117 TCGA-B2-3923 
       28.47         3.62        10.95        52.08        52.87        32.61 
TCGA-BP-4334 TCGA-BP-4352 TCGA-BP-4770 TCGA-BP-4994 TCGA-BP-5175 TCGA-CZ-4861 
       21.21        11.31        10.82        43.00        30.64        14.66 
TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9KH TCGA-AL-3466 TCGA-B9-A69E TCGA-BQ-5878 
       51.52        12.82        67.43         9.63        14.86        63.72 
TCGA-HE-7130 TCGA-Q2-A5QZ 
       58.19        14.07 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 
       23.28        28.80        47.21        38.47        34.29        31.07 
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       42.97        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       19.73        43.96        52.21        18.51       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 
       15.78        70.68       119.38       126.05        24.82        25.91 
TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 
        1.18         8.42        15.42       111.02        94.72        32.61 
TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 
        3.58        80.68        74.17        54.77        12.33        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 
       27.02        31.79        31.27        63.25       105.37        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 
       27.65       108.56        53.26       118.85        75.58       103.43 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 
       46.16         0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD 
       23.90        81.21        70.13        23.01        75.42        34.85 
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU 
       39.88        33.07        25.58        16.18        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ 
       67.17        61.05        21.37         0.89        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       19.23        26.04        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       29.26        19.73        17.75        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8326 TCGA-KL-8333 
       21.60        15.91        15.62         6.74       109.22        98.33 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 
       71.41        28.80        62.37        51.06        31.33        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8433 
       87.91        25.48        25.91         3.55         0.99        11.21 
TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E 
      100.87        10.68       103.10        99.88        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       36.82         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-A3-3326 
       37.15        49.58        48.59        36.36        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       48.82        62.01         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.87        28.31        65.52        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 
       22.65         0.10         0.10        11.18        10.62        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80       122.56       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
      109.51        46.78        48.36        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 
       37.58        38.40        82.45        72.89         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-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       65.10         7.82         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
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-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        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-B0-5092 TCGA-B0-5095 TCGA-B0-5096 
       11.90         7.30        25.32        15.09         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       21.86        15.95        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        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       41.88        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4098 
       79.89       131.15        89.49        91.46        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 
       31.96        21.30        31.30        31.66        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67        12.00         5.75         5.10         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 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       14.30        27.29        29.88        17.06         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
       17.36        16.27        14.17        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       27.78        62.07        37.25        15.62         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        62.86        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-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
        5.98        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         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-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       46.45        16.47        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       74.20        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        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       116.84        64.27 
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       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        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       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        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-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 
        1.35       105.93        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
       69.21        58.75         6.77        63.39        93.04       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       14.63        22.78        62.63        53.46        12.00        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
        3.91         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
        2.01        19.43        19.96        16.37        11.70         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-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       91.73        56.81        54.64        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW 
       31.20        29.36         5.29         0.13        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
       49.58        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       62.93        43.04        19.36        12.99        12.39        27.09 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI 
       43.99        22.06        17.23         0.16        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76        19.27         8.88        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
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        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21        16.31        81.93        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
       92.58        52.27        16.01        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                         2.50                          0.07 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       153.73                        194.79 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       52.570                        33.485 
[1] "2.5 - 153.7 (52.6)" "0.1 - 194.8 (33.5)"
[1] "hr=" "1.6"
D13V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  4(2Q22.1) MUTATED        21       26        18        9
  DEL PEAK  4(2Q22.1) WILD-TYPE     433       77       172       95
D13V3, multiclass
           clus
vv          DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  STAGE I                            21                           433
  STAGE II                           26                            77
  STAGE III                          18                           172
  STAGE IV                            9                            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  4(2Q22.1) MUTATED    23  26  24   2
  DEL PEAK  4(2Q22.1) WILD-TYPE 457 101 234  13
D13V4, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  T1                          23                           457
  T2                          26                           101
  T3                          24                           234
  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
  DEL PEAK  4(2Q22.1) MUTATED    39   6   2
  DEL PEAK  4(2Q22.1) WILD-TYPE 284  38   4
D13V5, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  N0                          39                           284
  N1                           6                            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"
D13V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED    46   5
  DEL PEAK  4(2Q22.1) WILD-TYPE 500  84
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED     46    5
  DEL PEAK  4(2Q22.1) WILD-TYPE  500   84
   clus
vv  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  0                          46                           500
  1                           5                            84
[1] 2 2
[1] FALSE
D13V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED    31  44
  DEL PEAK  4(2Q22.1) WILD-TYPE 261 546
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED     31   44
  DEL PEAK  4(2Q22.1) WILD-TYPE  261  546
        clus
vv       DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  FEMALE                          31                           261
  MALE                            44                           546
[1] 2 2
[1] FALSE
D13V8, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED    57   0
  DEL PEAK  4(2Q22.1) WILD-TYPE 351   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED     57    0
  DEL PEAK  4(2Q22.1) WILD-TYPE  351    3
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  NO                           57                           351
  YES                           0                             3
[1] 2 2
[1] FALSE
D13V9, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK  4(2Q22.1) MUTATED                   46
  DEL PEAK  4(2Q22.1) WILD-TYPE                 20
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK  4(2Q22.1) MUTATED                                  19
  DEL PEAK  4(2Q22.1) WILD-TYPE                               509
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  4(2Q22.1) MUTATED                                      10
  DEL PEAK  4(2Q22.1) WILD-TYPE                                   278
D13V10, multiclass
                                       clus
vv                                      DEL PEAK  4(2Q22.1) MUTATED
  KIDNEY CHROMOPHOBE                                             46
  KIDNEY CLEAR CELL RENAL CARCINOMA                              19
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          10
                                       clus
vv                                      DEL PEAK  4(2Q22.1) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               20
  KIDNEY CLEAR CELL RENAL CARCINOMA                               509
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous
D13V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2Q22.1) MUTATED                                  0     2
  DEL PEAK  4(2Q22.1) WILD-TYPE                                2    14
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q22.1) MUTATED                           7    63
  DEL PEAK  4(2Q22.1) WILD-TYPE                       114   656
D13V13, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     63
                                  clus
vv                                 DEL PEAK  4(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       14
  BLACK OR AFRICAN AMERICAN                                  114
  WHITE                                                      656
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V14, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     3  41
  DEL PEAK  4(2Q22.1) WILD-TYPE  39 581
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      3   41
  DEL PEAK  4(2Q22.1) WILD-TYPE   39  581
                        clus
vv                       DEL PEAK  4(2Q22.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          41
                        clus
vv                       DEL PEAK  4(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                39
  NOT HISPANIC OR LATINO                           581
[1] 2 2
[1] FALSE

Clustering(14) Variable = DEL PEAK  5(2Q37.3) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q37.3) MUTATED    87  23
  DEL PEAK  5(2Q37.3) WILD-TYPE 561 205
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                          110                           766 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           23                           205 
$`DEL PEAK  5(2Q37.3) MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3336 TCGA-AK-3425 
      102.81        28.11        47.24       130.13        34.29       109.91 
TCGA-BP-4782 TCGA-BP-5199 TCGA-CJ-6027 TCGA-CZ-4854 TCGA-MH-A855 TCGA-Y8-A8RZ 
       11.64        44.55       118.85        46.16        12.13         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
       38.07       153.73        23.84       137.06        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-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 
       44.84        86.56        66.54        24.79        73.91        54.74 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8424 
      151.96        44.91        49.97       123.12       129.37        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-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
       59.08       115.00        42.35       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 
      103.40        92.71        16.67       104.55       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3323 TCGA-A3-3374 TCGA-AK-3433 
       90.48        92.55        39.16        36.36        43.20       112.08 
TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4696 TCGA-B0-4699 
       94.19        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        41.88 
TCGA-B0-5117 TCGA-B0-5120 TCGA-B2-3923 TCGA-B2-5641 TCGA-B8-4620 TCGA-B8-5549 
       52.87        38.43        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-4991 TCGA-BP-4994 TCGA-BP-5008 TCGA-BP-5175 TCGA-BP-5177 TCGA-CJ-4643 
       46.45        43.00        35.21        30.64         9.63        58.95 
TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4881 TCGA-CJ-4902 TCGA-CW-6090 TCGA-CZ-5453 
       21.24        49.25        66.21        49.97        83.90        79.53 
TCGA-CZ-5468 TCGA-CZ-5985 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-4A-A93X TCGA-5P-A9KH 
        1.94        65.65        22.78        62.63        12.82        67.43 
TCGA-A4-7585 TCGA-A4-A5Y0 TCGA-B3-4104 TCGA-B9-4117 TCGA-B9-A69E TCGA-BQ-5878 
       35.18         8.28        34.49         0.46        14.86        63.72 
TCGA-HE-7130 TCGA-Q2-A5QZ 
       58.19        14.07 

$`DEL PEAK  5(2Q37.3) WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3343 TCGA-A3-3358 
       23.28        28.80        47.21        38.47        31.07        42.97 
TCGA-A3-3359 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
       82.32        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5201 
       48.10        62.86        49.15        27.02        31.79        31.27 
TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       63.25       105.37        26.93        27.65       108.56        53.26 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 
       75.58       103.43         0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 
       56.84        23.90        81.21        70.13        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       67.17        16.34        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-KL-8326 
       62.83        86.37        21.60        15.91        15.62       109.22 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 
       71.41        28.80        62.37        51.06        31.33        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 TCGA-KN-8437 
       87.91        25.48        25.91         3.55        11.21       100.87 
TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 
      103.10        99.88        12.66        11.90        36.82         0.53 
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-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
       28.70        74.63        74.76        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        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       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       73.68        68.61       109.51        46.78        48.36        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
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        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        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-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4842 TCGA-B0-4843 
       40.70        45.30        27.42        53.88        56.68        10.52 
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-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 
        7.30        25.32        15.09        10.95         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       52.08        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-B0-5119 
       58.59        19.30        66.05        38.63        52.73        51.02 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       91.46        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       31.66        32.98        16.67        12.00         5.75         5.10 
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        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       17.19        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       24.23        50.14        16.60        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
       14.30        27.29        29.88         4.93        17.36        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.17        85.51        90.28       101.06        93.34        99.85 
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-4329 TCGA-BP-4330 TCGA-BP-4335 
       54.90        97.45        53.42        27.78        62.07        15.62 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
        0.07        93.99        18.48        52.24        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       12.30        72.59        77.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       13.15        61.68        10.82         5.33        61.97        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-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 
       36.39        10.98        36.95         6.71        47.97        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         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-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 
       31.30        36.95         3.88        16.47        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       38.70        37.02        37.48        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
        2.04        74.20        52.27        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       54.61        11.05        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       116.84        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 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       47.67        51.29        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       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        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       122.83        62.10        73.35        67.00 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35       105.93        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75         6.77        14.66        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
      107.41        63.42        58.82        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 
       21.76        69.96        84.30        22.52         2.40        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-DV-A4VX 
       12.69        80.19        67.96        12.26        14.63        53.46 
TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       12.00        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC 
       10.29        35.87         2.01        19.43        19.96        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
        0.13        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.99        12.39        27.09        18.21        19.63         0.10 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 
       15.75        12.46         9.63        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
       12.46        50.50        28.18        26.40        20.61         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI 
       43.99        22.06        17.23         0.16        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76        19.27         8.88        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
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        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21        16.31        81.93        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
       92.58        52.27        16.01        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                         0.43                          0.07 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                       153.73                        194.79 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                       44.695                        33.290 
[1] "0.4 - 153.7 (44.7)" "0.1 - 194.8 (33.3)"
[1] "hr=" "1.6"
D14V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  5(2Q37.3) MUTATED        38       32        28       11
  DEL PEAK  5(2Q37.3) WILD-TYPE     416       71       162       93
D14V3, multiclass
           clus
vv          DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  STAGE I                            38                           416
  STAGE II                           32                            71
  STAGE III                          28                           162
  STAGE IV                           11                            93
[1] 4 2
[1] 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(2Q37.3) MUTATED    39  34  35   3
  DEL PEAK  5(2Q37.3) WILD-TYPE 441  93 223  12
D14V4, multiclass
    clus
vv   DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  T1                          39                           441
  T2                          34                            93
  T3                          35                           223
  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  5(2Q37.3) MUTATED    55   6   2
  DEL PEAK  5(2Q37.3) WILD-TYPE 268  38   4
D14V5, multiclass
    clus
vv   DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  N0                          55                           268
  N1                           6                            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"
D14V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED    75   6
  DEL PEAK  5(2Q37.3) WILD-TYPE 471  83
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED     75    6
  DEL PEAK  5(2Q37.3) WILD-TYPE  471   83
   clus
vv  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  0                          75                           471
  1                           6                            83
[1] 2 2
[1] FALSE
D14V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED    40  71
  DEL PEAK  5(2Q37.3) WILD-TYPE 252 519
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED     40   71
  DEL PEAK  5(2Q37.3) WILD-TYPE  252  519
        clus
vv       DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  FEMALE                          40                           252
  MALE                            71                           519
[1] 2 2
[1] FALSE
D14V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED    70   0
  DEL PEAK  5(2Q37.3) WILD-TYPE 338   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED     70    0
  DEL PEAK  5(2Q37.3) WILD-TYPE  338    3
     clus
vv    DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  NO                           70                           338
  YES                           0                             3
[1] 2 2
[1] FALSE
D14V9, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK  5(2Q37.3) MUTATED                   49
  DEL PEAK  5(2Q37.3) WILD-TYPE                 17
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK  5(2Q37.3) MUTATED                                  50
  DEL PEAK  5(2Q37.3) WILD-TYPE                               478
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  5(2Q37.3) MUTATED                                      12
  DEL PEAK  5(2Q37.3) WILD-TYPE                                   276
D14V10, multiclass
                                       clus
vv                                      DEL PEAK  5(2Q37.3) MUTATED
  KIDNEY CHROMOPHOBE                                             49
  KIDNEY CLEAR CELL RENAL CARCINOMA                              50
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          12
                                       clus
vv                                      DEL PEAK  5(2Q37.3) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               17
  KIDNEY CLEAR CELL RENAL CARCINOMA                               478
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           276
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, continuous
D14V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(2Q37.3) MUTATED                                  0     3
  DEL PEAK  5(2Q37.3) WILD-TYPE                                2    13
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q37.3) MUTATED                          11    93
  DEL PEAK  5(2Q37.3) WILD-TYPE                       110   626
D14V13, multiclass
                                  clus
vv                                 DEL PEAK  5(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     93
                                  clus
vv                                 DEL PEAK  5(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       13
  BLACK OR AFRICAN AMERICAN                                  110
  WHITE                                                      626
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     4  65
  DEL PEAK  5(2Q37.3) WILD-TYPE  38 557
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      4   65
  DEL PEAK  5(2Q37.3) WILD-TYPE   38  557
                        clus
vv                       DEL PEAK  5(2Q37.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          65
                        clus
vv                       DEL PEAK  5(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           557
[1] 2 2
[1] FALSE

Clustering(15) Variable = DEL PEAK  6(3P26.3) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P26.3) MUTATED   329 159
  DEL PEAK  6(3P26.3) WILD-TYPE 319  69
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                          488                           388 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                          159                            69 
$`DEL PEAK  6(3P26.3) MUTATED`
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B8-5162 TCGA-B8-A54H TCGA-BP-4158 TCGA-BP-4160 
      119.38       126.05         1.18         8.42       111.02        94.72 
TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 
       32.61         3.58        80.68        74.17        54.77        12.33 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4986 
       44.15        60.59        11.64         6.94        61.51        25.81 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 
       62.86        49.15        27.02        44.55        31.27        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 
      105.37        26.93        27.65       108.56        53.26       118.85 
TCGA-CJ-6030 TCGA-CZ-4856 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       75.58         0.59         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-A4W0 TCGA-G6-A8L7 
       11.67        37.15        66.28        56.84        81.21        70.13 
TCGA-MM-A84U TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-BQ-5892 TCGA-Y8-A8RZ TCGA-KL-8324 
       23.01        12.99        11.87        11.97         6.74       153.73 
TCGA-KL-8333 TCGA-KL-8335 TCGA-KN-8421 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8432 
       98.33        92.55        87.91       104.52         0.99         2.50 
TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3308 
      104.55       105.60        96.62        12.66        36.82         0.53 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
       39.16        24.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       48.59        36.36        38.99        37.38        48.82        62.01 
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-A3-3362 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-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3387 
       55.76        20.71        18.64        18.87        28.31        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       10.62        29.10       122.56       109.41        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 
      112.08        68.61       109.51        48.36        78.64        94.29 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       38.40        82.45        72.89         1.41         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4703 
        2.53         3.48        28.47        19.00         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        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-B0-4819 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-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4841 
       10.09        78.44        40.70        45.30        27.42         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       56.68        10.52        65.29        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-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 
       25.32        15.09        10.95         8.05        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       15.95        90.87        90.48        30.48        58.59        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       38.63        52.73        41.88        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        42.41       111.52       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 
      130.65        79.89       131.15        89.49        91.46        35.90 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 
       31.96        21.30        31.30        31.66        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       16.67        12.00         5.10         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        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 
       42.71        25.05        45.37        25.55        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 
       27.02         0.85        24.23         6.38         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       14.30        27.29        17.06         1.74         4.93        17.36 
TCGA-B8-A7U6 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4166 
       16.27        85.51        90.28       101.06        93.34         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-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 
       53.42        27.78        62.07        37.25        15.62         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 
       93.99        18.48        52.24        62.86        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       12.23        31.89        11.31        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
        5.33        61.97        13.51        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
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-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-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 
       31.30        36.95         3.88        46.45        16.47        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       74.27        75.06        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-4892 
       57.83       113.46        64.18        30.64        51.52        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        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       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         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-6088 
       85.78        73.18        66.31        78.18        74.66       105.93 
TCGA-CW-6090 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       83.90        25.45        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       14.66        63.39        93.04       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        94.45        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        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-A4VX TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       62.63        53.46        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC 
       10.29        35.87         2.01        19.43        19.96        16.37 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-5P-A9K9 TCGA-A4-A57E TCGA-AL-3473 
       54.64        51.52        38.99        19.36         8.48        62.66 
TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5882 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-7501 
       14.86         8.88        21.63        79.86         4.01        20.52 
TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-SX-A7SU 
       23.08         3.68         2.04        10.55        14.07        43.76 
TCGA-UZ-A9PQ TCGA-WN-A9G9 
       86.27        26.01 

$`DEL PEAK  6(3P26.3) WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-A54K TCGA-BP-4760 TCGA-BP-4795 TCGA-BP-4799 
       24.82        25.91        15.42        77.62        20.38        37.25 
TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-5191 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4862 
       53.65        27.22        31.79       103.43        46.16       107.54 
TCGA-DV-5567 TCGA-DV-5576 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       65.88        23.90        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
       21.37         0.89        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       21.07        10.16        21.86        19.23        26.04        13.25 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       137.06        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.96        84.89        96.95        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       62.37       151.96        44.91        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
       31.33       129.37        23.47        25.48        25.91        65.19 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 
        3.55        52.27        87.12        19.33        11.21        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       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8416 
      103.40        92.71        16.67       103.10        99.88        90.48 
TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3385 TCGA-AK-3427 
       92.55        11.90        10.49        43.20        65.52       117.80 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 
       94.19        46.78        40.01        83.21        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        52.87        56.98        32.61         1.68 
TCGA-B4-5378 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 
        5.75        17.19        50.14        50.14        16.60        48.53 
TCGA-B8-A54E TCGA-B8-A8YJ TCGA-BP-4165 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4334 
       29.88        14.17        99.85        62.24        54.90        21.21 
TCGA-BP-4756 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4784 TCGA-BP-4804 TCGA-BP-4967 
       12.30        61.68        10.82        60.95        47.97         6.74 
TCGA-BP-4994 TCGA-CJ-4875 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4920 TCGA-CJ-5681 
       43.00       116.84        63.98       115.69         4.57        18.15 
TCGA-CW-6087 TCGA-CW-6097 TCGA-DV-A4VZ TCGA-EU-5905 TCGA-T7-A92I TCGA-2K-A9WE 
        1.35        18.77        12.00         3.91        11.70         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-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       91.73        56.81        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       43.04        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
       16.96        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       70.19        49.32        66.71        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
       17.23         0.16        17.49        12.30        86.76        19.27 
TCGA-BQ-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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       10.68        13.08         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 
       90.90        11.05        39.25        71.44        25.15        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD 
       22.26        21.34        12.36        12.76        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        78.90        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       53.10        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
      110.73        51.35        31.73        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                         0.07                          0.10 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                       153.73                        194.79 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                       38.665                        29.180 
[1] "0.1 - 153.7 (38.7)" "0.1 - 194.8 (29.2)"
[1] "hr=" "1.7"
D15V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  6(3P26.3) MUTATED       227       57       128       74
  DEL PEAK  6(3P26.3) WILD-TYPE     227       46        62       30
D15V3, multiclass
           clus
vv          DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  STAGE I                           227                           227
  STAGE II                           57                            46
  STAGE III                         128                            62
  STAGE IV                           74                            30
[1] 4 2
[1] 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(3P26.3) MUTATED   234  71 177   7
  DEL PEAK  6(3P26.3) WILD-TYPE 246  56  81   8
D15V4, multiclass
    clus
vv   DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  T1                         234                           246
  T2                          71                            56
  T3                         177                            81
  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(3P26.3) MUTATED   214  22   2
  DEL PEAK  6(3P26.3) WILD-TYPE 109  22   4
D15V5, multiclass
    clus
vv   DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  N0                         214                           109
  N1                          22                            22
  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"
D15V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED   374  69
  DEL PEAK  6(3P26.3) WILD-TYPE 172  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED    374   69
  DEL PEAK  6(3P26.3) WILD-TYPE  172   20
   clus
vv  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  0                         374                           172
  1                          69                            20
[1] 2 2
[1] FALSE
D15V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED   176 313
  DEL PEAK  6(3P26.3) WILD-TYPE 116 277
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED    176  313
  DEL PEAK  6(3P26.3) WILD-TYPE  116  277
        clus
vv       DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  FEMALE                         176                           116
  MALE                           313                           277
[1] 2 2
[1] FALSE
D15V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED   140   2
  DEL PEAK  6(3P26.3) WILD-TYPE 268   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED    140    2
  DEL PEAK  6(3P26.3) WILD-TYPE  268    1
     clus
vv    DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  NO                          140                           268
  YES                           2                             1
[1] 2 2
[1] FALSE
D15V9, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK  6(3P26.3) MUTATED                   10
  DEL PEAK  6(3P26.3) WILD-TYPE                 56
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK  6(3P26.3) MUTATED                                 455
  DEL PEAK  6(3P26.3) WILD-TYPE                                73
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  6(3P26.3) MUTATED                                      24
  DEL PEAK  6(3P26.3) WILD-TYPE                                   264
D15V10, multiclass
                                       clus
vv                                      DEL PEAK  6(3P26.3) MUTATED
  KIDNEY CHROMOPHOBE                                             10
  KIDNEY CLEAR CELL RENAL CARCINOMA                             455
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          24
                                       clus
vv                                      DEL PEAK  6(3P26.3) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               56
  KIDNEY CLEAR CELL RENAL CARCINOMA                                73
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           264
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, continuous
D15V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(3P26.3) MUTATED                                  0     7
  DEL PEAK  6(3P26.3) WILD-TYPE                                2     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P26.3) MUTATED                          43   430
  DEL PEAK  6(3P26.3) WILD-TYPE                        78   289
D15V13, multiclass
                                  clus
vv                                 DEL PEAK  6(3P26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 43
  WHITE                                                    430
                                  clus
vv                                 DEL PEAK  6(3P26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   78
  WHITE                                                      289
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED    26 319
  DEL PEAK  6(3P26.3) WILD-TYPE  16 303
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED     26  319
  DEL PEAK  6(3P26.3) WILD-TYPE   16  303
                        clus
vv                       DEL PEAK  6(3P26.3) MUTATED
  HISPANIC OR LATINO                              26
  NOT HISPANIC OR LATINO                         319
                        clus
vv                       DEL PEAK  6(3P26.3) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           303
[1] 2 2
[1] FALSE

Clustering(16) Variable = DEL PEAK  7(3P21.2) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P21.2) MUTATED   331 171
  DEL PEAK  7(3P21.2) WILD-TYPE 317  57
  DEL PEAK  7(3P21.2) MUTATED DEL PEAK  7(3P21.2) WILD-TYPE 
                          502                           374 
  DEL PEAK  7(3P21.2) MUTATED DEL PEAK  7(3P21.2) WILD-TYPE 
                          171                            57 
$`DEL PEAK  7(3P21.2) MUTATED`
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       52.21        18.51       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B8-5162 TCGA-B8-A54H TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 
      126.05         1.18         8.42       111.02        94.72        32.61 
TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4762 
        3.58        80.68        74.17        54.77        12.33        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4986 TCGA-BP-4993 
       60.59        11.64         6.94        61.51        25.81         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 
       45.07        41.62        27.62        35.90        48.10        62.86 
TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 
       49.15        27.02        31.79        44.55        31.27        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 
      105.37        26.93        27.65       108.56        53.26       118.85 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4865 TCGA-DV-5565 
       75.58       103.43        46.16         0.59         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-BQ-5892 
       81.21        70.13        23.01        12.99        11.87        11.97 
TCGA-Y8-A8RZ TCGA-KL-8324 TCGA-KL-8333 TCGA-KL-8341 TCGA-KN-8421 TCGA-KN-8425 
        6.74       153.73        98.33        24.79        87.91       104.52 
TCGA-KN-8427 TCGA-KN-8432 TCGA-KN-8436 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 
        0.99         2.50        42.35       104.55       105.60        96.62 
TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       12.66        36.82         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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       37.38        48.82        62.01         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 
       29.92        18.44        88.37        51.25        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        28.31        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 
        0.10         0.10        11.18        10.62        29.10       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
      109.41        15.78        73.68       112.08        68.61       109.51 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 
       78.64        94.29        38.40        82.45        72.89         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-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
        7.82         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        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-B0-4836 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-B0-4844 TCGA-B0-4845 
       27.42         6.71        56.68        10.52        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-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 
       20.94        43.30        11.90         7.30        25.32        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        58.59        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        41.88        51.02        38.43        48.82        46.39 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 
       79.89       131.15        89.49        91.46        35.90        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       21.30        31.30        31.66        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
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        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       25.05        45.37        25.55        50.14        40.04        23.74 
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        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       34.39        14.30        27.29        17.06         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       17.36        16.27        85.51        90.28       101.06        93.34 
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-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       64.27        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       33.99        31.33        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       71.80        48.07        13.15         5.33        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4798 
       56.91        68.38        15.78        48.95        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       16.47        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        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       116.84        64.27 
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       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       30.64        51.52        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       49.28        50.33        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       131.08        72.00       129.40       133.71        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       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         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-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 
       66.31        78.18        74.66       105.93        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
       25.45        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       107.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       94.45        10.85        10.22        21.76        69.96        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        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-A4VX TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       53.46        18.12         6.77         4.18         7.96        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-2Z-A9JG 
       35.87         2.01        19.43        19.96        16.37        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-5P-A9K3 TCGA-5P-A9K9 TCGA-A4-A57E TCGA-AL-3466 
       51.52        38.99        15.48        19.36         8.48         9.63 
TCGA-AL-3473 TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5890 TCGA-DZ-6131 
       62.66        14.86         8.88        21.63         7.66        79.86 
TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y 
        4.01        20.52        23.08        16.90         3.68         2.04 
TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UZ-A9PQ TCGA-WN-A9G9 
       10.55        14.07        86.27        26.01 

$`DEL PEAK  7(3P21.2) WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-B0-5691 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-A54K TCGA-BP-4760 TCGA-BP-4795 
      112.80        24.82        25.91        15.42        77.62        20.38 
TCGA-BP-4799 TCGA-BP-4976 TCGA-BP-4988 TCGA-CZ-4862 TCGA-DV-5567 TCGA-DV-5576 
       37.25        53.65        27.22       107.54        65.88        23.90 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7049 
       21.86        19.23        26.04        13.25        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-KL-8323 TCGA-KL-8325 
       86.37        21.60        15.91        15.62        38.07        23.84 
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
      109.22       137.06        90.48       108.62        98.96        84.89 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
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-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8428 
       23.47        25.48        25.91        65.19         3.55        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 
       87.12        19.33        11.21        59.08       115.00       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      105.47        10.68       100.47       103.40        92.71        16.67 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3363 
      103.10        99.88        90.48        92.55        11.90        10.49 
TCGA-A3-3374 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       43.20        65.52       117.80        94.19        46.78        48.36 
TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4688 
       40.01        83.21        37.58        12.13        40.70         3.32 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4834 TCGA-B0-4839 TCGA-B0-5080 
        1.38         3.62        65.10        68.71        53.88        11.24 
TCGA-B0-5100 TCGA-B0-5106 TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5400 TCGA-B2-3923 
       62.89        52.54        19.30        52.87        56.98        32.61 
TCGA-B2-4098 TCGA-B4-5378 TCGA-B8-4619 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-A54E 
        1.68         5.75        17.19        50.14        16.60        29.88 
TCGA-B8-A8YJ TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4756 TCGA-BP-4769 TCGA-BP-4770 
       14.17        62.24        54.90        12.30        61.68        10.82 
TCGA-BP-4784 TCGA-BP-4790 TCGA-BP-4804 TCGA-BP-4967 TCGA-BP-4994 TCGA-CJ-4889 
       60.95        36.53        47.97         6.74        43.00        63.98 
TCGA-CJ-4890 TCGA-CJ-4912 TCGA-CW-6087 TCGA-DV-A4VZ TCGA-EU-5905 TCGA-T7-A92I 
      115.69        54.48         1.35        12.00         3.91        11.70 
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-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
        4.57        91.73        56.81        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       43.04        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
       16.96        16.31        15.75         8.28        12.46        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       49.32        66.71        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
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-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       25.35        10.82         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
        7.04         7.17         3.81        40.77        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       39.25        71.44        25.15        25.84        25.25        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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.76        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
       92.58        52.27        16.01        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       31.73        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  DEL PEAK  7(3P21.2) MUTATED DEL PEAK  7(3P21.2) WILD-TYPE 
                         0.07                          0.10 
  DEL PEAK  7(3P21.2) MUTATED DEL PEAK  7(3P21.2) WILD-TYPE 
                       153.73                        194.79 
  DEL PEAK  7(3P21.2) MUTATED DEL PEAK  7(3P21.2) WILD-TYPE 
                       38.415                        30.065 
[1] "0.1 - 153.7 (38.4)" "0.1 - 194.8 (30.1)"
[1] "hr=" "2.1"
D16V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  7(3P21.2) MUTATED       227       57       134       81
  DEL PEAK  7(3P21.2) WILD-TYPE     227       46        56       23
D16V3, multiclass
           clus
vv          DEL PEAK  7(3P21.2) MUTATED DEL PEAK  7(3P21.2) WILD-TYPE
  STAGE I                           227                           227
  STAGE II                           57                            46
  STAGE III                         134                            56
  STAGE IV                           81                            23
[1] 4 2
[1] 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(3P21.2) MUTATED   234  72 190   7
  DEL PEAK  7(3P21.2) WILD-TYPE 246  55  68   8
D16V4, multiclass
    clus
vv   DEL PEAK  7(3P21.2) MUTATED DEL PEAK  7(3P21.2) WILD-TYPE
  T1                         234                           246
  T2                          72                            55
  T3                         190                            68
  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  7(3P21.2) MUTATED   220  25   3
  DEL PEAK  7(3P21.2) WILD-TYPE 103  19   3
D16V5, multiclass
    clus
vv   DEL PEAK  7(3P21.2) MUTATED DEL PEAK  7(3P21.2) WILD-TYPE
  N0                         220                           103
  N1                          25                            19
  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"
D16V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P21.2) MUTATED   379  75
  DEL PEAK  7(3P21.2) WILD-TYPE 167  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P21.2) MUTATED    379   75
  DEL PEAK  7(3P21.2) WILD-TYPE  167   14
   clus
vv  DEL PEAK  7(3P21.2) MUTATED DEL PEAK  7(3P21.2) WILD-TYPE
  0                         379                           167
  1                          75                            14
[1] 2 2
[1] FALSE
D16V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P21.2) MUTATED   178 325
  DEL PEAK  7(3P21.2) WILD-TYPE 114 265
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P21.2) MUTATED    178  325
  DEL PEAK  7(3P21.2) WILD-TYPE  114  265
        clus
vv       DEL PEAK  7(3P21.2) MUTATED DEL PEAK  7(3P21.2) WILD-TYPE
  FEMALE                         178                           114
  MALE                           325                           265
[1] 2 2
[1] FALSE
D16V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P21.2) MUTATED   146   2
  DEL PEAK  7(3P21.2) WILD-TYPE 262   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P21.2) MUTATED    146    2
  DEL PEAK  7(3P21.2) WILD-TYPE  262    1
     clus
vv    DEL PEAK  7(3P21.2) MUTATED DEL PEAK  7(3P21.2) WILD-TYPE
  NO                          146                           262
  YES                           2                             1
[1] 2 2
[1] FALSE
D16V9, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK  7(3P21.2) MUTATED                   11
  DEL PEAK  7(3P21.2) WILD-TYPE                 55
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK  7(3P21.2) MUTATED                                 465
  DEL PEAK  7(3P21.2) WILD-TYPE                                63
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  7(3P21.2) MUTATED                                      27
  DEL PEAK  7(3P21.2) WILD-TYPE                                   261
D16V10, multiclass
                                       clus
vv                                      DEL PEAK  7(3P21.2) MUTATED
  KIDNEY CHROMOPHOBE                                             11
  KIDNEY CLEAR CELL RENAL CARCINOMA                             465
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          27
                                       clus
vv                                      DEL PEAK  7(3P21.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               55
  KIDNEY CLEAR CELL RENAL CARCINOMA                                63
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           261
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, continuous
D16V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3P21.2) MUTATED                                  0     8
  DEL PEAK  7(3P21.2) WILD-TYPE                                2     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P21.2) MUTATED                          43   444
  DEL PEAK  7(3P21.2) WILD-TYPE                        78   275
D16V13, multiclass
                                  clus
vv                                 DEL PEAK  7(3P21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 43
  WHITE                                                    444
                                  clus
vv                                 DEL PEAK  7(3P21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   78
  WHITE                                                      275
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P21.2) MUTATED    24 333
  DEL PEAK  7(3P21.2) WILD-TYPE  18 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P21.2) MUTATED     24  333
  DEL PEAK  7(3P21.2) WILD-TYPE   18  289
                        clus
vv                       DEL PEAK  7(3P21.2) MUTATED
  HISPANIC OR LATINO                              24
  NOT HISPANIC OR LATINO                         333
                        clus
vv                       DEL PEAK  7(3P21.2) WILD-TYPE
  HISPANIC OR LATINO                                18
  NOT HISPANIC OR LATINO                           289
[1] 2 2
[1] FALSE

Clustering(17) Variable = DEL PEAK  8(3P14.1) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3P14.1) MUTATED   272 136
  DEL PEAK  8(3P14.1) WILD-TYPE 376  92
  DEL PEAK  8(3P14.1) MUTATED DEL PEAK  8(3P14.1) WILD-TYPE 
                          408                           468 
  DEL PEAK  8(3P14.1) MUTATED DEL PEAK  8(3P14.1) WILD-TYPE 
                          136                            92 
$`DEL PEAK  8(3P14.1) MUTATED`
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       47.21        38.47        34.29        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       58.49        28.73        22.45        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5698 TCGA-B8-5162 TCGA-B8-A54H 
       18.51       133.94        15.78       119.38         1.18         8.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 
      111.02        94.72        32.61         3.58        80.68        74.17 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4782 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4986 
       54.77        12.33        11.64         6.94        61.51        25.81 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5178 
        5.82        45.07        41.62        27.62        48.10        62.86 
TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 
       49.15        27.02        31.79        44.55        31.27        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 
      105.37        26.93        27.65       108.56        53.26       118.85 
TCGA-CJ-6030 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 
       75.58        46.16         0.59         5.46        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-A4W0 TCGA-MM-A84U 
       12.16        37.15        66.28        56.84        81.21        23.01 
TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-BQ-5892 TCGA-Y8-A8RZ TCGA-KL-8324 TCGA-KL-8333 
       12.99        11.87        11.97         6.74       153.73        98.33 
TCGA-KL-8341 TCGA-KN-8421 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8432 TCGA-KN-8436 
       24.79        87.91       104.52         0.99         2.50        42.35 
TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3311 
      104.55       105.60        96.62        12.66        36.82        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-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 
       36.36        38.99        48.82        62.01         4.50        52.93 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3429 TCGA-AK-3430 
        0.10        11.18        10.62        29.10       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3451 
       73.68       112.08        68.61       109.51        78.64        94.29 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4693 
       38.40        82.45        72.89         1.41         1.41         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        28.47        19.00         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4817 
        6.64        15.72        46.59         0.59        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-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4841 
       10.09        78.44        40.70        45.30        27.42         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       56.68        10.52        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5084 TCGA-B0-5092 
        2.27        70.52        20.94        43.30         7.30        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-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       90.87        90.48        58.59        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 
       41.88        51.02        38.43        46.39        42.41       111.52 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       73.84       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 
       91.46        35.90        31.96        31.66        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       16.67        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4620 
        0.36         0.23        23.31        16.80        49.97        25.55 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5549 TCGA-B8-5551 
       50.14        23.74        27.02         0.85         6.38         0.53 
TCGA-B8-5552 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       34.39        27.29        17.06         1.74         4.93        17.36 
TCGA-BP-4159 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       85.51        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4332 
       77.03        61.78        64.27        97.45        27.78        37.25 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 
       93.99        18.48        52.24        62.86        49.08        44.94 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4758 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       31.89        11.31        72.59         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       48.07        13.15         5.33        61.97        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       68.38        48.95        36.39        10.98        36.95         6.71 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4971 
       87.45        71.41        63.62        58.68        60.30        48.89 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
        6.94        47.11        14.93        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 
       36.95         3.88        46.45        16.47        30.64        18.51 
TCGA-BP-5004 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5173 TCGA-BP-5174 
       37.02        35.21        28.87         6.35         2.04        74.20 
TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       52.27        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4640 
       19.82        34.95       115.00        46.55        73.22       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       79.66        74.27        75.06        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4892 TCGA-CJ-4893 
       61.91        64.18        30.64        51.52        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
       50.33        45.14       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       25.71        18.87        22.32       122.83        62.10        73.35 
TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5584 
       53.42       119.64         7.36        64.57        81.83         5.39 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 
       73.18        66.31        78.18        74.66       105.93        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       18.77        25.45        47.08        69.21        58.75         6.77 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 
       63.39        93.04        63.42        58.82        79.53        18.44 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        69.96        84.30        22.52         1.94        31.10 
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-A4VX TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L8 
       62.63        53.46         6.77         4.18        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-2Z-A9JG TCGA-2Z-A9JI 
        2.01        19.43        19.96        16.37        54.64        51.52 
TCGA-2Z-A9JK TCGA-5P-A9K9 TCGA-A4-A57E TCGA-AL-3473 TCGA-B9-A69E TCGA-BQ-5877 
       38.99        19.36         8.48        62.66        14.86         8.88 
TCGA-BQ-5882 TCGA-BQ-5890 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-A8LC TCGA-G7-A8LD 
       21.63         7.66        79.86         4.01        23.08        16.90 
TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UZ-A9PQ TCGA-WN-A9G9 
        3.68         2.04        10.55        14.07        86.27        26.01 

$`DEL PEAK  8(3P14.1) WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3343 TCGA-B0-5691 TCGA-B0-5695 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 
       31.07       112.80        70.68       126.05        24.82        25.91 
TCGA-B8-A54K TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4795 TCGA-BP-4799 
       15.42        77.62        44.15        60.59        20.38        37.25 
TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-5009 TCGA-CW-6093 TCGA-CZ-4862 TCGA-DV-5567 
       53.65        27.22        35.90       103.43       107.54        65.88 
TCGA-DV-5569 TCGA-DV-5576 TCGA-G6-A8L7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        23.90        70.13        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       61.05        21.37         0.89        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 
       27.68        21.07        10.16        21.86        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       13.25        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       15.62        38.07        23.84       109.22       137.06        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-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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 
       51.06        31.33       129.37        23.47        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 
       65.19         3.55        52.27        87.12        19.33        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
       59.08       115.00       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8416 
      103.40        92.71        16.67       103.10        99.88        90.48 
TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3326 TCGA-A3-3349 TCGA-A3-3362 
       92.55        11.90         0.53        37.38        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       117.80       122.56        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 
       46.78        48.36        40.01        83.21        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        58.45         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        52.87        48.82 
TCGA-B0-5400 TCGA-B0-5705 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4101 TCGA-B2-4102 
       56.98       149.16        32.61         1.68        21.30        31.30 
TCGA-B4-5378 TCGA-B4-5838 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
        5.75         5.46        42.71        25.05        45.37        17.19 
TCGA-B8-5158 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5553 
       40.04        24.23        50.14        16.60        48.53        14.30 
TCGA-B8-A54E TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4173 
       29.88        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        15.62         0.07 
TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4759 TCGA-BP-4769 
       12.23        33.99        31.33        12.30        77.98        61.68 
TCGA-BP-4770 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4804 TCGA-BP-4964 
       10.82        60.95        15.78        36.53        47.97        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        58.98        14.24        49.38        45.50 
TCGA-BP-4981 TCGA-BP-4994 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5170 TCGA-BP-5175 
       36.07        43.00        38.70        37.48        79.30        30.64 
TCGA-BP-5177 TCGA-BP-5186 TCGA-BP-5202 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4872 
        9.63        22.78         0.95        14.17       106.16        47.18 
TCGA-CJ-4875 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4897 
      116.84        57.83       113.46        63.98       115.69       109.84 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4918 TCGA-CJ-4920 
       49.18        49.28        54.48        38.56         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CW-5581 
       18.81        25.25        18.15        67.00        62.66        92.02 
TCGA-CW-5585 TCGA-CW-6087 TCGA-CZ-4861 TCGA-CZ-4866 TCGA-CZ-5454 TCGA-CZ-5456 
       85.78         1.35        14.66       107.41        23.74        79.63 
TCGA-CZ-5467 TCGA-CZ-5470 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-G6-A5PC 
        2.40        12.69        12.00        18.12         3.91         7.96 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.91         4.57        91.73        56.81        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       14.33        12.46        16.96        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 
       12.46         9.63        70.19        49.32        66.71        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI 
       43.99        22.06        17.23         0.16        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76        19.27        63.72        22.92        43.20        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 
       40.83        26.04        30.28        25.35        10.82         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       40.77        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 
       20.52        25.84        25.25        17.98        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25        25.22        16.80        19.99        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 
       96.69        22.26        21.34        12.36        12.76        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.09        42.94         6.61        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        78.90        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-AB4C 
       47.47        65.13       110.73        51.35        31.73        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  DEL PEAK  8(3P14.1) MUTATED DEL PEAK  8(3P14.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK  8(3P14.1) MUTATED DEL PEAK  8(3P14.1) WILD-TYPE 
                       153.73                        194.79 
  DEL PEAK  8(3P14.1) MUTATED DEL PEAK  8(3P14.1) WILD-TYPE 
                       38.990                        30.655 
[1] "0.1 - 153.7 (39.0)" "0.1 - 194.8 (30.7)"
[1] "hr=" "1.6"
D17V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  8(3P14.1) MUTATED       187       49       110       59
  DEL PEAK  8(3P14.1) WILD-TYPE     267       54        80       45
D17V3, multiclass
           clus
vv          DEL PEAK  8(3P14.1) MUTATED DEL PEAK  8(3P14.1) WILD-TYPE
  STAGE I                           187                           267
  STAGE II                           49                            54
  STAGE III                         110                            80
  STAGE IV                           59                            45
[1] 4 2
[1] 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(3P14.1) MUTATED   192  60 151   5
  DEL PEAK  8(3P14.1) WILD-TYPE 288  67 107  10
D17V4, multiclass
    clus
vv   DEL PEAK  8(3P14.1) MUTATED DEL PEAK  8(3P14.1) WILD-TYPE
  T1                         192                           288
  T2                          60                            67
  T3                         151                           107
  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  8(3P14.1) MUTATED   179  18   3
  DEL PEAK  8(3P14.1) WILD-TYPE 144  26   3
D17V5, multiclass
    clus
vv   DEL PEAK  8(3P14.1) MUTATED DEL PEAK  8(3P14.1) WILD-TYPE
  N0                         179                           144
  N1                          18                            26
  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"
D17V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.1) MUTATED   310  54
  DEL PEAK  8(3P14.1) WILD-TYPE 236  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.1) MUTATED    310   54
  DEL PEAK  8(3P14.1) WILD-TYPE  236   35
   clus
vv  DEL PEAK  8(3P14.1) MUTATED DEL PEAK  8(3P14.1) WILD-TYPE
  0                         310                           236
  1                          54                            35
[1] 2 2
[1] FALSE
D17V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.1) MUTATED   127 281
  DEL PEAK  8(3P14.1) WILD-TYPE 165 309
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.1) MUTATED    127  281
  DEL PEAK  8(3P14.1) WILD-TYPE  165  309
        clus
vv       DEL PEAK  8(3P14.1) MUTATED DEL PEAK  8(3P14.1) WILD-TYPE
  FEMALE                         127                           165
  MALE                           281                           309
[1] 2 2
[1] FALSE
D17V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.1) MUTATED   123   2
  DEL PEAK  8(3P14.1) WILD-TYPE 285   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.1) MUTATED    123    2
  DEL PEAK  8(3P14.1) WILD-TYPE  285    1
     clus
vv    DEL PEAK  8(3P14.1) MUTATED DEL PEAK  8(3P14.1) WILD-TYPE
  NO                          123                           285
  YES                           2                             1
[1] 2 2
[1] FALSE
D17V9, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK  8(3P14.1) MUTATED                   11
  DEL PEAK  8(3P14.1) WILD-TYPE                 55
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK  8(3P14.1) MUTATED                                 373
  DEL PEAK  8(3P14.1) WILD-TYPE                               155
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  8(3P14.1) MUTATED                                      24
  DEL PEAK  8(3P14.1) WILD-TYPE                                   264
D17V10, multiclass
                                       clus
vv                                      DEL PEAK  8(3P14.1) MUTATED
  KIDNEY CHROMOPHOBE                                             11
  KIDNEY CLEAR CELL RENAL CARCINOMA                             373
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          24
                                       clus
vv                                      DEL PEAK  8(3P14.1) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               55
  KIDNEY CLEAR CELL RENAL CARCINOMA                               155
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           264
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
D17V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(3P14.1) MUTATED                                  0     7
  DEL PEAK  8(3P14.1) WILD-TYPE                                2     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3P14.1) MUTATED                          37   357
  DEL PEAK  8(3P14.1) WILD-TYPE                        84   362
D17V13, multiclass
                                  clus
vv                                 DEL PEAK  8(3P14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 37
  WHITE                                                    357
                                  clus
vv                                 DEL PEAK  8(3P14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   84
  WHITE                                                      362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V14, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.1) MUTATED    20 271
  DEL PEAK  8(3P14.1) WILD-TYPE  22 351
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.1) MUTATED     20  271
  DEL PEAK  8(3P14.1) WILD-TYPE   22  351
                        clus
vv                       DEL PEAK  8(3P14.1) MUTATED
  HISPANIC OR LATINO                              20
  NOT HISPANIC OR LATINO                         271
                        clus
vv                       DEL PEAK  8(3P14.1) WILD-TYPE
  HISPANIC OR LATINO                                22
  NOT HISPANIC OR LATINO                           351
[1] 2 2
[1] FALSE

Clustering(18) Variable = DEL PEAK  9(3P12.2) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(3P12.2) MUTATED   219 117
  DEL PEAK  9(3P12.2) WILD-TYPE 429 111
  DEL PEAK  9(3P12.2) MUTATED DEL PEAK  9(3P12.2) WILD-TYPE 
                          336                           540 
  DEL PEAK  9(3P12.2) MUTATED DEL PEAK  9(3P12.2) WILD-TYPE 
                          117                           111 
$`DEL PEAK  9(3P12.2) MUTATED`
TCGA-A3-3325 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 
       38.47        42.97        82.32       109.91        58.49        28.73 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5693 TCGA-B0-5694 TCGA-B8-5162 
       19.73        43.96        52.21       133.94        15.78         1.18 
TCGA-B8-A54H TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
        8.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4807 TCGA-BP-4986 TCGA-BP-4993 
       74.17        54.77        12.33         6.94        25.81         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       45.07        41.62        27.62        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 
       27.02        31.79        44.55        31.27        63.25       105.37 
TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
       26.93        27.65       108.56        53.26       118.85        75.58 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       46.16         0.59         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-A4W0 TCGA-A4-A5Y1 
       11.67        37.15        66.28        56.84        81.21        12.99 
TCGA-B9-A44B TCGA-BQ-5892 TCGA-Y8-A8RZ TCGA-KL-8324 TCGA-KL-8333 TCGA-KL-8341 
       11.87        11.97         6.74       153.73        98.33        24.79 
TCGA-KN-8421 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8432 TCGA-KN-8436 TCGA-KO-8409 
       87.91       104.52         0.99         2.50        42.35       104.55 
TCGA-KO-8414 TCGA-KO-8415 TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3313 
      105.60        96.62        12.66        36.82        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-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3357 
       48.82        62.01         4.50        52.93        18.44        88.37 
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-3429 TCGA-AK-3430 
        0.10         0.10        11.18        10.62       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3451 
       73.68       112.08        68.61       109.51        78.64        94.29 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4693 
       38.40        82.45        72.89         1.41         1.41         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4810 
        3.48        28.47         5.98         2.14         6.64        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4817 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       46.59         0.59        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        10.52        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        58.59 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 
       38.63        52.73        41.88        51.02        38.43        46.39 
TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5706 
       42.41       129.67        86.47       126.28        73.84       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5712 TCGA-B2-3924 TCGA-B2-5633 TCGA-B2-5639 
      130.65        79.89        89.49        35.90        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B8-4148 
       21.57        16.67        12.00         5.10         1.25        49.97 
TCGA-B8-4620 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 
       25.55        27.02         0.85         6.38         0.53        34.39 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-BP-4166 TCGA-BP-4169 
       27.29        17.06         1.74         4.93         0.43        23.05 
TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4332 
       77.03        61.78        64.27        97.45        27.78        37.25 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4351 
       93.99        18.48        62.86        49.08        44.94        31.89 
TCGA-BP-4352 TCGA-BP-4758 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4768 
       11.31        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-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4971 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4985 TCGA-BP-4987 
       60.30        48.89         6.94        47.11        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5004 
        3.88        46.45        16.47        30.64        18.51        37.02 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5180 
       35.21        28.87         2.04        74.20        52.27        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5190 
       38.30        42.44        37.25        37.22        13.35        33.24 
TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4640 
       24.62        19.82        34.95       115.00        46.55       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4887 
       74.27        64.27        66.21        61.91        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       51.52        50.01        24.66        39.45        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5677 
       47.67        49.97        51.29       131.08        72.00        25.71 
TCGA-CJ-5679 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-6028 TCGA-CJ-6032 
       22.32        18.15       122.83        62.10        53.42       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5589 
        7.36        64.57        81.83         5.39        73.18        78.18 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4858 TCGA-CZ-4859 
       74.66       105.93        83.90        18.77        69.21        58.75 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 
       63.39        93.04        63.42        58.82        79.53        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       91.69        55.33        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5982 TCGA-CZ-5984 
       84.30        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-A4VX 
       65.65        12.26        14.63        22.78        62.63        53.46 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        6.77         4.18        10.29        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MW-A4EC TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-5P-A9K9 
       19.96        16.37        54.64        51.52        38.99        19.36 
TCGA-A4-A57E TCGA-AL-3473 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5890 TCGA-G7-6789 
        8.48        62.66         8.88        21.63         7.66         4.01 
TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UZ-A9PQ 
       23.08         3.68         2.04        10.55        14.07        86.27 

$`DEL PEAK  9(3P12.2) WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3336 TCGA-A3-3343 TCGA-AK-3455 TCGA-B0-5088 TCGA-B0-5691 
       47.21        34.29        31.07        22.45        18.51       112.80 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-A54K 
       70.68       119.38       126.05        24.82        25.91        15.42 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 
       77.62        44.15        60.59        11.64        20.38        37.25 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-5009 TCGA-CW-6093 TCGA-CZ-4862 
       61.51        53.65        27.22        35.90       103.43       107.54 
TCGA-DV-5567 TCGA-DV-5576 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD 
       65.88        23.90        70.13        23.01        75.42        34.85 
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU 
       39.88        33.07        25.58        16.18        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ 
       67.17        61.05        21.37         0.89        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 
       21.67        27.68        21.07        10.16        21.86        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       26.04        13.25        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
       15.91        15.62        38.07        23.84       109.22       137.06 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 
       90.48       108.62        98.96        84.89        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       30.25        44.84        86.56        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 
      123.12        51.06        31.33       129.37        23.47        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       25.91        65.19         3.55        52.27        87.12        19.33 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       11.21        59.08       115.00       100.87       105.47        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8413 
      100.47       103.40        92.71        16.67       103.10        99.88 
TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3326 
       90.48        92.55        11.90         0.53        49.08        37.38 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3376 
       45.53        29.92        51.25        10.49        43.20        55.76 
TCGA-A3-3385 TCGA-A3-A6NI TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3440 
       65.52        33.47        29.10       117.80       122.56        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 
       46.78        48.36        40.01        83.21        37.58        12.13 
TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
       40.70         3.32         4.57        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4814 
       65.10         7.82        57.70         3.25        58.45         5.52 
TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4834 TCGA-B0-4839 TCGA-B0-4844 
       45.07        16.77         6.02        68.71        53.88        10.29 
TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 
       26.07        36.85        20.94        11.24        11.90        25.32 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
        2.24        21.86        62.89        90.48        52.54        30.48 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5117 TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5690 
       19.30        66.05        52.87        48.82        56.98       111.52 
TCGA-B0-5696 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5711 TCGA-B0-5713 
       85.78        80.91        71.41       149.16       131.15        91.46 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B4-5378 
       32.61         1.68        31.96        21.30        31.30         5.75 
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-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 
       16.80        42.71        25.05        45.37        17.19        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 
       40.04        23.74        24.23        50.14        16.60        48.53 
TCGA-B8-5553 TCGA-B8-A54E TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
       14.30        29.88        17.36        16.27        14.17        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4173 
       90.28       101.06        93.34        99.85        89.36        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        15.62         0.07 
TCGA-BP-4341 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4759 
       52.24        12.23        33.99        31.33        12.30        77.98 
TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4776 TCGA-BP-4784 TCGA-BP-4787 
       71.80        61.68        10.82        13.51        60.95        15.78 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4804 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       36.53        36.39        47.97        61.22         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4981 
       58.98        14.24        49.38        45.50        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4994 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5169 
       33.34        46.45        43.00        38.70        37.48         6.35 
TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5186 TCGA-BP-5192 TCGA-BP-5194 
       79.30        30.64         9.63        22.78        23.47        13.41 
TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4871 
       33.47         0.95        73.22        14.17       106.16        79.66 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 
       47.18        75.06       116.84        71.87        57.83       113.46 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4897 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       63.98       115.69       109.84        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-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5684 TCGA-CJ-5686 
      129.40       133.71        18.87        25.25        73.35        67.00 
TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-6087 TCGA-CZ-4853 
       62.66        92.02        85.78        66.31         1.35        25.45 
TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4866 TCGA-CZ-5454 TCGA-CZ-5455 
       47.08         6.77        14.66       107.41        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-DV-A4VZ TCGA-EU-5904 
       79.63        94.45         2.40        12.69        12.00        18.12 
TCGA-EU-5905 TCGA-G6-A5PC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
        3.91         7.96        11.70         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       78.64        15.48        71.80        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU 
       19.63        19.73        14.33        12.46        16.96        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 
       15.75         8.28        12.46         9.63        70.19        49.32 
TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       66.71        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
       14.86        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-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       25.35        10.82         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
       13.08         2.40         1.18         0.43        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD 
       22.26        21.34        12.36        12.76        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        78.90        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  DEL PEAK  9(3P12.2) MUTATED DEL PEAK  9(3P12.2) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK  9(3P12.2) MUTATED DEL PEAK  9(3P12.2) WILD-TYPE 
                       153.73                        194.79 
  DEL PEAK  9(3P12.2) MUTATED DEL PEAK  9(3P12.2) WILD-TYPE 
                       38.990                        31.315 
[1] "0.1 - 153.7 (39.0)" "0.1 - 194.8 (31.3)"
[1] "hr=" "1.6"
D18V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  9(3P12.2) MUTATED       155       42        87       49
  DEL PEAK  9(3P12.2) WILD-TYPE     299       61       103       55
D18V3, multiclass
           clus
vv          DEL PEAK  9(3P12.2) MUTATED DEL PEAK  9(3P12.2) WILD-TYPE
  STAGE I                           155                           299
  STAGE II                           42                            61
  STAGE III                          87                           103
  STAGE IV                           49                            55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  9(3P12.2) MUTATED   160  51 121   4
  DEL PEAK  9(3P12.2) WILD-TYPE 320  76 137  11
D18V4, multiclass
    clus
vv   DEL PEAK  9(3P12.2) MUTATED DEL PEAK  9(3P12.2) WILD-TYPE
  T1                         160                           320
  T2                          51                            76
  T3                         121                           137
  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  9(3P12.2) MUTATED   148  15   3
  DEL PEAK  9(3P12.2) WILD-TYPE 175  29   3
D18V5, multiclass
    clus
vv   DEL PEAK  9(3P12.2) MUTATED DEL PEAK  9(3P12.2) WILD-TYPE
  N0                         148                           175
  N1                          15                            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"
D18V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P12.2) MUTATED   255  44
  DEL PEAK  9(3P12.2) WILD-TYPE 291  45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P12.2) MUTATED    255   44
  DEL PEAK  9(3P12.2) WILD-TYPE  291   45
   clus
vv  DEL PEAK  9(3P12.2) MUTATED DEL PEAK  9(3P12.2) WILD-TYPE
  0                         255                           291
  1                          44                            45
[1] 2 2
[1] FALSE
D18V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P12.2) MUTATED   101 235
  DEL PEAK  9(3P12.2) WILD-TYPE 191 355
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P12.2) MUTATED    101  235
  DEL PEAK  9(3P12.2) WILD-TYPE  191  355
        clus
vv       DEL PEAK  9(3P12.2) MUTATED DEL PEAK  9(3P12.2) WILD-TYPE
  FEMALE                         101                           191
  MALE                           235                           355
[1] 2 2
[1] FALSE
D18V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P12.2) MUTATED    97   2
  DEL PEAK  9(3P12.2) WILD-TYPE 311   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P12.2) MUTATED     97    2
  DEL PEAK  9(3P12.2) WILD-TYPE  311    1
     clus
vv    DEL PEAK  9(3P12.2) MUTATED DEL PEAK  9(3P12.2) WILD-TYPE
  NO                           97                           311
  YES                           2                             1
[1] 2 2
[1] FALSE
D18V9, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK  9(3P12.2) MUTATED                   11
  DEL PEAK  9(3P12.2) WILD-TYPE                 55
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK  9(3P12.2) MUTATED                                 305
  DEL PEAK  9(3P12.2) WILD-TYPE                               223
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK  9(3P12.2) MUTATED                                      20
  DEL PEAK  9(3P12.2) WILD-TYPE                                   268
D18V10, multiclass
                                       clus
vv                                      DEL PEAK  9(3P12.2) MUTATED
  KIDNEY CHROMOPHOBE                                             11
  KIDNEY CLEAR CELL RENAL CARCINOMA                             305
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          20
                                       clus
vv                                      DEL PEAK  9(3P12.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               55
  KIDNEY CLEAR CELL RENAL CARCINOMA                               223
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           268
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
D18V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(3P12.2) MUTATED                                  0     6
  DEL PEAK  9(3P12.2) WILD-TYPE                                2    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3P12.2) MUTATED                          31   293
  DEL PEAK  9(3P12.2) WILD-TYPE                        90   426
D18V13, multiclass
                                  clus
vv                                 DEL PEAK  9(3P12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 31
  WHITE                                                    293
                                  clus
vv                                 DEL PEAK  9(3P12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   90
  WHITE                                                      426
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P12.2) MUTATED    14 226
  DEL PEAK  9(3P12.2) WILD-TYPE  28 396
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P12.2) MUTATED     14  226
  DEL PEAK  9(3P12.2) WILD-TYPE   28  396
                        clus
vv                       DEL PEAK  9(3P12.2) MUTATED
  HISPANIC OR LATINO                              14
  NOT HISPANIC OR LATINO                         226
                        clus
vv                       DEL PEAK  9(3P12.2) WILD-TYPE
  HISPANIC OR LATINO                                28
  NOT HISPANIC OR LATINO                           396
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEL PEAK 10(4Q34.3) MUTATION ANALYSIS
D19V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4Q34.3) MUTATED    58  55
  DEL PEAK 10(4Q34.3) WILD-TYPE 590 173
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                          113                           763 
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                           55                           173 
$`DEL PEAK 10(4Q34.3) MUTATED`
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5691 TCGA-B8-5162 TCGA-BP-4164 
       19.73        43.96        52.21       112.80         1.18        32.61 
TCGA-BP-4353 TCGA-CJ-4636 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-KN-8427 TCGA-KN-8428 
       12.33        63.25        12.99        49.25         0.99        52.27 
TCGA-KO-8408 TCGA-A3-3316 TCGA-A3-3320 TCGA-A3-3346 TCGA-A3-3352 TCGA-A3-3367 
       16.67        49.08        49.58         4.50        18.44        74.63 
TCGA-A3-3380 TCGA-AK-3436 TCGA-AK-3458 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4698 
       18.64       109.51        38.40         3.32         1.41         1.38 
TCGA-B0-4710 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4821 TCGA-B0-4822 
       57.70        46.59         0.59         5.52        40.44        36.53 
TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-5084 
       10.09        40.70        10.29        65.29        36.85         7.30 
TCGA-B0-5095 TCGA-B0-5098 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5699 TCGA-B0-5701 
        8.05        52.08        38.63        41.88       126.28        80.91 
TCGA-B0-5709 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-5158 TCGA-B8-5549 
      130.65         5.46        23.31        16.80        40.04         6.38 
TCGA-BP-4161 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4787 
       90.28        62.86        31.89        13.15        10.82        15.78 
TCGA-BP-4985 TCGA-BP-5173 TCGA-BP-5183 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4643 
       31.30         2.04        42.44        33.47        19.82        58.95 
TCGA-CJ-4644 TCGA-CJ-4870 TCGA-CJ-4881 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4907 
       11.05        49.25        66.21       109.84        51.29        49.28 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6028 TCGA-CW-5580 TCGA-CW-5588 
      133.71        25.71        22.32        53.42        64.57        66.31 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4866 
       83.90        18.77        47.08        69.21         6.77       107.41 
TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-EU-5907 TCGA-2Z-A9JI 
       90.54        10.85        84.30        31.10         4.18        51.52 
TCGA-4A-A93X TCGA-5P-A9K3 TCGA-5P-A9K9 TCGA-A4-7287 TCGA-A4-8098 TCGA-A4-A57E 
       12.82        15.48        19.36        19.63        29.46         8.48 
TCGA-B1-7332 TCGA-B3-3926 TCGA-B3-4104 TCGA-BQ-5876 TCGA-BQ-5882 TCGA-BQ-5890 
       37.51        29.03        34.49        19.27        21.63         7.66 
TCGA-BQ-5894 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-7501 
        2.76        79.86        10.68        13.08         0.43        20.52 
TCGA-GL-7966 TCGA-HE-7130 TCGA-HE-A5NK TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5E8 
        3.68        58.19        73.25         2.04        10.55        42.94 
TCGA-P4-A5EA TCGA-P4-AAVK TCGA-Q2-A5QZ TCGA-SX-A7SS TCGA-UN-AAZ9 
        6.61        52.27        14.07        53.10        18.02 

$`DEL PEAK 10(4Q34.3) WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-5088 TCGA-B0-5693 
      109.91        58.49        28.73        22.45        18.51       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 
       15.78        70.68       119.38       126.05        24.82        25.91 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4327 TCGA-BP-4331 
        8.42        15.42       111.02        94.72         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       74.17        54.77        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       31.27       105.37        26.93        27.65       108.56        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      118.85        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
        0.89        76.64        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        49.97       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-8434 
        3.55        87.12        19.33         2.50        11.21        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       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
      103.40        92.71       104.55       103.10        99.88       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
       96.62        90.48        92.55        12.66        11.90        36.82 
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-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3347 
       36.36        38.99        37.38        48.82        62.01        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        29.92        88.37        51.25        10.49        28.70 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.76        24.16        53.29        43.20        55.76        20.71 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.87        28.31        65.52        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 
       22.65         0.10         0.10        11.18        10.62        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
      117.80       122.56       109.41        15.78        73.68       112.08 
TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       68.61        94.19        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       94.29        83.21        37.58        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
       40.70         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
       19.00         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4816 TCGA-B0-4817 
        6.64         3.25        58.45        15.72        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 
       16.77         6.02        14.93        54.48        29.10        78.44 
TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       68.71        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 
       10.52        39.45        26.07        29.03         2.27        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5092 
       20.94        43.30        11.24        11.90        25.32        15.09 
TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
       10.95         2.24        21.86        15.95        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        58.59        19.30        66.05 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       56.98        42.41       111.52       129.67        85.78        86.47 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5710 TCGA-B0-5711 
       71.41        73.84       149.16       105.37        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       21.30        31.30        31.66        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       12.00         5.75         5.10         1.25         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.36         0.23        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       17.19        25.55        50.14        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       24.23        50.14        16.60        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       14.30        27.29        29.88        17.06         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 
       17.36        16.27        14.17        85.51       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-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        37.25        21.21        15.62         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 
       18.48        52.24        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-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 
       41.75        71.80        48.07        61.68         5.33        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 
       13.51        56.91        68.38        60.95        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 
       36.39        10.98        36.95         6.71        47.97        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         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-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
        6.35        79.30        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       74.40        38.30        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5200 TCGA-BP-5202 
       33.24        23.47        13.41        24.62        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       54.61        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       116.84        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 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       50.01        24.66        39.45        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.97        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       131.08        72.00       129.40 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 
       67.00        62.66       119.64         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-CZ-4853 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
      105.93        25.45        58.75        14.66        63.39        93.04 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       91.69        55.33        94.45        10.22        21.76        69.96 
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-A4VX 
       65.65        12.26        14.63        22.78        62.63        53.46 
TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 
       12.00        18.12         3.91         6.77         7.96        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.43        19.96        16.37        11.70 
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-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JK TCGA-2Z-A9JM 
        4.57        91.73        56.81        54.64        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y 
       24.33        31.20        29.36         5.29         0.13        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 
      106.55        49.58        90.21        22.26        78.64        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       18.21         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       16.64        30.48        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
       36.49        20.25        16.77        20.32        33.83        30.58 
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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         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-5887 
       43.20        47.80        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
       10.82         0.95         7.92       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
        3.81        40.77        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
       19.00        24.89         2.40         1.18         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 
       90.90        11.05        39.25        71.44        25.15        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
       16.31        81.93        26.01        11.84        56.75        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        12.36        12.76        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
       17.62        31.13        15.48        99.78        87.09        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        78.90        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       41.62        26.47        43.76        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      125.29        37.35        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                         0.43                          0.07 
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                       133.71                        194.79 
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                        31.30                         36.39 
[1] "0.4 - 133.7 (31.3)" "0.1 - 194.8 (36.4)"
[1] "hr=" "2.5"
D19V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 10(4Q34.3) MUTATED        26       10        48       26
  DEL PEAK 10(4Q34.3) WILD-TYPE     428       93       142       78
D19V3, multiclass
           clus
vv          DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  STAGE I                            26                           428
  STAGE II                           10                            93
  STAGE III                          48                           142
  STAGE IV                           26                            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 10(4Q34.3) MUTATED    29  15  62   7
  DEL PEAK 10(4Q34.3) WILD-TYPE 451 112 196   8
D19V4, multiclass
    clus
vv   DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  T1                          29                           451
  T2                          15                           112
  T3                          62                           196
  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 10(4Q34.3) MUTATED    40  15   1
  DEL PEAK 10(4Q34.3) WILD-TYPE 283  29   5
D19V5, multiclass
    clus
vv   DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  N0                          40                           283
  N1                          15                            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"
D19V6, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q34.3) MUTATED    71  21
  DEL PEAK 10(4Q34.3) WILD-TYPE 475  68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q34.3) MUTATED     71   21
  DEL PEAK 10(4Q34.3) WILD-TYPE  475   68
   clus
vv  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  0                          71                           475
  1                          21                            68
[1] 2 2
[1] FALSE
D19V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q34.3) MUTATED    39  74
  DEL PEAK 10(4Q34.3) WILD-TYPE 253 516
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q34.3) MUTATED     39   74
  DEL PEAK 10(4Q34.3) WILD-TYPE  253  516
        clus
vv       DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  FEMALE                          39                           253
  MALE                            74                           516
[1] 2 2
[1] FALSE
D19V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q34.3) MUTATED    41   0
  DEL PEAK 10(4Q34.3) WILD-TYPE 367   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q34.3) MUTATED     41    0
  DEL PEAK 10(4Q34.3) WILD-TYPE  367    3
     clus
vv    DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  NO                           41                           367
  YES                           0                             3
[1] 2 2
[1] FALSE
D19V9, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK 10(4Q34.3) MUTATED                    3
  DEL PEAK 10(4Q34.3) WILD-TYPE                 63
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 10(4Q34.3) MUTATED                                  78
  DEL PEAK 10(4Q34.3) WILD-TYPE                               450
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 10(4Q34.3) MUTATED                                      32
  DEL PEAK 10(4Q34.3) WILD-TYPE                                   256
D19V10, multiclass
                                       clus
vv                                      DEL PEAK 10(4Q34.3) MUTATED
  KIDNEY CHROMOPHOBE                                              3
  KIDNEY CLEAR CELL RENAL CARCINOMA                              78
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          32
                                       clus
vv                                      DEL PEAK 10(4Q34.3) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               63
  KIDNEY CLEAR CELL RENAL CARCINOMA                               450
  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"
D19V11, continuous
D19V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(4Q34.3) MUTATED                                  0     4
  DEL PEAK 10(4Q34.3) WILD-TYPE                                2    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(4Q34.3) MUTATED                           8    95
  DEL PEAK 10(4Q34.3) WILD-TYPE                       113   624
D19V13, multiclass
                                  clus
vv                                 DEL PEAK 10(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     95
                                  clus
vv                                 DEL PEAK 10(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                  113
  WHITE                                                      624
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q34.3) MUTATED     7  80
  DEL PEAK 10(4Q34.3) WILD-TYPE  35 542
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q34.3) MUTATED      7   80
  DEL PEAK 10(4Q34.3) WILD-TYPE   35  542
                        clus
vv                       DEL PEAK 10(4Q34.3) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                          80
                        clus
vv                       DEL PEAK 10(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                35
  NOT HISPANIC OR LATINO                           542
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK 11(5P15.33) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 11(5P15.33) MUTATED    21   9
  DEL PEAK 11(5P15.33) WILD-TYPE 627 219
  DEL PEAK 11(5P15.33) MUTATED DEL PEAK 11(5P15.33) WILD-TYPE 
                            30                            846 
  DEL PEAK 11(5P15.33) MUTATED DEL PEAK 11(5P15.33) WILD-TYPE 
                             9                            219 
$`DEL PEAK 11(5P15.33) MUTATED`
TCGA-KM-8442 TCGA-2Z-A9JJ TCGA-KL-8324 TCGA-KL-8330 TCGA-KL-8341 TCGA-KL-8346 
       47.24        39.88       153.73       108.62        24.79        62.37 
TCGA-KM-8438 TCGA-KN-8431 TCGA-KO-8405 TCGA-KO-8409 TCGA-AK-3433 TCGA-B0-5107 
      151.96        19.33       100.47       104.55       112.08        30.48 
TCGA-B8-4143 TCGA-BP-4332 TCGA-BP-5010 TCGA-CJ-4901 TCGA-CZ-5469 TCGA-CZ-5988 
       23.31        37.25        28.87        47.67        31.10        22.78 
TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-A4-7286 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5894 
       59.01        91.73        18.21        63.72        22.92         2.76 
TCGA-F9-A4JJ TCGA-G7-6793 TCGA-GL-7773 TCGA-HE-7129 TCGA-P4-A5E6 TCGA-P4-A5EA 
       10.68        11.05        12.92        81.93        99.78         6.61 

$`DEL PEAK 11(5P15.33) WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KO-8411 TCGA-A3-3307 
      102.81        28.11        23.28        28.80       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       38.47        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       58.49        28.73        22.45        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 
      111.02        94.72        32.61         3.58        80.68        74.17 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       54.77        12.33        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
       53.26       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       70.13        23.01        75.42        34.85        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 
       15.91        15.62         6.74        38.07        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
      137.06        90.48        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-8342 
       92.55        30.25        44.84        86.56        66.54        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       71.41        28.80        54.74        44.91        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-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       87.12         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87       105.47        10.68       103.40        92.71        16.67 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        99.88       105.60        96.62        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82         0.53        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        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       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       48.36        78.64        40.01        94.29        83.21        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        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-B0-4819 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        10.52        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-B0-5092 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-B0-5108 
       15.95        62.89        90.87        90.48        52.54        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
      111.52       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 
       31.96        21.30        31.30        31.66        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67        12.00         5.75         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
        4.64         5.46         0.36         0.23        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         4.93        17.36 
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-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-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       62.07        21.21        15.62         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       52.24        62.86        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
        5.98        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        13.51        56.91        68.38 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       60.95        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       58.68        60.30        61.22         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         6.94        47.11 
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-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 
       38.70        37.02        37.48        35.21         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
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-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      106.16       114.41        54.61        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 
      116.84        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 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        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       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        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       122.83        62.10        73.35        67.00 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35       105.93        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 
       47.08        69.21        58.75         6.77        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        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-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       12.26        14.63        62.63        53.46        12.00        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
        3.91         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
        2.01        19.43        19.96        16.37        11.70         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE 
       75.55        58.22       100.27        56.91         4.57        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
       49.58        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       62.93        43.04        19.36        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       67.43        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46         9.63        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5880 
       17.49        12.30        86.76        19.27         8.88        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 
       10.82         7.66         0.95         7.92       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF 
       74.60        34.19        19.00        24.89        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
        1.18         0.43         4.01        51.78        90.90        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 
       23.08        16.90        80.65       194.79         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7130 
        1.05        12.43        12.89        11.21        16.31        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5E8 
       20.25        17.62        31.13        15.48        87.09        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  DEL PEAK 11(5P15.33) MUTATED DEL PEAK 11(5P15.33) WILD-TYPE 
                          2.76                           0.07 
  DEL PEAK 11(5P15.33) MUTATED DEL PEAK 11(5P15.33) WILD-TYPE 
                        153.73                         194.79 
  DEL PEAK 11(5P15.33) MUTATED DEL PEAK 11(5P15.33) WILD-TYPE 
                        38.565                         35.885 
[1] "2.8 - 153.7 (38.6)" "0.1 - 194.8 (35.9)"
[1] "hr=" "1"  
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 11(5P15.33) MUTATED         6       10         9        5
  DEL PEAK 11(5P15.33) WILD-TYPE     448       93       181       99
D20V3, multiclass
           clus
vv          DEL PEAK 11(5P15.33) MUTATED DEL PEAK 11(5P15.33) WILD-TYPE
  STAGE I                              6                            448
  STAGE II                            10                             93
  STAGE III                            9                            181
  STAGE IV                             5                             99
[1] 4 2
[1] 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(5P15.33) MUTATED     7  11  13   0
  DEL PEAK 11(5P15.33) WILD-TYPE 473 116 245  15
D20V4, multiclass
    clus
vv   DEL PEAK 11(5P15.33) MUTATED DEL PEAK 11(5P15.33) WILD-TYPE
  T1                            7                            473
  T2                           11                            116
  T3                           13                            245
  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 11(5P15.33) MUTATED    13   5   2
  DEL PEAK 11(5P15.33) WILD-TYPE 310  39   4
D20V5, multiclass
    clus
vv   DEL PEAK 11(5P15.33) MUTATED DEL PEAK 11(5P15.33) WILD-TYPE
  N0                           13                            310
  N1                            5                             39
  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 11(5P15.33) MUTATED    16   3
  DEL PEAK 11(5P15.33) WILD-TYPE 530  86
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(5P15.33) MUTATED     16    3
  DEL PEAK 11(5P15.33) WILD-TYPE  530   86
   clus
vv  DEL PEAK 11(5P15.33) MUTATED DEL PEAK 11(5P15.33) WILD-TYPE
  0                           16                            530
  1                            3                             86
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                               0   1
  DEL PEAK 11(5P15.33) MUTATED    14  17
  DEL PEAK 11(5P15.33) WILD-TYPE 278 573
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(5P15.33) MUTATED     14   17
  DEL PEAK 11(5P15.33) WILD-TYPE  278  573
        clus
vv       DEL PEAK 11(5P15.33) MUTATED DEL PEAK 11(5P15.33) WILD-TYPE
  FEMALE                           14                            278
  MALE                             17                            573
[1] 2 2
[1] FALSE
D20V8, binary
                                cls
clus                               0   1
  DEL PEAK 11(5P15.33) MUTATED    20   0
  DEL PEAK 11(5P15.33) WILD-TYPE 388   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(5P15.33) MUTATED     20    0
  DEL PEAK 11(5P15.33) WILD-TYPE  388    3
     clus
vv    DEL PEAK 11(5P15.33) MUTATED DEL PEAK 11(5P15.33) WILD-TYPE
  NO                            20                            388
  YES                            0                              3
[1] 2 2
[1] FALSE
D20V9, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  DEL PEAK 11(5P15.33) MUTATED                   10
  DEL PEAK 11(5P15.33) WILD-TYPE                 56
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 11(5P15.33) MUTATED                                   8
  DEL PEAK 11(5P15.33) WILD-TYPE                               520
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 11(5P15.33) MUTATED                                      13
  DEL PEAK 11(5P15.33) WILD-TYPE                                   275
D20V10, multiclass
                                       clus
vv                                      DEL PEAK 11(5P15.33) MUTATED
  KIDNEY CHROMOPHOBE                                              10
  KIDNEY CLEAR CELL RENAL CARCINOMA                                8
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           13
                                       clus
vv                                      DEL PEAK 11(5P15.33) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                56
  KIDNEY CLEAR CELL RENAL CARCINOMA                                520
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            275
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, continuous
D20V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(5P15.33) MUTATED                                  0     1
  DEL PEAK 11(5P15.33) WILD-TYPE                                2    15
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(5P15.33) MUTATED                           3    23
  DEL PEAK 11(5P15.33) WILD-TYPE                       118   696
D20V13, multiclass
                                  clus
vv                                 DEL PEAK 11(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      23
                                  clus
vv                                 DEL PEAK 11(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        15
  BLACK OR AFRICAN AMERICAN                                   118
  WHITE                                                       696
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V14, binary
                                cls
clus                               0   1
  DEL PEAK 11(5P15.33) MUTATED     3  18
  DEL PEAK 11(5P15.33) WILD-TYPE  39 604
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(5P15.33) MUTATED      3   18
  DEL PEAK 11(5P15.33) WILD-TYPE   39  604
                        clus
vv                       DEL PEAK 11(5P15.33) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           18
                        clus
vv                       DEL PEAK 11(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                 39
  NOT HISPANIC OR LATINO                            604
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK 12(6Q26) MUTATION ANALYSIS
D21V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 12(6Q26) MUTATED   168  64
  DEL PEAK 12(6Q26) WILD-TYPE 480 164
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        232                         644 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                         64                         164 
$`DEL PEAK 12(6Q26) MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3336 TCGA-AK-3454 
      102.81        28.11        47.24       130.13        34.29        28.73 
TCGA-B0-4707 TCGA-B0-4712 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       19.73        43.96        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4353 TCGA-BP-4775 TCGA-BP-4986 TCGA-BP-4993 TCGA-BP-5178 
       74.17        12.33        60.59        25.81         5.82        62.86 
TCGA-BP-5181 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-DV-5565 
       49.15        31.79        31.27       108.56       118.85        43.69 
TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5575 TCGA-G6-A8L7 TCGA-2Z-A9JJ TCGA-5P-A9JU 
       12.16        37.15        56.84        70.13        39.88        12.26 
TCGA-B9-A44B TCGA-BQ-5888 TCGA-BQ-7056 TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       11.87        13.25        20.12        38.07       153.73        23.84 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       24.79        73.91        54.74       151.96        44.91        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       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       92.71        16.67       104.55       105.60        96.62        90.48 
TCGA-KO-8417 TCGA-A3-3306 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
       92.55        36.82        24.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3374 
       49.58        62.01         4.50        52.93        18.44        43.20 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3426 TCGA-AK-3430 TCGA-AK-3433 
       18.64        18.87         0.10        29.10        15.78       112.08 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3458 TCGA-AK-3461 
       68.61       109.51        94.19        40.01        38.40        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4698 
       12.13        40.70         1.41         3.48        28.47         1.38 
TCGA-B0-4699 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4828 
        3.62        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        58.59        52.87        51.02        42.41        71.41 
TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 
       32.61        21.57        12.00         5.10         0.53         5.46 
TCGA-B8-4143 TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-A54G TCGA-BP-4167 
       23.31        49.97        25.55        40.04         1.74        89.36 
TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4334 TCGA-BP-4346 TCGA-BP-4352 TCGA-BP-4761 
       64.27        97.45        21.21        49.08        11.31         5.98 
TCGA-BP-4768 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4959 
       13.15        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         6.94        46.45 
TCGA-BP-4987 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 
       36.95        16.47        43.00        18.51         6.35        30.64 
TCGA-BP-5180 TCGA-BP-5185 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4643 TCGA-CJ-4871 
       74.40        37.22       115.00        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-4907 TCGA-CJ-5675 
       24.66        39.45       109.84        47.67        49.28       129.40 
TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5584 
      133.71        22.32        25.25        53.42       119.64         5.39 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4864 
       85.78        66.31        25.45        69.21        58.75        93.04 
TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5465 
      107.41        58.82        79.63        94.45        10.22        84.30 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-EU-5907 TCGA-G6-A8L8 
       80.19        67.96        65.65        14.63         4.18        35.87 
TCGA-MM-A563 TCGA-MW-A4EC TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-5P-A9K9 
       19.43        16.37        91.73        54.64        51.52        19.36 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-B3-3926 TCGA-BQ-5875 TCGA-BQ-5882 TCGA-BQ-5890 
       67.43        18.21        29.03        86.76        21.63         7.66 
TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LC 
       19.00        13.08         4.01        11.05        25.84        23.08 
TCGA-GL-7966 TCGA-HE-7130 TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EB TCGA-Q2-A5QZ 
        3.68        58.19         2.04        10.55        99.12        14.07 
TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-UZ-A9PQ TCGA-Y8-A896 
       27.06        18.02        86.27        18.64 

$`DEL PEAK 12(6Q26) WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3343 TCGA-A3-3358 
       23.28        28.80        47.21        38.47        31.07        42.97 
TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3455 TCGA-B0-4815 TCGA-B0-5088 
       82.32       109.91        58.49        22.45        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
       24.82        25.91         1.18         8.42        15.42       111.02 
TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 
       54.77        77.62        44.15        11.64        20.38        37.25 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4995 TCGA-BP-4999 
        6.94        61.51        53.65        27.22        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5189 TCGA-BP-5199 TCGA-CJ-4636 
       27.62        35.90        48.10        27.02        44.55        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CW-6093 
      105.37        26.93        27.65        53.26        75.58       103.43 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5566 TCGA-DV-5567 
       46.16         0.59       107.54         5.46        45.96        65.88 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-MM-A84U TCGA-2Z-A9J9 
       11.67        66.28        23.90        81.21        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JV 
       34.85        33.07        25.58        16.18        22.49        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 
       21.67        27.68        21.07        10.16        21.86        19.23 
TCGA-BQ-5886 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7058 
       26.04        11.97        96.92        44.84        26.27        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8326 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 
       15.62         6.74       109.22        71.41        28.80        62.37 
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-A3-3308 
      100.87       103.10        99.88        12.66        11.90         0.53 
TCGA-A3-3311 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
       39.16        48.59        36.36        38.99        37.38        48.82 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        29.92        88.37        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-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
        0.10        11.18        10.62       117.80       122.56       109.41 
TCGA-AK-3431 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
       73.68        46.78        48.36        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 
       37.58        82.45         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        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4816 
        6.64         3.25        58.45        46.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4827 
       33.50        16.77         6.02        40.44        14.93        29.10 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       78.44        68.71        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-4945 
       10.52        65.29        39.45        26.07        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5092 
       20.94        43.30        11.24        11.90        25.32        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-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5110 
       62.89        90.48        52.54        30.48        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       38.63        52.73        41.88        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       56.98       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       80.91        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
      131.15        89.49        91.46        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5378 
       21.30        31.30        31.66        32.98        16.67         5.75 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4151 
        1.25         4.64         0.36         0.23        16.80        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 
       25.05        45.37        17.19        50.14        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        4.93        17.36        16.27        14.17        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 
      101.06        93.34        99.85         0.43        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       62.24        61.78        54.90        53.42        27.78        62.07 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       37.25        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 
       62.86        44.94        12.23        31.89        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       12.30        72.59        77.98        41.75        71.80        48.07 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4784 
       61.68        10.82         5.33        61.97        13.51        60.95 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       48.95        36.53        10.98        36.95         6.71        47.97 
TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       63.62        61.22         6.74        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       49.38        45.50        47.11        14.93        36.07        33.34 
TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5004 
       31.30         3.88        46.45        30.64        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       37.48        35.21        28.87        79.30         2.04        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-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       19.82        34.95         0.95        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
      114.41        54.61        11.05        21.24        83.97        49.25 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       74.27        75.06       116.84        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4899 TCGA-CJ-4900 
       64.18        51.52        63.98       115.69        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       131.08        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       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       67.00        62.66         7.36        64.57        92.02        81.83 
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-6097 TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-5451 
       18.77        47.08         6.77        14.66        63.39        63.42 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        90.54        91.69        55.33 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.85        21.76        69.96        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX 
       31.10        12.69        12.26        22.78        62.63        53.46 
TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 
       12.00        18.12         3.91         6.77         7.96        10.29 
TCGA-GK-A6C7 TCGA-MM-A564 TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
        2.01        19.96        11.70         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JK 
       58.22       100.27        56.91         4.57        56.81        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       78.64        15.48        71.80        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       12.39        27.09        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 
        8.28        12.46         9.63        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       20.25        16.77        20.32        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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        12.30        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        47.80        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       10.82         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY 
       74.60        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        90.90        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       20.52        25.25        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        81.93        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD 
       22.26        21.34        12.36        12.76        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94         6.61        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM 
       78.90        47.90        49.45        44.61        28.80        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY 
       31.73        26.01        39.06        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        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 
                     153.73                      194.79 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                     44.400                      31.695 
[1] "0.1 - 153.7 (44.4)" "0.1 - 194.8 (31.7)"
[1] "hr=" "1.1"
D21V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 12(6Q26) MUTATED        93       43        58       35
  DEL PEAK 12(6Q26) WILD-TYPE     361       60       132       69
D21V3, multiclass
           clus
vv          DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  STAGE I                          93                         361
  STAGE II                         43                          60
  STAGE III                        58                         132
  STAGE IV                         35                          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 12(6Q26) MUTATED    96  46  85   6
  DEL PEAK 12(6Q26) WILD-TYPE 384  81 173   9
D21V4, multiclass
    clus
vv   DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  T1                        96                         384
  T2                        46                          81
  T3                        85                         173
  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    94  16   5
  DEL PEAK 12(6Q26) WILD-TYPE 229  28   1
D21V5, multiclass
    clus
vv   DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  N0                        94                         229
  N1                        16                          28
  N2                         5                           1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED   161  26
  DEL PEAK 12(6Q26) WILD-TYPE 385  63
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED    161   26
  DEL PEAK 12(6Q26) WILD-TYPE  385   63
   clus
vv  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  0                       161                         385
  1                        26                          63
[1] 2 2
[1] FALSE
D21V7, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED    81 152
  DEL PEAK 12(6Q26) WILD-TYPE 211 438
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     81  152
  DEL PEAK 12(6Q26) WILD-TYPE  211  438
        clus
vv       DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  FEMALE                        81                         211
  MALE                         152                         438
[1] 2 2
[1] FALSE
D21V8, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED   104   0
  DEL PEAK 12(6Q26) WILD-TYPE 304   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED    104    0
  DEL PEAK 12(6Q26) WILD-TYPE  304    3
     clus
vv    DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  NO                        104                         304
  YES                         0                           3
[1] 2 2
[1] FALSE
D21V9, 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                               377
                             vv
clus                          KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 12(6Q26) MUTATED                                      31
  DEL PEAK 12(6Q26) WILD-TYPE                                   257
D21V10, multiclass
                                       clus
vv                                      DEL PEAK 12(6Q26) MUTATED
  KIDNEY CHROMOPHOBE                                           51
  KIDNEY CLEAR CELL RENAL CARCINOMA                           151
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                        31
                                       clus
vv                                      DEL PEAK 12(6Q26) WILD-TYPE
  KIDNEY CHROMOPHOBE                                             15
  KIDNEY CLEAR CELL RENAL CARCINOMA                             377
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                         257
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous
D21V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(6Q26) MUTATED                                  0     6
  DEL PEAK 12(6Q26) WILD-TYPE                                2    10
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6Q26) MUTATED                          16   203
  DEL PEAK 12(6Q26) WILD-TYPE                       105   516
D21V13, multiclass
                                  clus
vv                                 DEL PEAK 12(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    6
  BLACK OR AFRICAN AMERICAN                               16
  WHITE                                                  203
                                  clus
vv                                 DEL PEAK 12(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                     10
  BLACK OR AFRICAN AMERICAN                                105
  WHITE                                                    516
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V14, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED    14 144
  DEL PEAK 12(6Q26) WILD-TYPE  28 478
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     14  144
  DEL PEAK 12(6Q26) WILD-TYPE   28  478
                        clus
vv                       DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  HISPANIC OR LATINO                            14                          28
  NOT HISPANIC OR LATINO                       144                         478
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK 13(6Q26) MUTATION ANALYSIS
D22V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 13(6Q26) MUTATED   169  64
  DEL PEAK 13(6Q26) WILD-TYPE 479 164
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                        233                         643 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         64                         164 
$`DEL PEAK 13(6Q26) MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3336 TCGA-AK-3454 
      102.81        28.11        47.24       130.13        34.29        28.73 
TCGA-B0-4707 TCGA-B0-4712 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       19.73        43.96        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4353 TCGA-BP-4775 TCGA-BP-4986 TCGA-BP-4993 TCGA-BP-5178 
       74.17        12.33        60.59        25.81         5.82        62.86 
TCGA-BP-5181 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-DV-5565 
       49.15        31.79        31.27       108.56       118.85        43.69 
TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5575 TCGA-G6-A8L7 TCGA-2Z-A9JJ TCGA-5P-A9JU 
       12.16        37.15        56.84        70.13        39.88        12.26 
TCGA-B9-A44B TCGA-BQ-5888 TCGA-BQ-7056 TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       11.87        13.25        20.12        38.07       153.73        23.84 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       24.79        73.91        54.74       151.96        44.91        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       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       92.71        16.67       104.55       105.60        96.62        90.48 
TCGA-KO-8417 TCGA-A3-3306 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
       92.55        36.82        24.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3374 
       49.58        62.01         4.50        52.93        18.44        43.20 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3426 TCGA-AK-3430 TCGA-AK-3433 
       18.64        18.87         0.10        29.10        15.78       112.08 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3458 TCGA-AK-3461 
       68.61       109.51        94.19        40.01        38.40        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4698 
       12.13        40.70         1.41         3.48        28.47         1.38 
TCGA-B0-4699 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4828 
        3.62        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        58.59        52.87        51.02        42.41        71.41 
TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 
       32.61        21.57        12.00         5.10         0.53         5.46 
TCGA-B8-4143 TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-A54G TCGA-BP-4167 
       23.31        49.97        25.55        40.04         1.74        89.36 
TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4334 TCGA-BP-4346 TCGA-BP-4352 TCGA-BP-4761 
       64.27        97.45        21.21        49.08        11.31         5.98 
TCGA-BP-4768 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4959 
       13.15        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         6.94        46.45 
TCGA-BP-4987 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 
       36.95        16.47        43.00        18.51         6.35        30.64 
TCGA-BP-5180 TCGA-BP-5185 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4643 TCGA-CJ-4871 
       74.40        37.22       115.00        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-4907 TCGA-CJ-5675 
       24.66        39.45       109.84        47.67        49.28       129.40 
TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5584 TCGA-CW-5585 
      133.71        22.32        53.42       119.64         5.39        85.78 
TCGA-CW-5588 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4864 TCGA-CZ-4866 
       66.31        25.45        69.21        58.75        93.04       107.41 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5468 
       58.82        79.63        94.45        10.22        84.30         1.94 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-EU-5907 TCGA-G6-A8L8 
       80.19        67.96        65.65        14.63         4.18        35.87 
TCGA-MM-A563 TCGA-MW-A4EC TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-5P-A9K9 
       19.43        16.37        91.73        54.64        51.52        19.36 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-B3-3926 TCGA-BQ-5875 TCGA-BQ-5882 TCGA-BQ-5890 
       67.43        18.21        29.03        86.76        21.63         7.66 
TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LC 
       19.00        13.08         4.01        11.05        25.84        23.08 
TCGA-GL-7966 TCGA-HE-7130 TCGA-IA-A40Y TCGA-J7-8537 TCGA-MH-A55W TCGA-P4-A5EB 
        3.68        58.19         2.04        10.55        34.29        99.12 
TCGA-Q2-A5QZ TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-UZ-A9PQ TCGA-Y8-A896 
       14.07        27.06        18.02        86.27        18.64 

$`DEL PEAK 13(6Q26) WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3343 TCGA-A3-3358 
       23.28        28.80        47.21        38.47        31.07        42.97 
TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3455 TCGA-B0-4815 TCGA-B0-5088 
       82.32       109.91        58.49        22.45        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
       24.82        25.91         1.18         8.42        15.42       111.02 
TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 
       54.77        77.62        44.15        11.64        20.38        37.25 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4995 TCGA-BP-4999 
        6.94        61.51        53.65        27.22        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5189 TCGA-BP-5199 TCGA-CJ-4636 
       27.62        35.90        48.10        27.02        44.55        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CW-6093 
      105.37        26.93        27.65        53.26        75.58       103.43 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5566 TCGA-DV-5567 
       46.16         0.59       107.54         5.46        45.96        65.88 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-MM-A84U TCGA-2Z-A9J9 
       11.67        66.28        23.90        81.21        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JV 
       34.85        33.07        25.58        16.18        22.49        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 
       21.67        27.68        21.07        10.16        21.86        19.23 
TCGA-BQ-5886 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7058 
       26.04        11.97        96.92        44.84        26.27        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8326 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 
       15.62         6.74       109.22        71.41        28.80        62.37 
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-A3-3308 
      100.87       103.10        99.88        12.66        11.90         0.53 
TCGA-A3-3311 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
       39.16        48.59        36.36        38.99        37.38        48.82 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        29.92        88.37        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-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
        0.10        11.18        10.62       117.80       122.56       109.41 
TCGA-AK-3431 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
       73.68        46.78        48.36        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 
       37.58        82.45         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        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4816 
        6.64         3.25        58.45        46.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4827 
       33.50        16.77         6.02        40.44        14.93        29.10 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       78.44        68.71        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-4945 
       10.52        65.29        39.45        26.07        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5092 
       20.94        43.30        11.24        11.90        25.32        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-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5110 
       62.89        90.48        52.54        30.48        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       38.63        52.73        41.88        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       56.98       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       80.91        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
      131.15        89.49        91.46        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5378 
       21.30        31.30        31.66        32.98        16.67         5.75 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4151 
        1.25         4.64         0.36         0.23        16.80        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 
       25.05        45.37        17.19        50.14        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        4.93        17.36        16.27        14.17        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 
      101.06        93.34        99.85         0.43        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       62.24        61.78        54.90        53.42        27.78        62.07 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       37.25        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 
       62.86        44.94        12.23        31.89        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       12.30        72.59        77.98        41.75        71.80        48.07 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4784 
       61.68        10.82         5.33        61.97        13.51        60.95 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       48.95        36.53        10.98        36.95         6.71        47.97 
TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       63.62        61.22         6.74        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       49.38        45.50        47.11        14.93        36.07        33.34 
TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5004 
       31.30         3.88        46.45        30.64        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       37.48        35.21        28.87        79.30         2.04        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-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       19.82        34.95         0.95        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
      114.41        54.61        11.05        21.24        83.97        49.25 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       74.27        75.06       116.84        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4899 TCGA-CJ-4900 
       64.18        51.52        63.98       115.69        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       131.08        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       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       73.35        67.00        62.66         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       81.83        73.18        78.18        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 
       83.90        18.77        47.08         6.77        14.66        63.39 
TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       63.42        79.53        23.74        18.44        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 
       55.33        10.85        21.76        69.96        22.52         2.40 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX 
       31.10        12.69        12.26        22.78        62.63        53.46 
TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 
       12.00        18.12         3.91         6.77         7.96        10.29 
TCGA-GK-A6C7 TCGA-MM-A564 TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
        2.01        19.96        11.70         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JK 
       58.22       100.27        56.91         4.57        56.81        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       78.64        15.48        71.80        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       12.39        27.09        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 
        8.28        12.46         9.63        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       20.25        16.77        20.32        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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        12.30        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        47.80        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       10.82         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY 
       74.60        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        90.90        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       20.52        25.25        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        81.93        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD 
       22.26        21.34        12.36        12.76        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        11.41        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
        6.61        92.58        52.27        16.01        50.60        78.90 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        49.45        44.61        28.80        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ 
       16.31        41.62        26.47        53.10        43.76        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       26.01        39.06        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       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 
                     153.73                      194.79 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                      43.96                       31.66 
[1] "0.1 - 153.7 (44.0)" "0.1 - 194.8 (31.7)"
[1] "hr=" "1.1"
D22V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 13(6Q26) MUTATED        94       43        58       35
  DEL PEAK 13(6Q26) WILD-TYPE     360       60       132       69
D22V3, multiclass
           clus
vv          DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  STAGE I                          94                         360
  STAGE II                         43                          60
  STAGE III                        58                         132
  STAGE IV                         35                          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 13(6Q26) MUTATED    97  46  85   6
  DEL PEAK 13(6Q26) WILD-TYPE 383  81 173   9
D22V4, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  T1                        97                         383
  T2                        46                          81
  T3                        85                         173
  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    94  16   5
  DEL PEAK 13(6Q26) WILD-TYPE 229  28   1
D22V5, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  N0                        94                         229
  N1                        16                          28
  N2                         5                           1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED   161  26
  DEL PEAK 13(6Q26) WILD-TYPE 385  63
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED    161   26
  DEL PEAK 13(6Q26) WILD-TYPE  385   63
   clus
vv  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  0                       161                         385
  1                        26                          63
[1] 2 2
[1] FALSE
D22V7, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED    80 154
  DEL PEAK 13(6Q26) WILD-TYPE 212 436
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     80  154
  DEL PEAK 13(6Q26) WILD-TYPE  212  436
        clus
vv       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  FEMALE                        80                         212
  MALE                         154                         436
[1] 2 2
[1] FALSE
D22V8, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED   105   0
  DEL PEAK 13(6Q26) WILD-TYPE 303   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED    105    0
  DEL PEAK 13(6Q26) WILD-TYPE  303    3
     clus
vv    DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  NO                        105                         303
  YES                         0                           3
[1] 2 2
[1] FALSE
D22V9, 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                               377
                             vv
clus                          KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 13(6Q26) MUTATED                                      32
  DEL PEAK 13(6Q26) WILD-TYPE                                   256
D22V10, multiclass
                                       clus
vv                                      DEL PEAK 13(6Q26) MUTATED
  KIDNEY CHROMOPHOBE                                           51
  KIDNEY CLEAR CELL RENAL CARCINOMA                           151
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                        32
                                       clus
vv                                      DEL PEAK 13(6Q26) WILD-TYPE
  KIDNEY CHROMOPHOBE                                             15
  KIDNEY CLEAR CELL RENAL CARCINOMA                             377
  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"
D22V11, continuous
D22V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(6Q26) MUTATED                                  0     6
  DEL PEAK 13(6Q26) WILD-TYPE                                2    10
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(6Q26) MUTATED                          17   203
  DEL PEAK 13(6Q26) WILD-TYPE                       104   516
D22V13, multiclass
                                  clus
vv                                 DEL PEAK 13(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    6
  BLACK OR AFRICAN AMERICAN                               17
  WHITE                                                  203
                                  clus
vv                                 DEL PEAK 13(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                     10
  BLACK OR AFRICAN AMERICAN                                104
  WHITE                                                    516
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED    14 145
  DEL PEAK 13(6Q26) WILD-TYPE  28 477
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     14  145
  DEL PEAK 13(6Q26) WILD-TYPE   28  477
                        clus
vv                       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  HISPANIC OR LATINO                            14                          28
  NOT HISPANIC OR LATINO                       145                         477
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK 14(8P23.2) MUTATION ANALYSIS
D23V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(8P23.2) MUTATED   115  69
  DEL PEAK 14(8P23.2) WILD-TYPE 533 159
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                          184                           692 
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                           69                           159 
$`DEL PEAK 14(8P23.2) MUTATED`
TCGA-KO-8411 TCGA-A3-3325 TCGA-A3-3336 TCGA-AK-3425 TCGA-B0-4707 TCGA-B0-4712 
      130.13        38.47        34.29       109.91        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5695 TCGA-B8-A54H TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4353 
       52.21        70.68         8.42        32.61         3.58        12.33 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4986 
       60.59        11.64        20.38        37.25         6.94        25.81 
TCGA-BP-5201 TCGA-CJ-4642 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 
       31.27       105.37        27.65       108.56        53.26       118.85 
TCGA-CJ-6030 TCGA-CZ-4854 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5574 
       75.58        46.16       107.54         5.46        43.69        66.28 
TCGA-DV-5575 TCGA-5P-A9JV TCGA-A4-A5Y1 TCGA-DW-5560 TCGA-SX-A7SO TCGA-KL-8327 
       56.84        67.17        12.99        48.85        41.33       137.06 
TCGA-KL-8337 TCGA-KM-8476 TCGA-KN-8424 TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8436 
       44.84       123.12        65.19         2.50       115.00        42.35 
TCGA-KO-8404 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3319 TCGA-A3-3346 
       10.68       105.60        90.48        92.55        37.15         4.50 
TCGA-A3-3365 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3382 TCGA-A3-A6NN TCGA-AK-3426 
       28.70        24.16        53.29        18.87         0.10        29.10 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3458 
       68.61       109.51        94.19        78.64        40.01        38.40 
TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4699 TCGA-B0-4703 
       40.70         3.32         1.41         4.57         3.62         5.98 
TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4819 TCGA-B0-4821 
        6.64        58.45         0.59        45.07         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4845 TCGA-B0-4849 
       36.53        40.70        27.42        53.88        65.29         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5094 TCGA-B0-5097 TCGA-B0-5102 TCGA-B0-5108 
       36.85        70.52        10.95        21.86        90.87        58.59 
TCGA-B0-5696 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 
       85.78        89.49        91.46        16.67        12.00         5.10 
TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4151 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5164 
        5.46        23.31        42.71        40.04        27.02         0.85 
TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4169 TCGA-BP-4174 
       50.14         6.38         0.53         4.93        23.05        61.78 
TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       64.27        53.42        93.99        18.48        52.24        62.86 
TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4787 
       44.94        31.89        11.31        13.15        68.38        15.78 
TCGA-BP-4798 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       10.98        87.45        71.41         6.74        57.40        14.24 
TCGA-BP-4973 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
       45.50        46.45        31.30        43.00        30.64        18.51 
TCGA-BP-5004 TCGA-BP-5169 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5182 
       37.02         6.35         2.04        30.64         9.63        38.30 
TCGA-BP-5196 TCGA-BP-5200 TCGA-CJ-4637 TCGA-CJ-4640 TCGA-CJ-4643 TCGA-CJ-4868 
       33.47        34.95        73.22       114.41        58.95        21.24 
TCGA-CJ-4870 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 
       49.25        64.27        71.87        66.21        57.83       113.46 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4912 
       51.52        63.98       109.84        51.29        49.28        54.48 
TCGA-CJ-5672 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6033 TCGA-CW-6088 TCGA-CW-6090 
       72.00        25.71        22.32         7.36       105.93        83.90 
TCGA-CZ-4860 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
        6.77        79.53        90.54        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       22.52         1.94        12.69        12.26        14.63        22.78 
TCGA-G6-A8L8 TCGA-MM-A563 TCGA-2Z-A9J3 TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-AL-3466 
       35.87        19.43        58.22        15.48        43.04         9.63 
TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4117 TCGA-BQ-5889 TCGA-F9-A7Q0 TCGA-F9-A8NY 
       37.51        29.03         0.46        10.82        13.08         1.18 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-J7-8537 TCGA-UN-AAZ9 
       23.08        16.90        10.55        18.02 

$`DEL PEAK 14(8P23.2) WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-A3-3307 
      102.81        28.11        23.28        28.80        47.24        47.21 
TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       31.07        42.97        82.32        58.49        28.73        22.45 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5698 TCGA-B0-5812 
       18.51       112.80       133.94        15.78       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 
       24.82        25.91         1.18        15.42       111.02        94.72 
TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4965 
       80.68        74.17        54.77        77.62        44.15        61.51 
TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       53.65        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       35.90        48.10        62.86        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CW-6093 TCGA-CZ-4856 TCGA-DV-5566 
       44.55        63.25        26.93       103.43         0.59        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5576 TCGA-DV-A4W0 
       65.88        12.16        11.67        37.15        23.90        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-A4-7288 TCGA-A4-7584 
       25.58        16.18        22.49        12.26        61.05        21.37 
TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
        0.89        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 
       38.07       153.73        23.84       109.22        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-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8477 
       54.74        62.37       151.96        44.91        49.97        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-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      104.52         3.55         0.99        52.27        87.12        19.33 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 
       11.21        59.08       100.87       105.47       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 
       92.71        16.67       104.55       103.10        99.88        96.62 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82         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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       37.38        48.82        62.01        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3367 TCGA-A3-3370 
       18.44        88.37        51.25        10.49        74.63        74.76 
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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        33.47        15.39        22.65         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       10.62       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
      112.08        46.78        48.36        94.29        83.21        37.58 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4694 
       82.45        72.89        12.13         1.41         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4706 
       28.47        19.00         1.38        65.10         7.82         2.14 
TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4817 
       57.70         3.25        15.72        46.59         5.52        33.50 
TCGA-B0-4818 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       16.77        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       68.71        45.30         6.71        56.68        10.52        10.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
       39.45        26.07        29.03        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 
       11.90         7.30        25.32        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        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      111.52       129.67        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       31.66        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        49.97        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5165 
       45.37        17.19        25.55        50.14        23.74        24.23 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       16.60        48.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
       17.06         1.74        17.36        16.27        14.17        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4330 
       77.03        62.24        54.90        97.45        27.78        62.07 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4346 TCGA-BP-4349 
       37.25        21.21        15.62         0.07        49.08        12.23 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
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-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 
       61.97        13.51        56.91        60.95        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 
       36.39        36.95         6.71        47.97        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 
       60.30        61.22        58.98        48.89        49.38         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4989 
       47.11        14.93        36.07        33.34        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       46.45        16.47        38.70        37.48        35.21        28.87 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5184 
       79.30        74.20        52.27        74.40        42.44        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-5198 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4638 
       24.62        19.82         0.95       115.00        46.55        14.17 
TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 
      106.16        54.61        11.05        83.97        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4887 
       74.27        75.06       116.84        61.91        64.18        30.64 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
      115.69        50.01        24.66        39.45        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 
       47.67        49.97        49.18        50.33        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 
        3.06         4.57        18.81       131.08       129.40       133.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 
       67.00        53.42        62.66       119.64        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
       74.66         1.35        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
       58.75        14.66        63.39        93.04       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 
       58.82        23.74        18.44        79.63        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5982 
       94.45        10.85        69.96         2.40        31.10        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       67.96        65.65        62.63        53.46        12.00        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-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        16.37        11.70         7.04        75.55        59.01 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 
       90.21        22.26        78.64        71.80        62.93        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
        8.48        16.31        15.75         8.28        12.46        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
       36.49        20.25        16.77        20.32        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       30.28        25.35         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       10.68         2.40         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       25.25        17.98        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 
       96.69        22.26        21.34        12.36        12.76        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.09        42.94         6.61        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       16.01        50.60        78.90        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       41.62        26.47        53.10        43.76        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
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 
                        37.20                         34.67 
[1] "0.1 - 137.1 (37.2)" "0.1 - 194.8 (34.7)"
[1] "hr=" "1.7"
D23V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 14(8P23.2) MUTATED        74       25        46       33
  DEL PEAK 14(8P23.2) WILD-TYPE     380       78       144       71
D23V3, multiclass
           clus
vv          DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  STAGE I                            74                           380
  STAGE II                           25                            78
  STAGE III                          46                           144
  STAGE IV                           33                            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 14(8P23.2) MUTATED    78  31  69   6
  DEL PEAK 14(8P23.2) WILD-TYPE 402  96 189   9
D23V4, multiclass
    clus
vv   DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  T1                          78                           402
  T2                          31                            96
  T3                          69                           189
  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    74  10   0
  DEL PEAK 14(8P23.2) WILD-TYPE 249  34   6
D23V5, multiclass
    clus
vv   DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  N0                          74                           249
  N1                          10                            34
  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"
D23V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED   131  32
  DEL PEAK 14(8P23.2) WILD-TYPE 415  57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED    131   32
  DEL PEAK 14(8P23.2) WILD-TYPE  415   57
   clus
vv  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  0                         131                           415
  1                          32                            57
[1] 2 2
[1] FALSE
D23V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED    63 121
  DEL PEAK 14(8P23.2) WILD-TYPE 229 469
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED     63  121
  DEL PEAK 14(8P23.2) WILD-TYPE  229  469
        clus
vv       DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  FEMALE                          63                           229
  MALE                           121                           469
[1] 2 2
[1] FALSE
D23V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED    56   0
  DEL PEAK 14(8P23.2) WILD-TYPE 352   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED     56    0
  DEL PEAK 14(8P23.2) WILD-TYPE  352    3
     clus
vv    DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  NO                           56                           352
  YES                           0                             3
[1] 2 2
[1] FALSE
D23V9, 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                               374
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 14(8P23.2) MUTATED                                      18
  DEL PEAK 14(8P23.2) WILD-TYPE                                   270
D23V10, multiclass
                                       clus
vv                                      DEL PEAK 14(8P23.2) MUTATED
  KIDNEY CHROMOPHOBE                                             12
  KIDNEY CLEAR CELL RENAL CARCINOMA                             154
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          18
                                       clus
vv                                      DEL PEAK 14(8P23.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               54
  KIDNEY CLEAR CELL RENAL CARCINOMA                               374
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           270
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous
D23V12, 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     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(8P23.2) MUTATED                          14   160
  DEL PEAK 14(8P23.2) WILD-TYPE                       107   559
D23V13, multiclass
                                  clus
vv                                 DEL PEAK 14(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    160
                                  clus
vv                                 DEL PEAK 14(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                  107
  WHITE                                                      559
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED    12 116
  DEL PEAK 14(8P23.2) WILD-TYPE  30 506
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED     12  116
  DEL PEAK 14(8P23.2) WILD-TYPE   30  506
                        clus
vv                       DEL PEAK 14(8P23.2) MUTATED
  HISPANIC OR LATINO                              12
  NOT HISPANIC OR LATINO                         116
                        clus
vv                       DEL PEAK 14(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                30
  NOT HISPANIC OR LATINO                           506
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK 15(9P23) MUTATION ANALYSIS
D24V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 15(9P23) MUTATED   104  92
  DEL PEAK 15(9P23) WILD-TYPE 544 136
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                        196                         680 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                         92                         136 
$`DEL PEAK 15(9P23) MUTATED`
TCGA-A3-3325 TCGA-AK-3425 TCGA-AK-3450 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       38.47       109.91        58.49        19.73        43.96        52.21 
TCGA-B0-5694 TCGA-BP-4164 TCGA-BP-4342 TCGA-BP-4353 TCGA-BP-4782 TCGA-BP-4986 
       15.78        32.61        74.17        12.33        11.64        25.81 
TCGA-BP-4995 TCGA-BP-5009 TCGA-BP-5178 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5201 
       45.07        35.90        62.86        27.02        31.79        31.27 
TCGA-CJ-4891 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CZ-4854 TCGA-DV-5576 
       26.93        53.26       118.85        75.58        46.16        23.90 
TCGA-DV-A4W0 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9JJ TCGA-A4-A5Y1 TCGA-AL-A5DJ 
       81.21        70.13        23.01        39.88        12.99        49.25 
TCGA-BQ-5888 TCGA-BQ-7056 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8332 TCGA-KL-8343 
       13.25        20.12       153.73        23.84        84.89        71.41 
TCGA-KL-8346 TCGA-KN-8427 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8415 TCGA-A3-3306 
       62.37         0.99        42.35        10.68        96.62        36.82 
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3347 
       39.16        49.08        49.02        37.15         4.50        52.93 
TCGA-A3-3352 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3426 TCGA-AK-3436 TCGA-AK-3445 
       18.44        24.16        18.87        29.10       109.51        78.64 
TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4698 TCGA-B0-4710 
       40.70         1.41         4.57         3.48         1.38        57.70 
TCGA-B0-4811 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 
       46.59        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-B0-5113 
        2.24        21.86        52.08        62.89        30.48        38.63 
TCGA-B0-5116 TCGA-B0-5402 TCGA-B0-5701 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5832 
       41.88        42.41        80.91        31.66        21.57         5.10 
TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5549 TCGA-B8-5551 
        5.46        25.55        50.14        40.04         6.38         0.53 
TCGA-BP-4161 TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 
       90.28        89.36        64.27        62.86        31.89        11.31 
TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4798 
       41.75        48.07        13.15        68.38        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-4983 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5010 TCGA-BP-5169 
       46.45        31.30        43.00        18.51        28.87         6.35 
TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4635 
       30.64        74.40        42.44        33.47        19.82        46.55 
TCGA-CJ-4638 TCGA-CJ-4871 TCGA-CJ-4881 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4895 
       14.17        79.66        66.21        51.52       115.69        39.45 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       56.35        47.67        49.28        50.33        54.48        38.56 
TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 
        4.57       131.08       133.71        25.71        22.32        25.25 
TCGA-CJ-5682 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5584 
      122.83        53.42        62.66         7.36        64.57         5.39 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 
       66.31        74.66        83.90        18.77        47.08        69.21 
TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 
        6.77        79.63        10.85        10.22        84.30        22.52 
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-DV-A4VX TCGA-G6-A5PC TCGA-MM-A563 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X 
       53.46         7.96        19.43        54.64        51.52        12.82 
TCGA-5P-A9K9 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-8516 TCGA-A4-A57E TCGA-AL-3466 
       19.36        18.21        19.63         0.76         8.48         9.63 
TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A69E TCGA-BQ-5879 TCGA-BQ-5889 TCGA-BQ-7048 
       29.03        20.61        14.86        22.92        10.82        93.34 
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        71.44        20.52 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-HE-7130 TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EA 
       23.08        16.90        58.19         2.04        10.55         6.61 
TCGA-P4-AAVL TCGA-UN-AAZ9 TCGA-UZ-A9PQ TCGA-Y8-A896 
       16.01        18.02        86.27        18.64 

$`DEL PEAK 15(9P23) WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3454 
       47.21        34.29        31.07        42.97        82.32        28.73 
TCGA-AK-3455 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 
       22.45        18.51       112.80       133.94        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4760 
      111.02        94.72         3.58        80.68        54.77        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       44.15        60.59        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 
       53.65        27.22         5.82        41.62        27.62        48.10 
TCGA-BP-5181 TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4894 TCGA-CJ-4904 
       49.15        44.55        63.25       105.37        27.65       108.56 
TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 
      103.43         0.59       107.54         5.46        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-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       75.42        34.85        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 
       12.26        67.17        61.05        21.37         0.89        76.64 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       19.23        26.04        11.97        96.92        44.84        26.27 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 
       15.91        15.62         6.74        38.07       109.22       137.06 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
       90.48       108.62        98.96        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-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       28.80        54.74       151.96        44.91        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-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 
       19.33         2.50        11.21        59.08       115.00       100.87 
TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
      105.47       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
      103.10        99.88       105.60        90.48        92.55        12.66 
TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       11.90         0.53        24.16        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3349 TCGA-A3-3351 
       38.99        37.38        48.82        62.01        45.53        29.92 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       88.37        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-A3-3383 
       53.29        43.20        55.76        20.71        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
        0.10        11.18        10.62       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68       112.08        68.61        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       48.36        40.01        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4693 
       82.45        72.89        12.13         1.41         3.32         2.53 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       28.47        19.00         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 
        2.14         6.64         3.25        58.45        15.72         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        5.52        45.07        16.77        14.93        54.48        29.10 
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-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 
       10.52        10.29        39.45        26.07         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-B0-5092 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       25.32        15.09        15.95        90.87        90.48        52.54 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
       58.59        19.30        66.05        52.73        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5692 
       38.43        48.82        46.39        56.98       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       85.78        86.47       126.28        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       32.98        16.67        12.00         5.75         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        4.64         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-5159 TCGA-B8-5163 
       42.71        25.05        45.37        17.19        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 
        0.85        24.23        50.14        16.60        48.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       14.30        27.29        29.88        17.06         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 
       17.36        16.27        14.17        85.51       101.06        93.34 
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-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.62         0.07        93.99        18.48        52.24 
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-4761 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 
       72.59        77.98         5.98        71.80        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4787 
        5.33        61.97        13.51        56.91        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4961 
       48.95        36.53        36.95        47.97        87.45        63.62 
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-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 
        6.94        47.11        14.93        36.07        33.34        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5004 
        3.88        46.45        16.47        30.64        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       37.48        35.21        79.30         2.04        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
        9.63        38.30        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5200 TCGA-BP-5202 
       33.24        23.47        13.41        24.62        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
      115.00        73.22       106.16       114.41        54.61        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       116.84        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 
      113.46        64.18        30.64        63.98        50.01        24.66 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4916 
      109.84        50.24        49.97        51.29        49.18        45.14 
TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5681 
        3.06        18.81        72.00       129.40        18.87        18.15 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
       62.10        73.35        67.00       119.64        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CZ-4853 
       85.78        73.18        78.18         1.35       105.93        25.45 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
       58.75        14.66        63.39        93.04       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5982 
       55.33        94.45        21.76        69.96         2.40        80.19 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       12.26        22.78        62.63        12.00        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 
        6.77         4.18        10.29        35.87         2.01        19.96 
TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       16.37        11.70         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JK 
      100.27        56.91         4.57        91.73        56.81        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       15.48        71.80        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       27.09        67.43         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 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        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
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-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-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       25.35         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       48.26        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        7.17         3.81        40.77        80.88        51.19        74.60 
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-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 
        0.43        51.78        90.90        39.25        25.15        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       25.25        17.98        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       81.93        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        12.36        12.76        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ 
       99.12        92.58        52.27        50.60        78.90        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY 
       31.73        26.01        39.06        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                       0.53                        0.07 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                     153.73                      194.79 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                     36.145                      35.885 
[1] "0.5 - 153.7 (36.1)" "0.1 - 194.8 (35.9)"
[1] "hr=" "2.6"
D24V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 15(9P23) MUTATED        63       16        68       46
  DEL PEAK 15(9P23) WILD-TYPE     391       87       122       58
D24V3, multiclass
           clus
vv          DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  STAGE I                          63                         391
  STAGE II                         16                          87
  STAGE III                        68                         122
  STAGE IV                         46                          58
[1] 4 2
[1] 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  23 100   7
  DEL PEAK 15(9P23) WILD-TYPE 412 104 158   8
D24V4, multiclass
    clus
vv   DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  T1                        68                         412
  T2                        23                         104
  T3                       100                         158
  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    73  20   3
  DEL PEAK 15(9P23) WILD-TYPE 250  24   3
D24V5, multiclass
    clus
vv   DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  N0                        73                         250
  N1                        20                          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"
D24V6, binary
                             cls
clus                            0   1
  DEL PEAK 15(9P23) MUTATED   126  38
  DEL PEAK 15(9P23) WILD-TYPE 420  51
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED    126   38
  DEL PEAK 15(9P23) WILD-TYPE  420   51
   clus
vv  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  0                       126                         420
  1                        38                          51
[1] 2 2
[1] FALSE
D24V7, binary
                             cls
clus                            0   1
  DEL PEAK 15(9P23) MUTATED    60 138
  DEL PEAK 15(9P23) WILD-TYPE 232 452
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED     60  138
  DEL PEAK 15(9P23) WILD-TYPE  232  452
        clus
vv       DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  FEMALE                        60                         232
  MALE                         138                         452
[1] 2 2
[1] FALSE
D24V8, binary
                             cls
clus                            0   1
  DEL PEAK 15(9P23) MUTATED    61   1
  DEL PEAK 15(9P23) WILD-TYPE 347   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED     61    1
  DEL PEAK 15(9P23) WILD-TYPE  347    2
     clus
vv    DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  NO                         61                         347
  YES                         1                           2
[1] 2 2
[1] FALSE
D24V9, 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                                 152
  DEL PEAK 15(9P23) WILD-TYPE                               376
                             vv
clus                          KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 15(9P23) MUTATED                                      36
  DEL PEAK 15(9P23) WILD-TYPE                                   252
D24V10, multiclass
                                       clus
vv                                      DEL PEAK 15(9P23) MUTATED
  KIDNEY CHROMOPHOBE                                           10
  KIDNEY CLEAR CELL RENAL CARCINOMA                           152
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                        36
                                       clus
vv                                      DEL PEAK 15(9P23) WILD-TYPE
  KIDNEY CHROMOPHOBE                                             56
  KIDNEY CLEAR CELL RENAL CARCINOMA                             376
  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"
D24V11, continuous
D24V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(9P23) MUTATED                                  0     4
  DEL PEAK 15(9P23) WILD-TYPE                                2    12
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(9P23) MUTATED                          15   173
  DEL PEAK 15(9P23) WILD-TYPE                       106   546
D24V13, multiclass
                                  clus
vv                                 DEL PEAK 15(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               15
  WHITE                                                  173
                                  clus
vv                                 DEL PEAK 15(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                     12
  BLACK OR AFRICAN AMERICAN                                106
  WHITE                                                    546
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                             cls
clus                            0   1
  DEL PEAK 15(9P23) MUTATED     8 136
  DEL PEAK 15(9P23) WILD-TYPE  34 486
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED      8  136
  DEL PEAK 15(9P23) WILD-TYPE   34  486
                        clus
vv                       DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  HISPANIC OR LATINO                             8                          34
  NOT HISPANIC OR LATINO                       136                         486
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK 16(9P21.3) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(9P21.3) MUTATED   107  99
  DEL PEAK 16(9P21.3) WILD-TYPE 541 129
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          206                           670 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                           99                           129 
$`DEL PEAK 16(9P21.3) MUTATED`
TCGA-A3-3325 TCGA-AK-3425 TCGA-AK-3450 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       38.47       109.91        58.49        19.73        43.96        52.21 
TCGA-B0-5694 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4342 TCGA-BP-4353 TCGA-BP-4782 
       15.78        94.72        32.61        74.17        12.33        11.64 
TCGA-BP-4986 TCGA-BP-4995 TCGA-BP-5009 TCGA-BP-5178 TCGA-BP-5189 TCGA-BP-5191 
       25.81        45.07        35.90        62.86        27.02        31.79 
TCGA-BP-5201 TCGA-CJ-4891 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CZ-4854 
       31.27        26.93        53.26       118.85        75.58        46.16 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9JJ TCGA-A4-A5Y1 
       23.90        81.21        70.13        23.01        39.88        12.99 
TCGA-AL-A5DJ TCGA-BQ-5888 TCGA-BQ-7056 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8332 
       49.25        13.25        20.12       153.73        23.84        84.89 
TCGA-KL-8343 TCGA-KL-8346 TCGA-KN-8427 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8415 
       71.41        62.37         0.99        42.35        10.68        96.62 
TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3346 
       36.82        39.16        49.08        49.02        37.15         4.50 
TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3426 TCGA-AK-3436 
       52.93        18.44        24.16        18.87        29.10       109.51 
TCGA-AK-3445 TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 
       78.64        40.70         3.32         1.41         4.57         3.48 
TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4710 TCGA-B0-4811 TCGA-B0-4817 TCGA-B0-4819 
       28.47         1.38        57.70        46.59        33.50         6.02 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4842 TCGA-B0-4845 
       40.44        36.53        10.09        40.70        56.68        65.29 
TCGA-B0-4848 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       29.03        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5100 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5121 
       62.89        30.48        19.30        38.63        41.88        48.82 
TCGA-B0-5402 TCGA-B0-5701 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5838 
       42.41        80.91        31.66        21.57         5.10         5.46 
TCGA-B8-4143 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5549 TCGA-B8-5550 
       23.31        25.55        50.14        40.04         6.38        48.53 
TCGA-B8-5551 TCGA-BP-4161 TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4343 TCGA-BP-4351 
        0.53        90.28        89.36        64.27        62.86        31.89 
TCGA-BP-4352 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4781 
       11.31         5.98        41.75        48.07        13.15        68.38 
TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4962 
       15.78        36.39        10.98         6.71        71.41        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5000 
       60.30        61.22        45.50        31.30        43.00        18.51 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5196 
       28.87         6.35        30.64        74.40        42.44        33.47 
TCGA-BP-5198 TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4868 TCGA-CJ-4871 TCGA-CJ-4881 
       19.82        46.55        14.17        21.24        79.66        66.21 
TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4907 
       51.52       115.69        39.45        56.35        47.67        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       50.33        54.48        38.56         4.57        18.81       131.08 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-6028 
      133.71        25.71        22.32        25.25       122.83        53.42 
TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-5588 TCGA-CW-6090 
       62.66         7.36        64.57         5.39        66.31        83.90 
TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5461 
       18.77        47.08        69.21         6.77        79.63        10.85 
TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 
       10.22        84.30        22.52         1.94        31.10        67.96 
TCGA-CZ-5985 TCGA-CZ-5987 TCGA-G6-A5PC TCGA-MM-A563 TCGA-2Z-A9JG TCGA-2Z-A9JI 
       65.65        14.63         7.96        19.43        54.64        51.52 
TCGA-4A-A93X TCGA-5P-A9K9 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-A57E TCGA-AL-3466 
       12.82        19.36        18.21        19.63         8.48         9.63 
TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5889 
       29.03        20.61        14.86         8.88        22.92        10.82 
TCGA-BQ-7048 TCGA-DZ-6131 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 
       93.34        79.86        13.08         4.01        11.05        71.44 
TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-HE-7130 TCGA-IA-A40Y 
       20.52        23.08        16.90         3.68        58.19         2.04 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-SX-A71V TCGA-UN-AAZ9 
       10.55        10.09         6.61        16.01        28.80        18.02 
TCGA-UZ-A9PQ TCGA-Y8-A896 
       86.27        18.64 

$`DEL PEAK 16(9P21.3) WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3454 
       47.21        34.29        31.07        42.97        82.32        28.73 
TCGA-AK-3455 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 
       22.45        18.51       112.80       133.94        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 
      111.02         3.58        80.68        54.77        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       60.59        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5181 
       27.22         5.82        41.62        27.62        48.10        49.15 
TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CW-6093 
       44.55        63.25       105.37        27.65       108.56       103.43 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        0.59       107.54         5.46        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-2Z-A9J9 
       12.16        11.67        37.15        66.28        56.84        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU 
       34.85        33.07        25.58        16.18        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-B1-A47M 
       67.17        61.05        21.37         0.89        76.64        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7058 
       26.04        11.97        96.92        44.84        26.27        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       15.62         6.74        38.07       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        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-8344 
       44.84        86.56        66.54        24.79        73.91        28.80 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       54.74       151.96        44.91        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-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-8437 TCGA-KO-8403 
        2.50        11.21        59.08       115.00       100.87       105.47 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
      100.47       103.40        92.71        16.67       104.55       103.10 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       99.88       105.60        90.48        92.55        12.66        11.90 
TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
        0.53        24.16        49.58        48.59        36.36        38.99 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
       37.38        48.82        62.01        45.53        29.92        88.37 
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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       11.18        10.62       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       73.68       112.08        68.61        94.19        46.78        48.36 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       40.01        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4699 
       72.89        12.13         1.41         2.53        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 
       58.45        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        10.52        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-B0-5092 TCGA-B0-5099 
       11.24        11.90         7.30        25.32        15.09        15.95 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 
       90.87        90.48        52.54        58.59        66.05        52.73 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 
       52.87        51.02        38.43        46.39        56.98       111.52 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 
      129.67        85.78        86.47       126.28        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       31.30        32.98        16.67        12.00         5.75         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
        0.53         4.64         0.36         0.23        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-5159 TCGA-B8-5163 
       42.71        25.05        45.37        17.19        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 
        0.85        24.23        50.14        16.60        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         4.93        17.36 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       16.27        14.17        85.51       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-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
       97.45        53.42        27.78        62.07        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 
       15.62         0.07        93.99        18.48        52.24        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       44.94        12.23        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       77.98        71.80        61.68        10.82         5.33        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4801 
       13.51        56.91        60.95        48.95        36.53        36.95 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       47.97        87.45        63.62         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       14.24        48.89        49.38         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       36.07        33.34        46.45        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       16.47        30.64        38.70        37.02        37.48        35.21 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5182 
       79.30         2.04        74.20        52.27         9.63        38.30 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4637 
       13.41        24.62        34.95         0.95       115.00        73.22 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4869 
      106.16       114.41        54.61        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       116.84        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       113.46        64.18        30.64 
TCGA-CJ-4889 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 
       63.98        50.01        24.66       109.84        50.24        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-5672 TCGA-CJ-5675 
       51.29        49.18        45.14         3.06        72.00       129.40 
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       119.64 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        73.18        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CZ-4853 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
        1.35       105.93        25.45        58.75        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 
       18.44        90.54        91.69        55.33        94.45        21.76 
TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 
       69.96         2.40        12.69        80.19        12.26        22.78 
TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       62.63        53.46        12.00        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        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM 
       56.91         4.57        91.73        56.81        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y 
       24.33        31.20        29.36         5.29         0.13        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       67.43         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
       16.96        16.31        15.75         8.28        12.46        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 
       17.49        12.30        86.76        19.27        63.72        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
        3.81        40.77        80.88        51.19        74.60        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        90.90        39.25        25.15        25.84        25.25 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH 
       12.43        12.89        11.21        16.31        81.93        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.09        42.94        99.12        92.58        52.27 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       53.10        43.76        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                         0.53                          0.07 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                       153.73                        194.79 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                        31.84                         36.51 
[1] "0.5 - 153.7 (31.8)" "0.1 - 194.8 (36.5)"
[1] "hr=" "2.8"
D25V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 16(9P21.3) MUTATED        66       15        73       50
  DEL PEAK 16(9P21.3) WILD-TYPE     388       88       117       54
D25V3, multiclass
           clus
vv          DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  STAGE I                            66                           388
  STAGE II                           15                            88
  STAGE III                          73                           117
  STAGE IV                           50                            54
[1] 4 2
[1] 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    71  22 108   8
  DEL PEAK 16(9P21.3) WILD-TYPE 409 105 150   7
D25V4, multiclass
    clus
vv   DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  T1                          71                           409
  T2                          22                           105
  T3                         108                           150
  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    79  25   3
  DEL PEAK 16(9P21.3) WILD-TYPE 244  19   3
D25V5, multiclass
    clus
vv   DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  N0                          79                           244
  N1                          25                            19
  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"
D25V6, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P21.3) MUTATED   132  43
  DEL PEAK 16(9P21.3) WILD-TYPE 414  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED    132   43
  DEL PEAK 16(9P21.3) WILD-TYPE  414   46
   clus
vv  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  0                         132                           414
  1                          43                            46
[1] 2 2
[1] FALSE
D25V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P21.3) MUTATED    62 147
  DEL PEAK 16(9P21.3) WILD-TYPE 230 443
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED     62  147
  DEL PEAK 16(9P21.3) WILD-TYPE  230  443
        clus
vv       DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  FEMALE                          62                           230
  MALE                           147                           443
[1] 2 2
[1] FALSE
D25V8, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P21.3) MUTATED    64   1
  DEL PEAK 16(9P21.3) WILD-TYPE 344   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED     64    1
  DEL PEAK 16(9P21.3) WILD-TYPE  344    2
     clus
vv    DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  NO                           64                           344
  YES                           1                             2
[1] 2 2
[1] FALSE
D25V9, 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                               369
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 16(9P21.3) MUTATED                                      40
  DEL PEAK 16(9P21.3) WILD-TYPE                                   248
D25V10, multiclass
                                       clus
vv                                      DEL PEAK 16(9P21.3) MUTATED
  KIDNEY CHROMOPHOBE                                             10
  KIDNEY CLEAR CELL RENAL CARCINOMA                             159
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          40
                                       clus
vv                                      DEL PEAK 16(9P21.3) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               56
  KIDNEY CLEAR CELL RENAL CARCINOMA                               369
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, continuous
D25V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(9P21.3) MUTATED                                  0     4
  DEL PEAK 16(9P21.3) WILD-TYPE                                2    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(9P21.3) MUTATED                          15   185
  DEL PEAK 16(9P21.3) WILD-TYPE                       106   534
D25V13, multiclass
                                  clus
vv                                 DEL PEAK 16(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                    185
                                  clus
vv                                 DEL PEAK 16(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                  106
  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"
D25V14, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P21.3) MUTATED     9 145
  DEL PEAK 16(9P21.3) WILD-TYPE  33 477
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED      9  145
  DEL PEAK 16(9P21.3) WILD-TYPE   33  477
                        clus
vv                       DEL PEAK 16(9P21.3) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         145
                        clus
vv                       DEL PEAK 16(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                33
  NOT HISPANIC OR LATINO                           477
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK 17(10Q23.31) MUTATION ANALYSIS
D26V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 17(10Q23.31) MUTATED   112  51
  DEL PEAK 17(10Q23.31) WILD-TYPE 536 177
  DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE 
                            163                             713 
  DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE 
                             51                             177 
$`DEL PEAK 17(10Q23.31) MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-B0-4712 TCGA-BP-4164 
      102.81        28.11        47.24       130.13        43.96        32.61 
TCGA-BP-4342 TCGA-BP-4775 TCGA-BP-5201 TCGA-CJ-4642 TCGA-DV-5565 TCGA-DV-5566 
       74.17        60.59        31.27       105.37        43.69        45.96 
TCGA-5P-A9JU TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-MH-A857 TCGA-KL-8323 TCGA-KL-8325 
       12.26        12.99        11.87        29.26        38.07        23.84 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8440 
       24.79        73.91        71.41        54.74        62.37        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       49.97       123.12       129.37        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
      104.52        52.27        87.12         2.50        59.08       115.00 
TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       42.35       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       16.67       104.55       105.60        96.62        90.48        92.55 
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       112.08        94.19        46.78        38.40 
TCGA-AK-3461 TCGA-AK-3465 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 
       72.89        12.13         3.32         1.41         3.48        28.47 
TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4819 TCGA-B0-4828 TCGA-B0-4836 
        3.62        58.45        46.59         6.02        10.09        40.70 
TCGA-B0-4837 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-5099 TCGA-B0-5117 
       45.30        10.52        10.29        65.29        15.95        52.87 
TCGA-B0-5402 TCGA-B0-5703 TCGA-B0-5706 TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5835 
       42.41        73.84       105.37        32.61        21.57         0.53 
TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-5158 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-A7U6 
        5.46        23.31        40.04         6.38        48.53        16.27 
TCGA-BP-4161 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4329 TCGA-BP-4334 TCGA-BP-4343 
       90.28         0.43        89.36        27.78        21.21        62.86 
TCGA-BP-4351 TCGA-BP-4766 TCGA-BP-4770 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4960 
       31.89        48.07        10.82        36.39         6.71        71.41 
TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5173 
       45.50        31.30        43.00        28.87         6.35         2.04 
TCGA-BP-5180 TCGA-BP-5185 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4635 TCGA-CJ-4644 
       74.40        37.22        33.47        19.82        46.55        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       109.84        47.67 
TCGA-CJ-4907 TCGA-CJ-4923 TCGA-CJ-5676 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-6090 
       49.28        18.81       133.71       119.64         7.36        83.90 
TCGA-CZ-4860 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 
        6.77        90.54        94.45        84.30         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-EU-5907 TCGA-G6-A8L8 TCGA-2Z-A9J8 TCGA-5P-A9KH 
       12.69        80.19         4.18        35.87        91.73        67.43 
TCGA-AL-3466 TCGA-BQ-5876 TCGA-BQ-5882 TCGA-DZ-6131 TCGA-F9-A97G TCGA-G7-6789 
        9.63        19.27        21.63        79.86         0.43         4.01 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-7130 TCGA-J7-8537 
       20.52        25.84        23.08         3.68        58.19        10.55 
TCGA-Q2-A5QZ 
       14.07 

$`DEL PEAK 17(10Q23.31) WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 
       23.28        28.80        47.21        38.47        34.29        31.07 
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       42.97        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-4707 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       19.73        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4327 TCGA-BP-4331 
        8.42        15.42       111.02        94.72         3.58        80.68 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4795 
       54.77        12.33        77.62        44.15        11.64        20.38 
TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       37.25         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4636 
       62.86        49.15        27.02        31.79        44.55        63.25 
TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
       26.93        27.65       108.56        53.26       118.85        75.58 
TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5567 
      103.43        46.16         0.59       107.54         5.46        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       81.21        70.13        23.01        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JV TCGA-A4-7288 
       33.07        25.58        16.18        22.49        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
       21.37         0.89        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       21.07        10.16        21.86        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       84.89        67.17        16.34        12.13        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8344 TCGA-KM-8438 TCGA-KM-8477 
        6.74       153.73       109.22        28.80       151.96        51.06 
TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8431 
       31.33        23.47        25.91         3.55         0.99        19.33 
TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E 
       11.21       100.87       103.10        99.88        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
       36.82         0.53        39.16        24.16        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3335 
       49.58        48.59        36.36        38.99        37.38        62.01 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        29.92        88.37        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
       28.70        74.63        74.76        24.16        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       20.71        18.87        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 
       15.39        22.65         0.10        11.18        10.62        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      117.80       122.56       109.41        73.68        68.61       109.51 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       48.36        78.64        40.01        94.29        83.21        37.58 
TCGA-AK-3460 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 
       82.45        40.70         1.41         4.57         2.53        19.00 
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        1.38        65.10         7.82         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
        6.64         3.25        15.72         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-B0-4833 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-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       52.08        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 
       51.02        38.43        48.82        46.39        56.98       111.52 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      149.16       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       32.98        16.67        12.00         5.75         5.10         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        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5159 
       25.05        45.37        17.19        25.55        50.14        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 
       27.02         0.85        24.23        50.14        16.60         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 
        4.93        17.36        14.17        85.51       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       99.85        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 
       54.90        97.45        53.42        62.07        37.25        15.62 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 
        0.07        93.99        18.48        52.24        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       12.23        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4768 TCGA-BP-4769 
       77.98         5.98        41.75        71.80        13.15        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4804 
       15.78        48.95        36.53        10.98        36.95        47.97 
TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       87.45        63.62        58.68        60.30        61.22         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         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 
       47.11        14.93        36.07        33.34        46.45        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
        3.88        46.45        16.47        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
       37.02        37.48        35.21        79.30        74.20        30.64 
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-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5200 
       13.35        33.24        23.47        13.41        24.62        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
        0.95       115.00        73.22        14.17       106.16       114.41 
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-4873 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 
       74.27       116.84        64.27        71.87        66.21        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       50.01        39.45        50.24        56.35        49.97        51.29 
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-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 
        4.57       131.08        72.00       129.40        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       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       67.00        53.42        62.66        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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35       105.93        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
       58.75        14.66        63.39        93.04       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        79.63        91.69 
TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
       55.33        10.85        10.22        21.76        69.96        22.52 
TCGA-CZ-5467 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
        2.40        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       62.63        53.46        12.00        18.12         3.91         6.77 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC 
        7.96        10.29         2.01        19.43        19.96        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
       56.91         4.57        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.99        12.39        27.09        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 
       16.31        15.75         8.28        12.46        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 
        0.16        14.86        17.49        12.30        86.76         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 
       10.68        13.08         2.40         1.18        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-A4TM TCGA-G7-A8LB 
       11.05        39.25        71.44        25.15        25.25        17.98 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       16.90        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH 
       12.43        12.89        11.21        16.31        81.93        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.36        12.76        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         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 
                          43.96                           33.83 
[1] "0.1 - 137.1 (44.0)" "0.1 - 194.8 (33.8)"
[1] "hr=" "1.1"
D26V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 17(10Q23.31) MUTATED        52       32        53       26
  DEL PEAK 17(10Q23.31) WILD-TYPE     402       71       137       78
D26V3, multiclass
           clus
vv          DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE
  STAGE I                              52                             402
  STAGE II                             32                              71
  STAGE III                            53                             137
  STAGE IV                             26                              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 17(10Q23.31) MUTATED    54  33  70   7
  DEL PEAK 17(10Q23.31) WILD-TYPE 426  94 188   8
D26V4, multiclass
    clus
vv   DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE
  T1                            54                             426
  T2                            33                              94
  T3                            70                             188
  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    77  10   3
  DEL PEAK 17(10Q23.31) WILD-TYPE 246  34   3
D26V5, multiclass
    clus
vv   DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE
  N0                            77                             246
  N1                            10                              34
  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"
D26V6, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10Q23.31) MUTATED   112  19
  DEL PEAK 17(10Q23.31) WILD-TYPE 434  70
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10Q23.31) MUTATED    112   19
  DEL PEAK 17(10Q23.31) WILD-TYPE  434   70
   clus
vv  DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE
  0                           112                             434
  1                            19                              70
[1] 2 2
[1] FALSE
D26V7, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10Q23.31) MUTATED    52 112
  DEL PEAK 17(10Q23.31) WILD-TYPE 240 478
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10Q23.31) MUTATED     52  112
  DEL PEAK 17(10Q23.31) WILD-TYPE  240  478
        clus
vv       DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE
  FEMALE                            52                             240
  MALE                             112                             478
[1] 2 2
[1] FALSE
D26V8, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10Q23.31) MUTATED    84   0
  DEL PEAK 17(10Q23.31) WILD-TYPE 324   3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10Q23.31) MUTATED     84    0
  DEL PEAK 17(10Q23.31) WILD-TYPE  324    3
     clus
vv    DEL PEAK 17(10Q23.31) MUTATED DEL PEAK 17(10Q23.31) WILD-TYPE
  NO                             84                             324
  YES                             0                               3
[1] 2 2
[1] FALSE
D26V9, 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                               432
                                 vv
clus                              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 17(10Q23.31) MUTATED                                      19
  DEL PEAK 17(10Q23.31) WILD-TYPE                                   269
D26V10, multiclass
                                       clus
vv                                      DEL PEAK 17(10Q23.31) MUTATED
  KIDNEY CHROMOPHOBE                                               49
  KIDNEY CLEAR CELL RENAL CARCINOMA                                96
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            19
                                       clus
vv                                      DEL PEAK 17(10Q23.31) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                 17
  KIDNEY CLEAR CELL RENAL CARCINOMA                                 432
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                             269
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous
D26V12, 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    12
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(10Q23.31) MUTATED                          13   141
  DEL PEAK 17(10Q23.31) WILD-TYPE                       108   578
D26V13, multiclass
                                  clus
vv                                 DEL PEAK 17(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                      141
                                  clus
vv                                 DEL PEAK 17(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                         12
  BLACK OR AFRICAN AMERICAN                                    108
  WHITE                                                        578
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10Q23.31) MUTATED     9  97
  DEL PEAK 17(10Q23.31) WILD-TYPE  33 525
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10Q23.31) MUTATED      9   97
  DEL PEAK 17(10Q23.31) WILD-TYPE   33  525
                        clus
vv                       DEL PEAK 17(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                            97
                        clus
vv                       DEL PEAK 17(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  33
  NOT HISPANIC OR LATINO                             525
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK 18(11Q23.1) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(11Q23.1) MUTATED    42  28
  DEL PEAK 18(11Q23.1) WILD-TYPE 606 200
  DEL PEAK 18(11Q23.1) MUTATED DEL PEAK 18(11Q23.1) WILD-TYPE 
                            70                            806 
  DEL PEAK 18(11Q23.1) MUTATED DEL PEAK 18(11Q23.1) WILD-TYPE 
                            28                            200 
$`DEL PEAK 18(11Q23.1) MUTATED`
TCGA-KL-8328 TCGA-AK-3425 TCGA-B0-4707 TCGA-BP-4986 TCGA-BP-5201 TCGA-G6-A8L7 
      102.81       109.91        19.73        25.81        31.27        70.13 
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-PJ-A5Z8 TCGA-KL-8331 TCGA-KL-8345 
       12.99        49.25        11.87        19.73        98.96        54.74 
TCGA-KM-8443 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8434 TCGA-KN-8436 TCGA-KO-8404 
       49.97         0.99        52.27        59.08        42.35        10.68 
TCGA-A3-3316 TCGA-A3-3346 TCGA-AK-3465 TCGA-B0-4690 TCGA-B0-4696 TCGA-B0-4819 
       49.08         4.50        12.13         1.41        28.47         6.02 
TCGA-B0-4822 TCGA-B0-5084 TCGA-B0-5094 TCGA-B0-5702 TCGA-B2-5641 TCGA-B4-5832 
       36.53         7.30        10.95        71.41        21.57         5.10 
TCGA-B4-5838 TCGA-BP-4352 TCGA-BP-4768 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-5173 
        5.46        11.31        13.15        46.45        31.30         2.04 
TCGA-CW-5588 TCGA-CW-6088 TCGA-CZ-5458 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 
       66.31       105.93        91.69        84.30         1.94        31.10 
TCGA-CZ-5985 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X 
       65.65         4.57        56.81        54.64        51.52        12.82 
TCGA-5P-A9K9 TCGA-B1-7332 TCGA-B3-4104 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5882 
       19.36        37.51        34.49        19.27         8.88        21.63 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6793 
       10.82         7.66       123.62         0.43         4.01        11.05 
TCGA-G7-7502 TCGA-G7-A8LD TCGA-HE-7130 TCGA-IA-A40Y TCGA-J7-8537 TCGA-UZ-A9PQ 
       25.84        16.90        58.19         2.04        10.55        86.27 
TCGA-UZ-A9PS TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8S1 
       71.24        18.64        18.64        13.28 

$`DEL PEAK 18(11Q23.1) WILD-TYPE`
TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
       28.11        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3450 
       38.47        34.29        31.07        42.97        82.32        58.49 
TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 
       28.73        22.45        43.96        52.21        18.51       112.80 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 
      133.94        15.78        70.68       119.38       126.05        24.82 
TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 
       25.91         1.18         8.42        15.42       111.02        94.72 
TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 
       32.61         3.58        80.68        74.17        54.77        12.33 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 
       77.62        44.15        60.59        11.64        20.38        37.25 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
        6.94        61.51        53.65        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 
       27.02        31.79        44.55        63.25       105.37        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 
       27.65       108.56        53.26       118.85        75.58       103.43 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 
       46.16         0.59       107.54         5.46        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-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       23.90        81.21        23.01        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O 
       61.05        21.37         0.89        76.64        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       21.07        10.16        21.86        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z9 
       84.89        67.17        16.34        12.13        29.26        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8476 
       71.41        28.80        62.37       151.96        44.91       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-8429 TCGA-KN-8431 
       25.91        65.19       104.52         3.55        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 
        2.50        11.21       115.00       100.87       105.47       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
      103.40        92.71        16.67       104.55       103.10        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
      105.60        96.62        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
       36.82         0.53        39.16        24.16        49.02        37.15 
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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
       62.01        52.93        45.53        29.92        18.44        88.37 
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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 
        0.10         0.10        11.18        10.62        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
      122.56       109.41        15.78        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
      109.51        94.19        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
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-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        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-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       40.44        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        10.52        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-B0-5085 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 
       11.24        11.90        25.32        15.09         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-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 
       46.39        56.98        42.41       111.52       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       86.47       126.28        80.91        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       32.98        16.67        12.00         5.75         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        4.64         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         4.93        17.36 
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-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-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        37.25        21.21        15.62         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        62.86        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-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
        5.98        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         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-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       36.07        33.34        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
       35.21        28.87         6.35        79.30        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        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-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
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       116.84        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       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
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       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         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-6090 
       85.78        73.18        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       18.77        25.45        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       14.66        63.39        93.04       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5459 
       79.53        23.74        18.44        79.63        90.54        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
       94.45        10.85        10.22        21.76        69.96        22.52 
TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5986 TCGA-CZ-5987 
        2.40        12.69        80.19        67.96        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       22.78        62.63        53.46        12.00        18.12         3.91 
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-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 
       19.43        19.96        16.37        11.70         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J8 TCGA-2Z-A9JK 
       59.01        58.22       100.27        56.91        91.73        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       15.48        71.80        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 
       15.75         8.28        12.46         9.63        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N 
       66.71        62.66        67.73         2.20        41.13        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         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-5887 TCGA-BQ-5891 
       47.80        40.83        26.04        30.28        25.35         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        7.92         2.76        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 
       24.89        10.68        13.08         2.40         1.18        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
       90.90        39.25        71.44        25.15        20.52        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.98        23.08        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       81.93        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        12.36        12.76        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       78.90        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
      125.29        37.35        98.96        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A897 
      110.73        51.35        31.73        26.01        39.06        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 
       25.28         6.02 

  DEL PEAK 18(11Q23.1) MUTATED DEL PEAK 18(11Q23.1) WILD-TYPE 
                          0.43                           0.07 
  DEL PEAK 18(11Q23.1) MUTATED DEL PEAK 18(11Q23.1) WILD-TYPE 
                        123.62                         194.79 
  DEL PEAK 18(11Q23.1) MUTATED DEL PEAK 18(11Q23.1) WILD-TYPE 
                        21.600                         36.835 
[1] "0.4 - 123.6 (21.6)" "0.1 - 194.8 (36.8)"
[1] "hr=" "2"  
D27V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 18(11Q23.1) MUTATED        18       13        23       16
  DEL PEAK 18(11Q23.1) WILD-TYPE     436       90       167       88
D27V3, multiclass
           clus
vv          DEL PEAK 18(11Q23.1) MUTATED DEL PEAK 18(11Q23.1) WILD-TYPE
  STAGE I                             18                            436
  STAGE II                            13                             90
  STAGE III                           23                            167
  STAGE IV                            16                             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(11Q23.1) MUTATED    19  15  34   3
  DEL PEAK 18(11Q23.1) WILD-TYPE 461 112 224  12
D27V4, multiclass
    clus
vv   DEL PEAK 18(11Q23.1) MUTATED DEL PEAK 18(11Q23.1) WILD-TYPE
  T1                           19                            461
  T2                           15                            112
  T3                           34                            224
  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 18(11Q23.1) MUTATED    24  12   3
  DEL PEAK 18(11Q23.1) WILD-TYPE 299  32   3
D27V5, multiclass
    clus
vv   DEL PEAK 18(11Q23.1) MUTATED DEL PEAK 18(11Q23.1) WILD-TYPE
  N0                           24                            299
  N1                           12                             32
  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"
D27V6, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q23.1) MUTATED    34  10
  DEL PEAK 18(11Q23.1) WILD-TYPE 512  79
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.1) MUTATED     34   10
  DEL PEAK 18(11Q23.1) WILD-TYPE  512   79
   clus
vv  DEL PEAK 18(11Q23.1) MUTATED DEL PEAK 18(11Q23.1) WILD-TYPE
  0                           34                            512
  1                           10                             79
[1] 2 2
[1] FALSE
D27V7, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q23.1) MUTATED    21  50
  DEL PEAK 18(11Q23.1) WILD-TYPE 271 540
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.1) MUTATED     21   50
  DEL PEAK 18(11Q23.1) WILD-TYPE  271  540
        clus
vv       DEL PEAK 18(11Q23.1) MUTATED DEL PEAK 18(11Q23.1) WILD-TYPE
  FEMALE                           21                            271
  MALE                             50                            540
[1] 2 2
[1] FALSE
D27V8, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q23.1) MUTATED    36   1
  DEL PEAK 18(11Q23.1) WILD-TYPE 372   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.1) MUTATED     36    1
  DEL PEAK 18(11Q23.1) WILD-TYPE  372    2
     clus
vv    DEL PEAK 18(11Q23.1) MUTATED DEL PEAK 18(11Q23.1) WILD-TYPE
  NO                            36                            372
  YES                            1                              2
[1] 2 2
[1] FALSE
D27V9, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  DEL PEAK 18(11Q23.1) MUTATED                    9
  DEL PEAK 18(11Q23.1) WILD-TYPE                 57
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 18(11Q23.1) MUTATED                                  30
  DEL PEAK 18(11Q23.1) WILD-TYPE                               498
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 18(11Q23.1) MUTATED                                      32
  DEL PEAK 18(11Q23.1) WILD-TYPE                                   256
D27V10, multiclass
                                       clus
vv                                      DEL PEAK 18(11Q23.1) MUTATED
  KIDNEY CHROMOPHOBE                                               9
  KIDNEY CLEAR CELL RENAL CARCINOMA                               30
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           32
                                       clus
vv                                      DEL PEAK 18(11Q23.1) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                57
  KIDNEY CLEAR CELL RENAL CARCINOMA                                498
  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"
D27V11, continuous
D27V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(11Q23.1) MUTATED                                  0     3
  DEL PEAK 18(11Q23.1) WILD-TYPE                                2    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(11Q23.1) MUTATED                           7    58
  DEL PEAK 18(11Q23.1) WILD-TYPE                       114   661
D27V13, multiclass
                                  clus
vv                                 DEL PEAK 18(11Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      58
                                  clus
vv                                 DEL PEAK 18(11Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        13
  BLACK OR AFRICAN AMERICAN                                   114
  WHITE                                                       661
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q23.1) MUTATED     1  53
  DEL PEAK 18(11Q23.1) WILD-TYPE  41 569
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q23.1) MUTATED      1   53
  DEL PEAK 18(11Q23.1) WILD-TYPE   41  569
                        clus
vv                       DEL PEAK 18(11Q23.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           53
                        clus
vv                       DEL PEAK 18(11Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 41
  NOT HISPANIC OR LATINO                            569
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK 19(13Q13.2) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(13Q13.2) MUTATED    92  55
  DEL PEAK 19(13Q13.2) WILD-TYPE 556 173
  DEL PEAK 19(13Q13.2) MUTATED DEL PEAK 19(13Q13.2) WILD-TYPE 
                           147                            729 
  DEL PEAK 19(13Q13.2) MUTATED DEL PEAK 19(13Q13.2) WILD-TYPE 
                            55                            173 
$`DEL PEAK 19(13Q13.2) MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
      102.81        28.11        47.24        19.73        43.96        52.21 
TCGA-BP-5191 TCGA-CZ-4854 TCGA-DV-5568 TCGA-G6-A8L7 TCGA-AL-A5DJ TCGA-B3-A6W5 
       31.79        46.16        12.16        70.13        49.25        10.16 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       153.73       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       84.89        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       66.54        24.79       151.96        44.91        49.97       123.12 
TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 
      129.37        87.91        25.48        65.19       104.52         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12        19.33         2.50        59.08       115.00 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      105.47        10.68       100.47       103.40        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3319 TCGA-A3-3346 
      104.55       105.60        90.48        92.55        37.15         4.50 
TCGA-A3-3347 TCGA-A3-3370 TCGA-A3-3374 TCGA-AK-3426 TCGA-AK-3433 TCGA-AK-3440 
       52.93        74.76        43.20        29.10       112.08        94.19 
TCGA-AK-3445 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4696 
       78.64        12.13        40.70         1.41         4.57        28.47 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4819 TCGA-B0-5092 
        1.38         3.62        57.70         6.64         6.02        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5099 TCGA-B0-5113 TCGA-B0-5117 TCGA-B4-5832 
       10.95         8.05        15.95        38.63        52.87         5.10 
TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-5163 TCGA-B8-5549 
        0.53         5.46        23.31        16.80        27.02         6.38 
TCGA-BP-4167 TCGA-BP-4334 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       89.36        21.21        62.86        31.89        11.31        33.99 
TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4787 TCGA-BP-4797 
        5.98        71.80        13.15        10.82        15.78        36.39 
TCGA-BP-4964 TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5004 
       61.22        57.40        45.50        31.30        43.00        37.02 
TCGA-BP-5175 TCGA-BP-5196 TCGA-CJ-4639 TCGA-CJ-4868 TCGA-CJ-4881 TCGA-CJ-4901 
       30.64        33.47       106.16        21.24        66.21        47.67 
TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 
       25.71        22.32        53.42        66.31        83.90        18.77 
TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5455 TCGA-CZ-5457 
       47.08         6.77        63.39       107.41        18.44        90.54 
TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-2Z-A9J8 TCGA-2Z-A9JI 
       84.30         1.94        31.10        67.96        91.73        51.52 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-A4-7287 TCGA-A4-7915 TCGA-B3-3926 TCGA-BQ-5875 
       43.04        19.36        19.63         0.23        29.03        86.76 
TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 
       22.92        21.63         2.76        10.68        13.08         4.01 
TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-J7-8537 
       11.05        25.84        23.08        16.90         3.68        10.55 
TCGA-P4-A5E8 TCGA-Q2-A5QZ TCGA-UN-AAZ9 
       42.94        14.07        18.02 

$`DEL PEAK 19(13Q13.2) WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-KO-8411 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 
       23.28        28.80       130.13        47.21        38.47        34.29 
TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 
       31.07        42.97        82.32       109.91        58.49        28.73 
TCGA-AK-3455 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       22.45        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5199 
       35.90        48.10        62.86        49.15        27.02        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 
       53.26       118.85        75.58       103.43         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5573 
        5.46        43.69        45.96        65.88        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-MM-A84U TCGA-2Z-A9J9 
       66.28        56.84        23.90        81.21        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B9-5155 TCGA-B9-A44B 
       76.64        21.67        27.68        21.07        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8325 
       86.37        21.60        15.91        15.62         6.74        23.84 
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
      109.22        98.33        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 
       62.37        51.06        31.33        23.47        25.91         3.55 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 
       11.21        42.35       100.87       103.10        99.88        96.62 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82         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-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       37.38        48.82        62.01        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3372 
       88.37        51.25        10.49        28.70        74.63        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
        0.10        11.18        10.62       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
       15.78        73.68        68.61       109.51        46.78        48.36 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       40.01        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       72.89         1.41         3.32         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4714 TCGA-B0-4718 
       65.10         7.82         5.98         2.14         3.25        58.45 
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        10.52        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-B0-5096 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-B0-5115 
       52.54        30.48        58.59        19.30        66.05        52.73 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       41.88        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
        1.68        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 
       21.57        16.67        12.00         5.75         1.25         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.36         0.23        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5164 
       17.19        25.55        50.14        40.04        23.74         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       24.23        50.14        16.60        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       14.30        27.29        29.88        17.06         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
       17.36        16.27        14.17        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       93.34        99.85         0.43        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-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       62.07        37.25        15.62         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4355 TCGA-BP-4756 
       52.24        49.08        44.94        12.23        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 
       72.59        77.98        41.75        48.07        61.68         5.33 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4789 
       61.97        13.51        56.91        68.38        60.95        48.95 
TCGA-BP-4790 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 
       36.53        10.98        36.95         6.71        47.97        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4969 
       71.41        63.62        58.68        60.30         6.74        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       14.24        48.89        49.38         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       36.07        33.34        46.45        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5008 
       16.47        30.64        18.51        38.70        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       28.87         6.35        79.30         2.04        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4869 
       14.17       114.41        54.61        58.95        11.05        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       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       64.27        71.87        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45       109.84        50.24        56.35        49.97        51.29 
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       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
      133.71        18.87        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       73.35        67.00        62.66       119.64         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-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 
       74.66         1.35       105.93        25.45        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       14.66        93.04        63.42        58.82        79.53        23.74 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       79.63        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 
       21.76        69.96        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-A4VX 
       65.65        12.26        14.63        22.78        62.63        53.46 
TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       12.00        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC 
       10.29        35.87         2.01        19.43        19.96        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JK TCGA-2Z-A9JM 
       56.91         4.57        56.81        54.64        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       15.48        71.80        62.93        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       67.43        18.21         0.10        35.18        19.13         7.82 
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-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       20.32        33.83        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        7.92       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        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        90.90 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
       39.25        71.44        25.15        20.52        25.25        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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.36        12.76        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB 
       31.13        15.48        99.78        87.09         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
       92.58        52.27        16.01        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ 
       16.31        41.62        26.47        53.10        43.76        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      117.40       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  DEL PEAK 19(13Q13.2) MUTATED DEL PEAK 19(13Q13.2) WILD-TYPE 
                          0.23                           0.07 
  DEL PEAK 19(13Q13.2) MUTATED DEL PEAK 19(13Q13.2) WILD-TYPE 
                        153.73                         194.79 
  DEL PEAK 19(13Q13.2) MUTATED DEL PEAK 19(13Q13.2) WILD-TYPE 
                         37.15                          35.21 
[1] "0.2 - 153.7 (37.1)" "0.1 - 194.8 (35.2)"
[1] "hr=" "1.5"
D28V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 19(13Q13.2) MUTATED        46       23        49       29
  DEL PEAK 19(13Q13.2) WILD-TYPE     408       80       141       75
D28V3, multiclass
           clus
vv          DEL PEAK 19(13Q13.2) MUTATED DEL PEAK 19(13Q13.2) WILD-TYPE
  STAGE I                             46                            408
  STAGE II                            23                             80
  STAGE III                           49                            141
  STAGE IV                            29                             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 19(13Q13.2) MUTATED    48  25  68   8
  DEL PEAK 19(13Q13.2) WILD-TYPE 432 102 190   7
D28V4, multiclass
    clus
vv   DEL PEAK 19(13Q13.2) MUTATED DEL PEAK 19(13Q13.2) WILD-TYPE
  T1                           48                            432
  T2                           25                            102
  T3                           68                            190
  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 19(13Q13.2) MUTATED    68  14   5
  DEL PEAK 19(13Q13.2) WILD-TYPE 255  30   1
D28V5, multiclass
    clus
vv   DEL PEAK 19(13Q13.2) MUTATED DEL PEAK 19(13Q13.2) WILD-TYPE
  N0                           68                            255
  N1                           14                             30
  N2                            5                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                                cls
clus                               0   1
  DEL PEAK 19(13Q13.2) MUTATED    89  20
  DEL PEAK 19(13Q13.2) WILD-TYPE 457  69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(13Q13.2) MUTATED     89   20
  DEL PEAK 19(13Q13.2) WILD-TYPE  457   69
   clus
vv  DEL PEAK 19(13Q13.2) MUTATED DEL PEAK 19(13Q13.2) WILD-TYPE
  0                           89                            457
  1                           20                             69
[1] 2 2
[1] FALSE
D28V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(13Q13.2) MUTATED    65  84
  DEL PEAK 19(13Q13.2) WILD-TYPE 227 506
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(13Q13.2) MUTATED     65   84
  DEL PEAK 19(13Q13.2) WILD-TYPE  227  506
        clus
vv       DEL PEAK 19(13Q13.2) MUTATED DEL PEAK 19(13Q13.2) WILD-TYPE
  FEMALE                           65                            227
  MALE                             84                            506
[1] 2 2
[1] FALSE
D28V8, binary
                                cls
clus                               0   1
  DEL PEAK 19(13Q13.2) MUTATED    76   0
  DEL PEAK 19(13Q13.2) WILD-TYPE 332   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(13Q13.2) MUTATED     76    0
  DEL PEAK 19(13Q13.2) WILD-TYPE  332    3
     clus
vv    DEL PEAK 19(13Q13.2) MUTATED DEL PEAK 19(13Q13.2) WILD-TYPE
  NO                            76                            332
  YES                            0                              3
[1] 2 2
[1] FALSE
D28V9, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  DEL PEAK 19(13Q13.2) MUTATED                   44
  DEL PEAK 19(13Q13.2) WILD-TYPE                 22
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 19(13Q13.2) MUTATED                                  80
  DEL PEAK 19(13Q13.2) WILD-TYPE                               448
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 19(13Q13.2) MUTATED                                      25
  DEL PEAK 19(13Q13.2) WILD-TYPE                                   263
D28V10, multiclass
                                       clus
vv                                      DEL PEAK 19(13Q13.2) MUTATED
  KIDNEY CHROMOPHOBE                                              44
  KIDNEY CLEAR CELL RENAL CARCINOMA                               80
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           25
                                       clus
vv                                      DEL PEAK 19(13Q13.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                22
  KIDNEY CLEAR CELL RENAL CARCINOMA                                448
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, continuous
D28V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(13Q13.2) MUTATED                                  0     4
  DEL PEAK 19(13Q13.2) WILD-TYPE                                2    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(13Q13.2) MUTATED                          12   128
  DEL PEAK 19(13Q13.2) WILD-TYPE                       109   591
D28V13, multiclass
                                  clus
vv                                 DEL PEAK 19(13Q13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                     128
                                  clus
vv                                 DEL PEAK 19(13Q13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        12
  BLACK OR AFRICAN AMERICAN                                   109
  WHITE                                                       591
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                                cls
clus                               0   1
  DEL PEAK 19(13Q13.2) MUTATED     4  95
  DEL PEAK 19(13Q13.2) WILD-TYPE  38 527
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(13Q13.2) MUTATED      4   95
  DEL PEAK 19(13Q13.2) WILD-TYPE   38  527
                        clus
vv                       DEL PEAK 19(13Q13.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           95
                        clus
vv                       DEL PEAK 19(13Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            527
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK 20(14Q31.1) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(14Q31.1) MUTATED   166 112
  DEL PEAK 20(14Q31.1) WILD-TYPE 482 116
  DEL PEAK 20(14Q31.1) MUTATED DEL PEAK 20(14Q31.1) WILD-TYPE 
                           278                            598 
  DEL PEAK 20(14Q31.1) MUTATED DEL PEAK 20(14Q31.1) WILD-TYPE 
                           112                            116 
$`DEL PEAK 20(14Q31.1) MUTATED`
TCGA-A3-3336 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
       34.29        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5694 TCGA-B0-5698 TCGA-B2-5635 TCGA-B8-5162 TCGA-BP-4164 
       52.21        15.78       119.38        24.82         1.18        32.61 
TCGA-BP-4331 TCGA-BP-4353 TCGA-BP-4965 TCGA-BP-4986 TCGA-BP-5009 TCGA-BP-5178 
       80.68        12.33        61.51        25.81        35.90        62.86 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 
       27.02        31.79        31.27        63.25       105.37        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CZ-4854 
       27.65       108.56        53.26       118.85        75.58        46.16 
TCGA-DV-5573 TCGA-MM-A84U TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-BQ-5888 TCGA-PJ-A5Z8 
       37.15        23.01        12.99        49.25        13.25        19.73 
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        62.01 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3378 
        4.50        52.93        45.53        29.92        88.37        20.71 
TCGA-A3-3382 TCGA-A3-3387 TCGA-A3-A6NI TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3429 
       18.87        20.28        33.47        29.10       117.80       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3458 
       15.78        73.68       109.51        78.64        94.29        38.40 
TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4703 TCGA-B0-4713 TCGA-B0-4814 TCGA-B0-4817 
        4.57         3.48         5.98         6.64         5.52        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        66.05        38.63        56.98       129.67 
TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-4098 
       86.47        80.91        79.89       131.15        89.49         1.68 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5836 
       31.30        31.66        32.98        21.57         5.10         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-4619 TCGA-B8-5158 TCGA-B8-5159 
        5.46         0.36        23.31        17.19        40.04        23.74 
TCGA-B8-5164 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54G 
        0.85        48.53         0.53        14.30        27.29         1.74 
TCGA-B8-A54I TCGA-BP-4163 TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        4.93        93.34        89.36        62.24        61.78        64.27 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4761 
       62.86        49.08        44.94        11.31        33.99         5.98 
TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       41.75        13.15         5.33        56.91        68.38        15.78 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4962 TCGA-BP-4970 
       36.39        10.98         6.71        87.45        58.68        14.24 
TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4983 TCGA-BP-4989 
       48.89        45.50        14.93        36.07        46.45         3.88 
TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       16.47        18.51        37.02         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5190 
       74.20        30.64        74.40        42.44        37.22        33.24 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 
       24.62        33.47        19.82        73.22        14.17       114.41 
TCGA-CJ-4641 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4873 
       54.61        11.05        21.24        83.97        79.66        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4888 
       75.06       116.84        64.27        66.21        57.83        51.52 
TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4900 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4908 
       24.66       109.84        56.35        51.29        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       54.48        38.56        45.14         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5686 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5584 
       25.25       122.83        67.00         7.36        64.57         5.39 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4858 
       73.18        66.31         1.35        83.90        18.77        69.21 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5452 
        6.77        14.66        63.39        93.04       107.41        58.82 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       18.44        79.63        10.85        10.22        21.76        84.30 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40         1.94        31.10        12.69        67.96        65.65 
TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-G6-A5PC TCGA-G6-A8L8 TCGA-MM-A563 
       14.63        62.63        53.46         7.96        35.87        19.43 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9K9 
       54.64        51.52        38.99        15.48        43.04        19.36 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3473 
       18.21        19.63         0.10        29.46         9.63        62.66 
TCGA-AL-7173 TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A5W8 
       67.73        37.51        16.77        29.03        20.61        17.23 
TCGA-BQ-5876 TCGA-BQ-5880 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-DZ-6131 
       19.27        43.20        30.28        10.82         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        71.44 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-8500 TCGA-HE-A5NK 
       20.52        25.84        23.08        16.90        27.65        73.25 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-MH-A854 TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UN-AAZ9 
       16.80         2.04        17.62         6.61        14.07        18.02 
TCGA-UZ-A9PN TCGA-WN-A9G9 
       37.35        26.01 

$`DEL PEAK 20(14Q31.1) WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       47.21        38.47        31.07        42.97        82.32       109.91 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5812 TCGA-B8-4621 
       18.51       112.80       133.94        70.68       126.05        25.91 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4327 TCGA-BP-4342 
        8.42        15.42       111.02        94.72         3.58        74.17 
TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 
       54.77        77.62        44.15        60.59        11.64        20.38 
TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       37.25         6.94        53.65        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5199 TCGA-CW-6093 
       41.62        27.62        48.10        49.15        44.55       103.43 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        0.59       107.54         5.46        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       12.16        11.67        66.28        56.84        23.90        81.21 
TCGA-G6-A8L7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       70.13        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
        0.89        76.64        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5892 TCGA-BQ-7046 
       21.86        11.87        19.23        26.04        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       16.34        12.13        29.26        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        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-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        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 
      105.47        10.68       100.47       103.40        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
      104.55       103.10        99.88       105.60        96.62        90.48 
TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3322 TCGA-A3-3323 
       92.55        11.90         0.53        24.16        48.59        36.36 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3352 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       37.38        48.82        18.44        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-3428 TCGA-AK-3433 TCGA-AK-3434 
        0.10        11.18        10.62       122.56       112.08        68.61 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 
       94.19        46.78        48.36        40.01        83.21        37.58 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
        1.41         2.53        28.47        19.00         1.38         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        57.70         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4821 
       15.72        46.59         0.59        45.07        16.77        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4834 TCGA-B0-4837 
       36.53        14.93        54.48        29.10        68.71        45.30 
TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4849 
        6.71        10.52        10.29        65.29        39.45         2.27 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5095 TCGA-B0-5098 TCGA-B0-5099 
       43.30        11.24        25.32         8.05        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5115 
       62.89        90.87        90.48        58.59        19.30        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5696 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 
       42.41       111.52        85.78       126.28        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
      149.16       105.37       130.65        91.46        32.61        35.90 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       31.96        21.30        16.67        12.00         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        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5545 
       45.37        25.55        50.14        27.02        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5552 TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54J 
       16.60         6.38        34.39        29.88        17.06        17.36 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 
       16.27        14.17        85.51        90.28       101.06        99.85 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
        0.43        23.05        77.03        54.90        97.45        53.42 
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        15.62         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4355 
       93.99        18.48        52.24        12.23        31.89        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
       12.30        72.59        77.98        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 
       10.82        61.97        13.51        60.95        48.95        36.53 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 
       36.95        47.97        71.41        63.62        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 
        6.74        57.40        58.98        49.38         6.94        47.11 
TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4994 TCGA-BP-4998 
       33.34        31.30        36.95        46.45        43.00        30.64 
TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5176 TCGA-BP-5177 
       38.70        37.48        35.21        28.87        52.27         9.63 
TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5192 TCGA-BP-5194 
       38.30        37.25        22.78        13.35        23.47        13.41 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4643 
       34.95         0.95       115.00        46.55       106.16        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       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4895 TCGA-CJ-4899 
       30.64        63.98       115.69        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       119.64        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CZ-4853 TCGA-CZ-4857 
       85.78        78.18        74.66       105.93        25.45        47.08 
TCGA-CZ-4859 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5457 TCGA-CZ-5458 
       58.75        63.42        79.53        23.74        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5982 TCGA-CZ-5986 
       55.33        94.45        69.96        22.52        80.19        12.26 
TCGA-CZ-5988 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        12.00        18.12         3.91         6.77         4.18 
TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
       10.29         2.01        19.96        16.37        11.70         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-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       91.73        56.81        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9KA 
       90.21        22.26        78.64        71.80        62.93        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       12.39        27.09        67.43        35.18        19.13         7.82 
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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N 
       70.19        49.32        66.71         2.20        41.13        36.49 
TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.25        20.32        33.83        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       50.50        28.18        26.40         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       22.06         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        63.72        22.92        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 
       26.04        25.35         7.66         0.95         7.92       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6133 TCGA-DZ-6135 
        7.04         7.17         3.81        40.77        51.19        74.60 
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-G7-6795 TCGA-G7-6797 TCGA-G7-A4TM TCGA-G7-A8LB 
       51.78        90.90        39.25        25.15        25.25        17.98 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       11.84        56.75        25.22        19.99        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       30.38        27.65        20.25        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       87.09        42.94        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        78.90        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       53.10        43.76        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
      110.73        51.35        31.73        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  DEL PEAK 20(14Q31.1) MUTATED DEL PEAK 20(14Q31.1) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 20(14Q31.1) MUTATED DEL PEAK 20(14Q31.1) WILD-TYPE 
                        133.71                         194.79 
  DEL PEAK 20(14Q31.1) MUTATED DEL PEAK 20(14Q31.1) WILD-TYPE 
                         33.11                          37.10 
[1] "0.1 - 133.7 (33.1)" "0.1 - 194.8 (37.1)"
[1] "hr=" "2.2"
D29V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 20(14Q31.1) MUTATED       103       31        81       56
  DEL PEAK 20(14Q31.1) WILD-TYPE     351       72       109       48
D29V3, multiclass
           clus
vv          DEL PEAK 20(14Q31.1) MUTATED DEL PEAK 20(14Q31.1) WILD-TYPE
  STAGE I                            103                            351
  STAGE II                            31                             72
  STAGE III                           81                            109
  STAGE IV                            56                             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 20(14Q31.1) MUTATED   111  41 122   5
  DEL PEAK 20(14Q31.1) WILD-TYPE 369  86 136  10
D29V4, multiclass
    clus
vv   DEL PEAK 20(14Q31.1) MUTATED DEL PEAK 20(14Q31.1) WILD-TYPE
  T1                          111                            369
  T2                           41                             86
  T3                          122                            136
  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 20(14Q31.1) MUTATED   110  25   4
  DEL PEAK 20(14Q31.1) WILD-TYPE 213  19   2
D29V5, multiclass
    clus
vv   DEL PEAK 20(14Q31.1) MUTATED DEL PEAK 20(14Q31.1) WILD-TYPE
  N0                          110                            213
  N1                           25                             19
  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"
D29V6, binary
                                cls
clus                               0   1
  DEL PEAK 20(14Q31.1) MUTATED   185  51
  DEL PEAK 20(14Q31.1) WILD-TYPE 361  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(14Q31.1) MUTATED    185   51
  DEL PEAK 20(14Q31.1) WILD-TYPE  361   38
   clus
vv  DEL PEAK 20(14Q31.1) MUTATED DEL PEAK 20(14Q31.1) WILD-TYPE
  0                          185                            361
  1                           51                             38
[1] 2 2
[1] FALSE
D29V7, binary
                                cls
clus                               0   1
  DEL PEAK 20(14Q31.1) MUTATED    96 183
  DEL PEAK 20(14Q31.1) WILD-TYPE 196 407
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(14Q31.1) MUTATED     96  183
  DEL PEAK 20(14Q31.1) WILD-TYPE  196  407
        clus
vv       DEL PEAK 20(14Q31.1) MUTATED DEL PEAK 20(14Q31.1) WILD-TYPE
  FEMALE                           96                            196
  MALE                            183                            407
[1] 2 2
[1] FALSE
D29V8, binary
                                cls
clus                               0   1
  DEL PEAK 20(14Q31.1) MUTATED    85   2
  DEL PEAK 20(14Q31.1) WILD-TYPE 323   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(14Q31.1) MUTATED     85    2
  DEL PEAK 20(14Q31.1) WILD-TYPE  323    1
     clus
vv    DEL PEAK 20(14Q31.1) MUTATED DEL PEAK 20(14Q31.1) WILD-TYPE
  NO                            85                            323
  YES                            2                              1
[1] 2 2
[1] FALSE
D29V9, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  DEL PEAK 20(14Q31.1) MUTATED                    3
  DEL PEAK 20(14Q31.1) WILD-TYPE                 63
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 20(14Q31.1) MUTATED                                 228
  DEL PEAK 20(14Q31.1) WILD-TYPE                               300
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 20(14Q31.1) MUTATED                                      48
  DEL PEAK 20(14Q31.1) WILD-TYPE                                   240
D29V10, multiclass
                                       clus
vv                                      DEL PEAK 20(14Q31.1) MUTATED
  KIDNEY CHROMOPHOBE                                               3
  KIDNEY CLEAR CELL RENAL CARCINOMA                              228
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           48
                                       clus
vv                                      DEL PEAK 20(14Q31.1) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                63
  KIDNEY CLEAR CELL RENAL CARCINOMA                                300
  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"
D29V11, continuous
D29V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(14Q31.1) MUTATED                                  0     3
  DEL PEAK 20(14Q31.1) WILD-TYPE                                2    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(14Q31.1) MUTATED                          26   243
  DEL PEAK 20(14Q31.1) WILD-TYPE                        95   476
D29V13, multiclass
                                  clus
vv                                 DEL PEAK 20(14Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  26
  WHITE                                                     243
                                  clus
vv                                 DEL PEAK 20(14Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        13
  BLACK OR AFRICAN AMERICAN                                    95
  WHITE                                                       476
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                                cls
clus                               0   1
  DEL PEAK 20(14Q31.1) MUTATED    13 199
  DEL PEAK 20(14Q31.1) WILD-TYPE  29 423
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(14Q31.1) MUTATED     13  199
  DEL PEAK 20(14Q31.1) WILD-TYPE   29  423
                        clus
vv                       DEL PEAK 20(14Q31.1) MUTATED
  HISPANIC OR LATINO                               13
  NOT HISPANIC OR LATINO                          199
                        clus
vv                       DEL PEAK 20(14Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 29
  NOT HISPANIC OR LATINO                            423
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK 21(16Q23.3) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(16Q23.3) MUTATED    19  18
  DEL PEAK 21(16Q23.3) WILD-TYPE 629 210
  DEL PEAK 21(16Q23.3) MUTATED DEL PEAK 21(16Q23.3) WILD-TYPE 
                            37                            839 
  DEL PEAK 21(16Q23.3) MUTATED DEL PEAK 21(16Q23.3) WILD-TYPE 
                            18                            210 
$`DEL PEAK 21(16Q23.3) MUTATED`
TCGA-KL-8339 TCGA-5P-A9JU TCGA-A4-A5Y1 TCGA-KL-8329 TCGA-KL-8336 TCGA-KN-8427 
       28.11        12.26        12.99        90.48        30.25         0.99 
TCGA-KN-8428 TCGA-KO-8408 TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-A6NN TCGA-B0-4688 
       52.27        16.67        36.82        49.08         0.10         3.32 
TCGA-B0-4822 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-5097 TCGA-B0-5402 TCGA-B8-4151 
       36.53        40.70        45.30        21.86        42.41        42.71 
TCGA-B8-5551 TCGA-BP-4354 TCGA-BP-4770 TCGA-BP-4797 TCGA-BP-4985 TCGA-BP-5185 
        0.53        33.99        10.82        36.39        31.30        37.22 
TCGA-CZ-5457 TCGA-CZ-5982 TCGA-G6-A8L8 TCGA-MM-A564 TCGA-2Z-A9JI TCGA-A4-7287 
       90.54        80.19        35.87        19.96        51.52        19.63 
TCGA-B9-A8YI TCGA-BQ-5882 TCGA-BQ-5893 TCGA-G7-6793 TCGA-G7-A8LD TCGA-HE-7130 
       12.30        21.63         7.92        11.05        16.90        58.19 
TCGA-IA-A40X 
       19.99 

$`DEL PEAK 21(16Q23.3) WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       38.47        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       58.49        28.73        22.45        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 
      111.02        94.72        32.61         3.58        80.68        74.17 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       54.77        12.33        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
       53.26       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       25.58        16.18        22.49        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
        0.89        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 
       15.62         6.74        38.07       153.73        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
      137.06       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       92.55        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-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
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-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       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       92.71       104.55       103.10        99.88       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3311 
       90.48        92.55        12.66        11.90         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        33.47        15.39        22.65         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       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       73.68       112.08        68.61       109.51        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       48.36        78.64        40.01        94.29        83.21        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       40.44        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       68.71        27.42        53.88         6.71        56.68        10.52 
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-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
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-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       56.98       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
        1.68        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         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-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       16.80        49.97        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
       50.14        16.60         6.38        48.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         4.93        17.36 
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-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-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        37.25        21.21        15.62         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        62.86        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       31.89        11.31        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
        5.98        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       15.78        48.95        36.53        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.22         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       33.34        46.45        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.25        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
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       116.84        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       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
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       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
      105.93        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
       58.75         6.77        14.66        63.39        93.04       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       69.96        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       12.69        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       62.63        53.46        12.00        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MW-A4EC 
        4.18         7.96        10.29         2.01        19.43        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JK 
       56.91         4.57        91.73        56.81        54.64        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 
       12.99        12.39        27.09        67.43        18.21         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5876 
       17.23         0.16        14.86        17.49        86.76        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        4.01        51.78        90.90        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       20.52        25.84        25.25        17.98        23.08        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI 
       12.89        11.21        16.31        81.93        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83S 
       56.75        73.25        25.22        16.80         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ 
       92.58        52.27        16.01        50.60        78.90        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  DEL PEAK 21(16Q23.3) MUTATED DEL PEAK 21(16Q23.3) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 21(16Q23.3) MUTATED DEL PEAK 21(16Q23.3) WILD-TYPE 
                         90.54                         194.79 
  DEL PEAK 21(16Q23.3) MUTATED DEL PEAK 21(16Q23.3) WILD-TYPE 
                         30.25                          36.36 
[1] "0.1 - 90.5 (30.2)"  "0.1 - 194.8 (36.4)"
[1] "hr=" "2.6"
D30V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 21(16Q23.3) MUTATED        11        4        12       10
  DEL PEAK 21(16Q23.3) WILD-TYPE     443       99       178       94
D30V3, multiclass
           clus
vv          DEL PEAK 21(16Q23.3) MUTATED DEL PEAK 21(16Q23.3) WILD-TYPE
  STAGE I                             11                            443
  STAGE II                             4                             99
  STAGE III                           12                            178
  STAGE IV                            10                             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
  DEL PEAK 21(16Q23.3) MUTATED    12   4  16   5
  DEL PEAK 21(16Q23.3) WILD-TYPE 468 123 242  10
D30V4, multiclass
    clus
vv   DEL PEAK 21(16Q23.3) MUTATED DEL PEAK 21(16Q23.3) WILD-TYPE
  T1                           12                            468
  T2                            4                            123
  T3                           16                            242
  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 21(16Q23.3) MUTATED    13   7   2
  DEL PEAK 21(16Q23.3) WILD-TYPE 310  37   4
D30V5, multiclass
    clus
vv   DEL PEAK 21(16Q23.3) MUTATED DEL PEAK 21(16Q23.3) WILD-TYPE
  N0                           13                            310
  N1                            7                             37
  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"
D30V6, binary
                                cls
clus                               0   1
  DEL PEAK 21(16Q23.3) MUTATED    19   5
  DEL PEAK 21(16Q23.3) WILD-TYPE 527  84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q23.3) MUTATED     19    5
  DEL PEAK 21(16Q23.3) WILD-TYPE  527   84
   clus
vv  DEL PEAK 21(16Q23.3) MUTATED DEL PEAK 21(16Q23.3) WILD-TYPE
  0                           19                            527
  1                            5                             84
[1] 2 2
[1] FALSE
D30V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(16Q23.3) MUTATED    12  25
  DEL PEAK 21(16Q23.3) WILD-TYPE 280 565
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q23.3) MUTATED     12   25
  DEL PEAK 21(16Q23.3) WILD-TYPE  280  565
        clus
vv       DEL PEAK 21(16Q23.3) MUTATED DEL PEAK 21(16Q23.3) WILD-TYPE
  FEMALE                           12                            280
  MALE                             25                            565
[1] 2 2
[1] FALSE
D30V8, binary
                                cls
clus                               0   1
  DEL PEAK 21(16Q23.3) MUTATED    19   0
  DEL PEAK 21(16Q23.3) WILD-TYPE 389   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q23.3) MUTATED     19    0
  DEL PEAK 21(16Q23.3) WILD-TYPE  389    3
     clus
vv    DEL PEAK 21(16Q23.3) MUTATED DEL PEAK 21(16Q23.3) WILD-TYPE
  NO                            19                            389
  YES                            0                              3
[1] 2 2
[1] FALSE
D30V9, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  DEL PEAK 21(16Q23.3) MUTATED                    6
  DEL PEAK 21(16Q23.3) WILD-TYPE                 60
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 21(16Q23.3) MUTATED                                  20
  DEL PEAK 21(16Q23.3) WILD-TYPE                               508
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 21(16Q23.3) MUTATED                                      11
  DEL PEAK 21(16Q23.3) WILD-TYPE                                   277
D30V10, multiclass
                                       clus
vv                                      DEL PEAK 21(16Q23.3) MUTATED
  KIDNEY CHROMOPHOBE                                               6
  KIDNEY CLEAR CELL RENAL CARCINOMA                               20
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           11
                                       clus
vv                                      DEL PEAK 21(16Q23.3) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                60
  KIDNEY CLEAR CELL RENAL CARCINOMA                                508
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            277
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, continuous
D30V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(16Q23.3) MUTATED                                  0     1
  DEL PEAK 21(16Q23.3) WILD-TYPE                                2    15
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(16Q23.3) MUTATED                           6    28
  DEL PEAK 21(16Q23.3) WILD-TYPE                       115   691
D30V13, multiclass
                                  clus
vv                                 DEL PEAK 21(16Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      28
                                  clus
vv                                 DEL PEAK 21(16Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        15
  BLACK OR AFRICAN AMERICAN                                   115
  WHITE                                                       691
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                                cls
clus                               0   1
  DEL PEAK 21(16Q23.3) MUTATED     1  24
  DEL PEAK 21(16Q23.3) WILD-TYPE  41 598
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q23.3) MUTATED      1   24
  DEL PEAK 21(16Q23.3) WILD-TYPE   41  598
                        clus
vv                       DEL PEAK 21(16Q23.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           24
                        clus
vv                       DEL PEAK 21(16Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 41
  NOT HISPANIC OR LATINO                            598
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK 22(19P13.3) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(19P13.3) MUTATED    19  24
  DEL PEAK 22(19P13.3) WILD-TYPE 629 204
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                            43                            833 
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                            24                            204 
$`DEL PEAK 22(19P13.3) MUTATED`
TCGA-AK-3425 TCGA-B0-4707 TCGA-BP-4164 TCGA-5P-A9JU TCGA-A4-A5Y1 TCGA-B9-A44B 
      109.91        19.73        32.61        12.26        12.99        11.87 
TCGA-B9-A5W7 TCGA-KL-8336 TCGA-KO-8404 TCGA-KO-8415 TCGA-A3-3319 TCGA-B0-4690 
       19.23        30.25        10.68        96.62        37.15         1.41 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4821 TCGA-B0-4828 TCGA-B0-5084 TCGA-B0-5098 
        3.48        28.47        40.44        10.09         7.30        52.08 
TCGA-B0-5109 TCGA-BP-4352 TCGA-BP-4770 TCGA-BP-4985 TCGA-CJ-5681 TCGA-CZ-4860 
       19.30        11.31        10.82        31.30        18.15         6.77 
TCGA-2Z-A9JG TCGA-5P-A9K9 TCGA-5P-A9KC TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-8517 
       54.64        19.36        12.39        18.21        25.64        19.63 
TCGA-AL-3466 TCGA-B1-7332 TCGA-BQ-5876 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-G7-6789 
        9.63        37.51        19.27         7.66         0.95         4.01 
TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UZ-A9PN 
       25.84        16.90         2.04        10.55        14.07        37.35 
TCGA-UZ-A9PP 
       98.96 

$`DEL PEAK 22(19P13.3) WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 
       58.49        28.73        22.45        43.96        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
       24.82        25.91         1.18         8.42        15.42       111.02 
TCGA-BP-4160 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 
       94.72         3.58        80.68        74.17        54.77        12.33 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 
       77.62        44.15        60.59        11.64        20.38        37.25 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 
        6.94        61.51        53.65        25.81        27.22         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 
       45.07        41.62        27.62        35.90        48.10        62.86 
TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 
       49.15        27.02        31.79        44.55        31.27        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 
      105.37        26.93        27.65       108.56        53.26       118.85 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
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-G6-A8L7 TCGA-MM-A84U 
       66.28        56.84        23.90        81.21        70.13        23.01 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 
       22.49        67.17        61.05        21.37         0.89        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       29.26        19.73        17.75        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
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-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       62.37       151.96        44.91        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-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       65.19       104.52         3.55         0.99        52.27        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-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87       105.47       100.47       103.40        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
      104.55       103.10        99.88       105.60        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82         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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       37.38        48.82        62.01         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       29.92        18.44        88.37        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-A3-3378 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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        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       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       73.68       112.08        68.61       109.51        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       48.36        78.64        40.01        94.29        83.21        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
        3.32         4.57         2.53        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       65.10         7.82         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
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        10.52        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-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       15.09        10.95         8.05         2.24        21.86        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        58.59 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       21.30        31.30        31.66        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       12.00         5.75         5.10         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        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         4.93        17.36 
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-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-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        37.25        21.21        15.62         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        62.86        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-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
        5.98        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         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-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       36.07        33.34        46.45        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        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       116.84 
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       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        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       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       25.25       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 
        1.35       105.93        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
       69.21        58.75        14.66        63.39        93.04       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       14.63        22.78        62.63        53.46        12.00        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
        3.91         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
        2.01        19.43        19.96        16.37        11.70         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-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       91.73        56.81        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KE TCGA-5P-A9KH 
       71.80        62.93        43.04        12.99        27.09        67.43 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       16.64        30.48        29.46        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
        0.76        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 
       16.31        15.75         8.28        12.46        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N 
       66.71        62.66        67.73         2.20        41.13        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 
       14.86        17.49        12.30        86.76         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       30.28        25.35        10.82         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
       13.08         2.40         1.18         0.43        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
       11.05        39.25        71.44        25.15        20.52        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.98        23.08        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD 
       22.26        21.34        12.36        12.76        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        78.90        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
      125.29        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                          0.95                           0.07 
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                        109.91                         194.79 
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                         18.21                          37.02 
[1] "0.9 - 109.9 (18.2)" "0.1 - 194.8 (37.0)"
[1] "hr=" "4"  
D31V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 22(19P13.3) MUTATED        10        1        18       11
  DEL PEAK 22(19P13.3) WILD-TYPE     444      102       172       93
D31V3, multiclass
           clus
vv          DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE
  STAGE I                             10                            444
  STAGE II                             1                            102
  STAGE III                           18                            172
  STAGE IV                            11                             93
[1] 4 2
[1] 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(19P13.3) MUTATED    12   2  25   4
  DEL PEAK 22(19P13.3) WILD-TYPE 468 125 233  11
D31V4, multiclass
    clus
vv   DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE
  T1                           12                            468
  T2                            2                            125
  T3                           25                            233
  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 22(19P13.3) MUTATED    11   7   3
  DEL PEAK 22(19P13.3) WILD-TYPE 312  37   3
D31V5, multiclass
    clus
vv   DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE
  N0                           11                            312
  N1                            7                             37
  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"
D31V6, binary
                                cls
clus                               0   1
  DEL PEAK 22(19P13.3) MUTATED    18   7
  DEL PEAK 22(19P13.3) WILD-TYPE 528  82
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(19P13.3) MUTATED     18    7
  DEL PEAK 22(19P13.3) WILD-TYPE  528   82
   clus
vv  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE
  0                           18                            528
  1                            7                             82
[1] 2 2
[1] FALSE
D31V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(19P13.3) MUTATED    16  27
  DEL PEAK 22(19P13.3) WILD-TYPE 276 563
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(19P13.3) MUTATED     16   27
  DEL PEAK 22(19P13.3) WILD-TYPE  276  563
        clus
vv       DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE
  FEMALE                           16                            276
  MALE                             27                            563
[1] 2 2
[1] FALSE
D31V8, binary
                                cls
clus                               0   1
  DEL PEAK 22(19P13.3) MUTATED    21   0
  DEL PEAK 22(19P13.3) WILD-TYPE 387   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(19P13.3) MUTATED     21    0
  DEL PEAK 22(19P13.3) WILD-TYPE  387    3
     clus
vv    DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE
  NO                            21                            387
  YES                            0                              3
[1] 2 2
[1] FALSE
D31V9, continuous
                                vv
clus                             KIDNEY CHROMOPHOBE
  DEL PEAK 22(19P13.3) MUTATED                    3
  DEL PEAK 22(19P13.3) WILD-TYPE                 63
                                vv
clus                             KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 22(19P13.3) MUTATED                                  17
  DEL PEAK 22(19P13.3) WILD-TYPE                               511
                                vv
clus                             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 22(19P13.3) MUTATED                                      23
  DEL PEAK 22(19P13.3) WILD-TYPE                                   265
D31V10, multiclass
                                       clus
vv                                      DEL PEAK 22(19P13.3) MUTATED
  KIDNEY CHROMOPHOBE                                               3
  KIDNEY CLEAR CELL RENAL CARCINOMA                               17
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           23
                                       clus
vv                                      DEL PEAK 22(19P13.3) WILD-TYPE
  KIDNEY CHROMOPHOBE                                                63
  KIDNEY CLEAR CELL RENAL CARCINOMA                                511
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                            265
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous
D31V12, continuous
[1] "Remove cluster labels:"       "DEL PEAK 22(19P13.3) MUTATED"
clus
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                             2                             72 
                    TCGA-DV-A4W0                     TCGA-G6-A8L7 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-MM-A84U                     TCGA-2Z-A9JD 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-DW-5561                     TCGA-PJ-A5Z9 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-UZ-A9PO                     TCGA-UZ-A9PR 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-Y8-A8RZ                     TCGA-KL-8330 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-KL-8335                     TCGA-KL-8341 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-KL-8345                     TCGA-KM-8639 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-KN-8433                     TCGA-KO-8408 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-KO-8409                     TCGA-A3-A8OV 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-A3-A8OW                     TCGA-AK-3445 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-AK-3451                     TCGA-B2-A4SR 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-B8-5158                     TCGA-B8-5550 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-MM-A563                     TCGA-T7-A92I 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-2Z-A9J3                     TCGA-2Z-A9J7 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-2Z-A9J8                     TCGA-2Z-A9JI 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-2Z-A9JN                     TCGA-2Z-A9JO 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-4A-A93W                     TCGA-4A-A93Y 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-A4-A48D                     TCGA-A4-A57E 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-A4-A5Y0                     TCGA-AL-3472 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-AL-7173                     TCGA-B1-A654 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-B9-4114                     TCGA-B9-4117 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-B9-A69E                     TCGA-DW-7963 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-F9-A97G                     TCGA-G7-6793 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-G7-6795                     TCGA-G7-7501 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-G7-A8LB                     TCGA-G7-A8LE 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-GL-7773                     TCGA-GL-A9DD 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-HE-A5NI                     TCGA-IA-A40U 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-MH-A854                     TCGA-MH-A856 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-P4-A5E6                     TCGA-P4-AAVK 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-SX-A71S                     TCGA-SX-A71U 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-SX-A7SL                     TCGA-SX-A7SM 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-SX-A7SR                     TCGA-SX-A7SS 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-UZ-A9PM                     TCGA-UZ-A9PS 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-UZ-A9PX                     TCGA-WN-A9G9 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-WN-AB4C                     TCGA-Y8-A894 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-Y8-A896                     TCGA-Y8-A8RY 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(19P13.3) MUTATED                                  0     2
  DEL PEAK 22(19P13.3) WILD-TYPE                                2    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(19P13.3) MUTATED                           5    36
  DEL PEAK 22(19P13.3) WILD-TYPE                       116   683
D31V13, multiclass
                                  clus
vv                                 DEL PEAK 22(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      36
                                  clus
vv                                 DEL PEAK 22(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        14
  BLACK OR AFRICAN AMERICAN                                   116
  WHITE                                                       683
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V14, binary
                                cls
clus                               0   1
  DEL PEAK 22(19P13.3) MUTATED     1  35
  DEL PEAK 22(19P13.3) WILD-TYPE  41 587
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(19P13.3) MUTATED      1   35
  DEL PEAK 22(19P13.3) WILD-TYPE   41  587
                        clus
vv                       DEL PEAK 22(19P13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           35
                        clus
vv                       DEL PEAK 22(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 41
  NOT HISPANIC OR LATINO                            587
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK 23(XP22.2) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 23(XP22.2) MUTATED    85  40
  DEL PEAK 23(XP22.2) WILD-TYPE 563 188
  DEL PEAK 23(XP22.2) MUTATED DEL PEAK 23(XP22.2) WILD-TYPE 
                          125                           751 
  DEL PEAK 23(XP22.2) MUTATED DEL PEAK 23(XP22.2) WILD-TYPE 
                           40                           188 
$`DEL PEAK 23(XP22.2) MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-BP-4164 TCGA-BP-4327 
      102.81        28.11        47.24       130.13        32.61         3.58 
TCGA-CJ-4894 TCGA-CJ-6027 TCGA-MM-A84U TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-KL-8323 
       27.65       118.85        23.01        12.99        11.87        38.07 
TCGA-KL-8325 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
       23.84        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 TCGA-KM-8440 TCGA-KM-8476 TCGA-KN-8418 
       73.91        71.41        54.74        44.91       123.12       129.37 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 
       87.91        25.48        65.19       104.52        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 
        2.50        59.08       115.00       105.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3306 TCGA-A3-3317 
       16.67        96.62        90.48        92.55        36.82        49.02 
TCGA-A3-3319 TCGA-A3-3383 TCGA-AK-3428 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 
       37.15        28.31       122.56        94.19        40.01        12.13 
TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-4813 
       40.70         3.32        28.47         3.62        58.45         0.59 
TCGA-B0-4827 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-5080 
       29.10        68.71        40.70        10.29        65.29        11.24 
TCGA-B0-5084 TCGA-B0-5098 TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5705 TCGA-B2-3923 
        7.30        52.08        52.87        42.41       149.16        32.61 
TCGA-B8-5159 TCGA-B8-5549 TCGA-B8-A54D TCGA-BP-4334 TCGA-BP-4761 TCGA-BP-4959 
       23.74         6.38        27.29        21.21         5.98        87.45 
TCGA-BP-5004 TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5196 TCGA-CJ-5680 
       37.02        52.27        74.40        42.44        33.47        25.25 
TCGA-CW-6090 TCGA-CZ-5458 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5985 TCGA-CZ-5986 
       83.90        91.69        21.76        84.30        65.65        12.26 
TCGA-CZ-5987 TCGA-EU-5907 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-2Z-A9J2 TCGA-2Z-A9J8 
       14.63         4.18        35.87        19.43        59.01        91.73 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K8 
       54.64        51.52        12.82        15.48        71.80        43.04 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 
       67.43        18.21        19.63        37.51        29.03        20.61 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-DZ-6131 
       19.27         8.88        22.92        21.63        25.35        79.86 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6793 TCGA-G7-6797 TCGA-G7-7501 
       10.68        13.08         0.43        11.05        25.15        20.52 
TCGA-G7-A8LD TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       16.90        10.55        14.07        18.02        86.27 

$`DEL PEAK 23(XP22.2) WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 
       23.28        28.80        47.21        38.47        34.29        31.07 
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       42.97        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       19.73        43.96        52.21        18.51       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 
       15.78        70.68       119.38       126.05        24.82        25.91 
TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4331 
        1.18         8.42        15.42       111.02        94.72        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       35.90        48.10        62.86        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4904 
       44.55        31.27        63.25       105.37        26.93       108.56 
TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
       53.26        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       21.86        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8341 TCGA-KL-8344 TCGA-KL-8346 
      153.73       109.22       137.06        24.79        28.80        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 
      151.96        49.97        51.06        31.33        23.47        25.91 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 TCGA-KN-8437 
        3.55         0.99        52.27        11.21        42.35       100.87 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       10.68       100.47       104.55       103.10        99.88       105.60 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       12.66        11.90         0.53        39.16        24.16        49.08 
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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       62.01         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       88.37        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-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 
        0.10         0.10        11.18        10.62        29.10       117.80 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
      109.41        15.78        73.68       112.08        68.61       109.51 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       46.78        48.36        78.64        94.29        83.21        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       38.40        82.45        72.89         1.41         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 
        2.53         3.48        19.00         1.38        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 
        5.98         2.14        57.70         6.64         3.25        15.72 
TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
       46.59         5.52        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        10.52 
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-B0-5092 TCGA-B0-5094 
       20.94        43.30        11.90        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        21.86        15.95        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        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       38.63        52.73        41.88        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98       111.52       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 
      126.28        80.91        71.41        73.84       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4098 
       79.89       131.15        89.49        91.46        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 
       31.96        21.30        31.30        31.66        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67        12.00         5.75         5.10         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 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       50.14        40.04        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54E 
       16.60        48.53         0.53        34.39        14.30        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
       17.06         1.74         4.93        17.36        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        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-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       15.62         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4765 
       31.33        12.30        72.59        77.98        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-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       13.51        56.91        68.38        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         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-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       30.64        18.51        38.70        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 
        6.35        79.30         2.04        74.20        30.64         9.63 
TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       38.30        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       23.47        13.41        24.62        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        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       116.84        64.27 
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       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        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       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5681 
      129.40       133.71        25.71        18.87        22.32        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
      105.93        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        6.77        14.66        63.39        93.04       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5464 TCGA-CZ-5466 
       55.33        94.45        10.85        10.22        69.96        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-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       22.78        62.63        53.46        12.00        18.12         3.91 
TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC 
        6.77         7.96        10.29         2.01        19.96        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
       11.70         7.04        75.55        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
        4.57        56.81        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
       29.36         5.29         0.13        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KA 
       90.21        22.26        78.64        62.93        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       12.39        27.09         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46         9.63        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
       67.73         2.20        41.13        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       20.32        33.83        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5878 TCGA-BQ-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-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
        7.04         7.17         3.81        40.77        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
       74.60        34.19        19.00        24.89         2.40         1.18 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 
        4.01        51.78        90.90        39.25        71.44        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        23.08        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S 
       52.27        16.01        50.60        78.90        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       41.62        26.47        53.10        43.76        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  DEL PEAK 23(XP22.2) MUTATED DEL PEAK 23(XP22.2) WILD-TYPE 
                         0.43                          0.07 
  DEL PEAK 23(XP22.2) MUTATED DEL PEAK 23(XP22.2) WILD-TYPE 
                       149.16                        194.79 
  DEL PEAK 23(XP22.2) MUTATED DEL PEAK 23(XP22.2) WILD-TYPE 
                        38.07                         34.85 
[1] "0.4 - 149.2 (38.1)" "0.1 - 194.8 (34.9)"
[1] "hr=" "1.1"
D32V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 23(XP22.2) MUTATED        41       23        39       15
  DEL PEAK 23(XP22.2) WILD-TYPE     413       80       151       89
D32V3, multiclass
           clus
vv          DEL PEAK 23(XP22.2) MUTATED DEL PEAK 23(XP22.2) WILD-TYPE
  STAGE I                            41                           413
  STAGE II                           23                            80
  STAGE III                          39                           151
  STAGE IV                           15                            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 23(XP22.2) MUTATED    45  26  51   3
  DEL PEAK 23(XP22.2) WILD-TYPE 435 101 207  12
D32V4, multiclass
    clus
vv   DEL PEAK 23(XP22.2) MUTATED DEL PEAK 23(XP22.2) WILD-TYPE
  T1                          45                           435
  T2                          26                           101
  T3                          51                           207
  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 23(XP22.2) MUTATED    47  12   2
  DEL PEAK 23(XP22.2) WILD-TYPE 276  32   4
D32V5, multiclass
    clus
vv   DEL PEAK 23(XP22.2) MUTATED DEL PEAK 23(XP22.2) WILD-TYPE
  N0                          47                           276
  N1                          12                            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 23(XP22.2) MUTATED    71  11
  DEL PEAK 23(XP22.2) WILD-TYPE 475  78
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(XP22.2) MUTATED     71   11
  DEL PEAK 23(XP22.2) WILD-TYPE  475   78
   clus
vv  DEL PEAK 23(XP22.2) MUTATED DEL PEAK 23(XP22.2) WILD-TYPE
  0                          71                           475
  1                          11                            78
[1] 2 2
[1] FALSE
D32V7, binary
                               cls
clus                              0   1
  DEL PEAK 23(XP22.2) MUTATED    45  80
  DEL PEAK 23(XP22.2) WILD-TYPE 247 510
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(XP22.2) MUTATED     45   80
  DEL PEAK 23(XP22.2) WILD-TYPE  247  510
        clus
vv       DEL PEAK 23(XP22.2) MUTATED DEL PEAK 23(XP22.2) WILD-TYPE
  FEMALE                          45                           247
  MALE                            80                           510
[1] 2 2
[1] FALSE
D32V8, binary
                               cls
clus                              0   1
  DEL PEAK 23(XP22.2) MUTATED    74   0
  DEL PEAK 23(XP22.2) WILD-TYPE 334   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(XP22.2) MUTATED     74    0
  DEL PEAK 23(XP22.2) WILD-TYPE  334    3
     clus
vv    DEL PEAK 23(XP22.2) MUTATED DEL PEAK 23(XP22.2) WILD-TYPE
  NO                           74                           334
  YES                           0                             3
[1] 2 2
[1] FALSE
D32V9, continuous
                               vv
clus                            KIDNEY CHROMOPHOBE
  DEL PEAK 23(XP22.2) MUTATED                   39
  DEL PEAK 23(XP22.2) WILD-TYPE                 27
                               vv
clus                            KIDNEY CLEAR CELL RENAL CARCINOMA
  DEL PEAK 23(XP22.2) MUTATED                                  53
  DEL PEAK 23(XP22.2) WILD-TYPE                               475
                               vv
clus                            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DEL PEAK 23(XP22.2) MUTATED                                      33
  DEL PEAK 23(XP22.2) WILD-TYPE                                   255
D32V10, multiclass
                                       clus
vv                                      DEL PEAK 23(XP22.2) MUTATED
  KIDNEY CHROMOPHOBE                                             39
  KIDNEY CLEAR CELL RENAL CARCINOMA                              53
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                          33
                                       clus
vv                                      DEL PEAK 23(XP22.2) WILD-TYPE
  KIDNEY CHROMOPHOBE                                               27
  KIDNEY CLEAR CELL RENAL CARCINOMA                               475
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                           255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, continuous
D32V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(XP22.2) MUTATED                                  0     4
  DEL PEAK 23(XP22.2) WILD-TYPE                                2    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(XP22.2) MUTATED                          18    98
  DEL PEAK 23(XP22.2) WILD-TYPE                       103   621
D32V13, multiclass
                                  clus
vv                                 DEL PEAK 23(XP22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 18
  WHITE                                                     98
                                  clus
vv                                 DEL PEAK 23(XP22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                  103
  WHITE                                                      621
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
                               cls
clus                              0   1
  DEL PEAK 23(XP22.2) MUTATED     3  77
  DEL PEAK 23(XP22.2) WILD-TYPE  39 545
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(XP22.2) MUTATED      3   77
  DEL PEAK 23(XP22.2) WILD-TYPE   39  545
                        clus
vv                       DEL PEAK 23(XP22.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          77
                        clus
vv                       DEL PEAK 23(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                39
  NOT HISPANIC OR LATINO                           545
[1] 2 2
[1] FALSE
