[1] "ofn"        "-oTTHCA-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/THCA-TP/22507188/THCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/22511444/transformed.cor.cli.txt"

nPatients in clinical file=503, in cluster file=499, common to both=499
[1] "Reduce the number of clustering variables from 42 to 36."
[1]  36 499
[1] "AMP PEAK 1(1Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(1Q31.2) MUTATED AMP PEAK 1(1Q31.2) WILD-TYPE 
                          29                          470 
  AMP PEAK 1(1Q31.2) MUTATED AMP PEAK 1(1Q31.2) WILD-TYPE 
                          29                          470 
[1] "AMP PEAK 3(4Q31.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(4Q31.21) MUTATED AMP PEAK 3(4Q31.21) WILD-TYPE 
                            9                           490 
  AMP PEAK 3(4Q31.21) MUTATED AMP PEAK 3(4Q31.21) WILD-TYPE 
                            9                           490 
[1] "AMP PEAK 4(5Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(5Q21.1) MUTATED AMP PEAK 4(5Q21.1) WILD-TYPE 
                          23                          476 
  AMP PEAK 4(5Q21.1) MUTATED AMP PEAK 4(5Q21.1) WILD-TYPE 
                          23                          476 
[1] "AMP PEAK 5(5Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 5(5Q33.1) MUTATED AMP PEAK 5(5Q33.1) WILD-TYPE 
                          21                          478 
  AMP PEAK 5(5Q33.1) MUTATED AMP PEAK 5(5Q33.1) WILD-TYPE 
                          21                          478 
[1] "AMP PEAK 6(13Q14.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 6(13Q14.2) MUTATED AMP PEAK 6(13Q14.2) WILD-TYPE 
                            6                           493 
  AMP PEAK 6(13Q14.2) MUTATED AMP PEAK 6(13Q14.2) WILD-TYPE 
                            6                           493 
[1] "AMP PEAK 7(22Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 7(22Q11.21) MUTATED AMP PEAK 7(22Q11.21) WILD-TYPE 
                             7                            492 
  AMP PEAK 7(22Q11.21) MUTATED AMP PEAK 7(22Q11.21) WILD-TYPE 
                             7                            492 
[1] "AMP PEAK 8(XP11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 8(XP11.22) MUTATED AMP PEAK 8(XP11.22) WILD-TYPE 
                            8                           491 
  AMP PEAK 8(XP11.22) MUTATED AMP PEAK 8(XP11.22) WILD-TYPE 
                            8                           491 
[1] "AMP PEAK 9(XQ22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 9(XQ22.3) MUTATED AMP PEAK 9(XQ22.3) WILD-TYPE 
                          15                          484 
  AMP PEAK 9(XQ22.3) MUTATED AMP PEAK 9(XQ22.3) WILD-TYPE 
                          15                          484 
[1] "DEL PEAK  1(1Q42.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1Q42.13) MUTATED DEL PEAK  1(1Q42.13) WILD-TYPE 
                             5                            494 
  DEL PEAK  1(1Q42.13) MUTATED DEL PEAK  1(1Q42.13) WILD-TYPE 
                             5                            494 
[1] "DEL PEAK  2(2P23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(2P23.1) MUTATED DEL PEAK  2(2P23.1) WILD-TYPE 
                           12                           487 
  DEL PEAK  2(2P23.1) MUTATED DEL PEAK  2(2P23.1) WILD-TYPE 
                           12                           487 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           10                           489 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           10                           489 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           13                           486 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           13                           486 
[1] "DEL PEAK  5(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                            5                           494 
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                            5                           494 
[1] "DEL PEAK  6(5P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE 
                            4                           495 
  DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE 
                            4                           495 
[1] "DEL PEAK 10(7Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE 
                          4                         495 
  DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE 
                          4                         495 
[1] "DEL PEAK 11(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                            4                           495 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                            4                           495 
[1] "DEL PEAK 12(8P22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE 
                          4                         495 
  DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE 
                          4                         495 
[1] "DEL PEAK 13(8P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE 
                          4                         495 
  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE 
                          4                         495 
[1] "DEL PEAK 14(8Q24.22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8Q24.22) MUTATED DEL PEAK 14(8Q24.22) WILD-TYPE 
                             7                            492 
  DEL PEAK 14(8Q24.22) MUTATED DEL PEAK 14(8Q24.22) WILD-TYPE 
                             7                            492 
[1] "DEL PEAK 15(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                           20                           479 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                           20                           479 
[1] "DEL PEAK 16(9Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(9Q22.33) MUTATED DEL PEAK 16(9Q22.33) WILD-TYPE 
                            27                            472 
  DEL PEAK 16(9Q22.33) MUTATED DEL PEAK 16(9Q22.33) WILD-TYPE 
                            27                            472 
[1] "DEL PEAK 17(10P12.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(10P12.31) MUTATED DEL PEAK 17(10P12.31) WILD-TYPE 
                              7                             492 
  DEL PEAK 17(10P12.31) MUTATED DEL PEAK 17(10P12.31) WILD-TYPE 
                              7                             492 
[1] "DEL PEAK 18(10Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10Q21.2) MUTATED DEL PEAK 18(10Q21.2) WILD-TYPE 
                            12                            487 
  DEL PEAK 18(10Q21.2) MUTATED DEL PEAK 18(10Q21.2) WILD-TYPE 
                            12                            487 
[1] "DEL PEAK 19(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                             12                             487 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                             12                             487 
[1] "DEL PEAK 20(13Q12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(13Q12.3) MUTATED DEL PEAK 20(13Q12.3) WILD-TYPE 
                            16                            483 
  DEL PEAK 20(13Q12.3) MUTATED DEL PEAK 20(13Q12.3) WILD-TYPE 
                            16                            483 
[1] "DEL PEAK 21(13Q14.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(13Q14.3) MUTATED DEL PEAK 21(13Q14.3) WILD-TYPE 
                            20                            479 
  DEL PEAK 21(13Q14.3) MUTATED DEL PEAK 21(13Q14.3) WILD-TYPE 
                            20                            479 
[1] "DEL PEAK 23(15Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(15Q25.3) MUTATED DEL PEAK 23(15Q25.3) WILD-TYPE 
                             8                            491 
  DEL PEAK 23(15Q25.3) MUTATED DEL PEAK 23(15Q25.3) WILD-TYPE 
                             8                            491 
[1] "DEL PEAK 24(16Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(16Q23.3) MUTATED DEL PEAK 24(16Q23.3) WILD-TYPE 
                             6                            493 
  DEL PEAK 24(16Q23.3) MUTATED DEL PEAK 24(16Q23.3) WILD-TYPE 
                             6                            493 
[1] "DEL PEAK 25(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(17P13.1) MUTATED DEL PEAK 25(17P13.1) WILD-TYPE 
                             8                            491 
  DEL PEAK 25(17P13.1) MUTATED DEL PEAK 25(17P13.1) WILD-TYPE 
                             8                            491 
[1] "DEL PEAK 26(18Q21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(18Q21.33) MUTATED DEL PEAK 26(18Q21.33) WILD-TYPE 
                              5                             494 
  DEL PEAK 26(18Q21.33) MUTATED DEL PEAK 26(18Q21.33) WILD-TYPE 
                              5                             494 
[1] "DEL PEAK 27(19P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE 
                             7                            492 
  DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE 
                             7                            492 
[1] "DEL PEAK 28(19P13.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE 
                              8                             491 
  DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE 
                              8                             491 
[1] "DEL PEAK 30(21Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(21Q21.1) MUTATED DEL PEAK 30(21Q21.1) WILD-TYPE 
                             9                            490 
  DEL PEAK 30(21Q21.1) MUTATED DEL PEAK 30(21Q21.1) WILD-TYPE 
                             9                            490 
[1] "DEL PEAK 31(22Q13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(22Q13.1) MUTATED DEL PEAK 31(22Q13.1) WILD-TYPE 
                            89                            410 
  DEL PEAK 31(22Q13.1) MUTATED DEL PEAK 31(22Q13.1) WILD-TYPE 
                            89                            410 
[1] "DEL PEAK 32(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             90                             409 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             90                             409 
[1] "DEL PEAK 33(XQ28) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE 
                          4                         495 
  DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE 
                          4                         495 
[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] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RADIATION_EXPOSURE"                  
[15] "EXTRATHYROIDAL_EXTENSION"            
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "MULTIFOCALITY"                       
[19] "TUMOR_SIZE"                          
[20] "RACE"                                
[21] "ETHNICITY"                           

Input Data has 21 rows and 499 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=73,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=16,	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=433,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	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=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATION_EXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'EXTRATHYROIDAL_EXTENSION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'TUMOR_SIZE':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[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 499 columns, 1 survival variables, and 16 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"        "HISTOLOGICAL_TYPE"       
 [9] "RADIATION_EXPOSURE"       "EXTRATHYROIDAL_EXTENSION"
[11] "RESIDUAL_TUMOR"           "NUMBER_OF_LYMPH_NODES"   
[13] "MULTIFOCALITY"            "TUMOR_SIZE"              
[15] "RACE"                     "ETHNICITY"               
YEARS_TO_BIRTH, nv=73, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
142 165 167  23 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
142 165 167  23 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
142 165 167  23 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
142 165 167  23 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATION_EXPOSURE, nv=2, binary=FALSE, numeric=FALSE
EXTRATHYROIDAL_EXTENSION, nv=4, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=28, binary=FALSE, numeric=TRUE
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SIZE, nv=61, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 1(1Q31.2) MUTATION ANALYSIS
D1V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 1(1Q31.2) MUTATED    27   2
  AMP PEAK 1(1Q31.2) WILD-TYPE 455  14
  AMP PEAK 1(1Q31.2) MUTATED AMP PEAK 1(1Q31.2) WILD-TYPE 
                          29                          469 
  AMP PEAK 1(1Q31.2) MUTATED AMP PEAK 1(1Q31.2) WILD-TYPE 
                           2                           14 
$`AMP PEAK 1(1Q31.2) MUTATED`
TCGA-BJ-A290 TCGA-4C-A93U TCGA-BJ-A192 TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       30.21         4.24        44.35        11.57        30.02        25.12 
TCGA-DJ-A13U TCGA-DO-A2HM TCGA-EL-A3GP TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3MZ 
       52.27         2.33        49.51       136.01        83.57        52.50 
TCGA-EL-A3T9 TCGA-EL-A3ZO TCGA-EL-A4JX TCGA-EM-A3O3 TCGA-ET-A39P TCGA-ET-A3BT 
        5.72        72.69        45.96        14.50        95.34        87.62 
TCGA-FE-A231 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A40L TCGA-FY-A4B0 TCGA-H2-A26U 
       31.59        29.10        19.56        23.87        13.81        17.00 
TCGA-IM-A3EB TCGA-IM-A3U2 TCGA-J8-A3O1 TCGA-KS-A4IB TCGA-L6-A4EU 
       48.92        18.51        27.19        84.72         9.50 

$`AMP PEAK 1(1Q31.2) WILD-TYPE`
TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L TCGA-DJ-A2PR 
       22.88        23.18        12.66        35.84         9.96        27.45 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK TCGA-E3-A3E5 
       23.44        59.57        42.54         3.12        24.76        39.95 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 TCGA-EL-A3GQ 
        7.66        45.53         4.18       139.86        57.11        50.24 
TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO 
       33.50       150.48        17.52       178.29        29.72        50.40 
TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET 
       75.42         1.05         1.68        17.23         2.60        21.83 
TCGA-MK-A84Z TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
       23.93        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       11.08        18.38        16.57        20.48        18.97        12.82 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       21.63        19.43        23.47        12.30        12.79        12.46 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 
       11.38        10.68        15.02        12.43        12.66        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        27.32        18.54        18.84        30.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
       18.58         8.71        56.19        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ 
       15.81        35.38        54.90        21.53        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
      115.10        65.39        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H7 TCGA-EL-A3MW 
      139.99        49.32        43.36        49.71       139.00       108.66 
TCGA-EL-A3MX TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       57.63        29.65       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       98.24        41.29       107.47        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZP 
       91.17        51.78        62.30        36.03        53.06        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       61.02        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.46        78.61        57.01        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33        12.53         9.24        27.02        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39R 
      107.41       108.46        84.89       123.32       100.57        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       31.40        73.74        71.44        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       17.82         7.82        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08        23.31        21.63        17.06        17.36        15.16 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A2K9 
       22.49        19.04        14.04        21.60        12.53        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3ED TCGA-IM-A3U3 
       12.46        11.01        20.05        18.61        47.41        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O2 
       21.83        31.10         8.22        25.64        43.17        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID 
       43.69        18.64        32.45        87.39        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV 
       33.40        40.37        36.10        32.45        30.21        12.89 
TCGA-E8-A418 
        3.02 

  AMP PEAK 1(1Q31.2) MUTATED AMP PEAK 1(1Q31.2) WILD-TYPE 
                        2.33                         0.20 
  AMP PEAK 1(1Q31.2) MUTATED AMP PEAK 1(1Q31.2) WILD-TYPE 
                      136.01                       178.29 
  AMP PEAK 1(1Q31.2) MUTATED AMP PEAK 1(1Q31.2) WILD-TYPE 
                       30.02                        31.27 
[1] "2.3 - 136.0 (30.0)" "0.2 - 178.3 (31.3)"
[1] "hr=" "2.4"
D1V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 1(1Q31.2) MUTATED         7        0        12        1         9
  AMP PEAK 1(1Q31.2) WILD-TYPE     275       50        99        1        37
                              vv
clus                           STAGE IVC
  AMP PEAK 1(1Q31.2) MUTATED           0
  AMP PEAK 1(1Q31.2) WILD-TYPE         6
D1V3, multiclass
           clus
vv          AMP PEAK 1(1Q31.2) MUTATED AMP PEAK 1(1Q31.2) WILD-TYPE
  STAGE I                            7                          275
  STAGE II                           0                           50
  STAGE III                         12                           99
  STAGE IV                           1                            1
  STAGE IVA                          9                           37
  STAGE IVC                          0                            6
[1] 6 2
[1] 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(1Q31.2) MUTATED     2   4  18   5
  AMP PEAK 1(1Q31.2) WILD-TYPE 140 161 149  18
D1V4, multiclass
    clus
vv   AMP PEAK 1(1Q31.2) MUTATED AMP PEAK 1(1Q31.2) WILD-TYPE
  T1                          2                          140
  T2                          4                          161
  T3                         18                          149
  T4                          5                           18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                              cls
clus                             0   1
  AMP PEAK 1(1Q31.2) MUTATED     5  22
  AMP PEAK 1(1Q31.2) WILD-TYPE 220 202
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q31.2) MUTATED      5   22
  AMP PEAK 1(1Q31.2) WILD-TYPE  220  202
   clus
vv  AMP PEAK 1(1Q31.2) MUTATED AMP PEAK 1(1Q31.2) WILD-TYPE
  0                          5                          220
  1                         22                          202
[1] 2 2
[1] FALSE
D1V6, binary
                              cls
clus                             0   1
  AMP PEAK 1(1Q31.2) MUTATED    14   0
  AMP PEAK 1(1Q31.2) WILD-TYPE 264   9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q31.2) MUTATED     14    0
  AMP PEAK 1(1Q31.2) WILD-TYPE  264    9
   clus
vv  AMP PEAK 1(1Q31.2) MUTATED AMP PEAK 1(1Q31.2) WILD-TYPE
  0                         14                          264
  1                          0                            9
[1] 2 2
[1] FALSE
D1V7, binary
                              cls
clus                             0   1
  AMP PEAK 1(1Q31.2) MUTATED    20   9
  AMP PEAK 1(1Q31.2) WILD-TYPE 345 125
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q31.2) MUTATED     20    9
  AMP PEAK 1(1Q31.2) WILD-TYPE  345  125
        clus
vv       AMP PEAK 1(1Q31.2) MUTATED AMP PEAK 1(1Q31.2) WILD-TYPE
  FEMALE                         20                          345
  MALE                            9                          125
[1] 2 2
[1] FALSE
D1V8, binary
                              cls
clus                             0   1
  AMP PEAK 1(1Q31.2) MUTATED     7  19
  AMP PEAK 1(1Q31.2) WILD-TYPE 173 284
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q31.2) MUTATED      7   19
  AMP PEAK 1(1Q31.2) WILD-TYPE  173  284
     clus
vv    AMP PEAK 1(1Q31.2) MUTATED AMP PEAK 1(1Q31.2) WILD-TYPE
  NO                           7                          173
  YES                         19                          284
[1] 2 2
[1] FALSE
                              vv
clus                           OTHER, SPECIFY
  AMP PEAK 1(1Q31.2) MUTATED                0
  AMP PEAK 1(1Q31.2) WILD-TYPE              7
                              vv
clus                           THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 1(1Q31.2) MUTATED                                              25
  AMP PEAK 1(1Q31.2) WILD-TYPE                                           331
                              vv
clus                           THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 1(1Q31.2) MUTATED                                                                        0
  AMP PEAK 1(1Q31.2) WILD-TYPE                                                                    100
                              vv
clus                           THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 1(1Q31.2) MUTATED                                                                     4
  AMP PEAK 1(1Q31.2) WILD-TYPE                                                                  32
D1V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 1(1Q31.2) MUTATED
  OTHER, SPECIFY                                                                                  0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  25
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             4
                                                                        clus
vv                                                                       AMP PEAK 1(1Q31.2) WILD-TYPE
  OTHER, SPECIFY                                                                                    7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   331
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
                              cls
clus                             0   1
  AMP PEAK 1(1Q31.2) MUTATED    26   1
  AMP PEAK 1(1Q31.2) WILD-TYPE 394  16
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q31.2) MUTATED     26    1
  AMP PEAK 1(1Q31.2) WILD-TYPE  394   16
     clus
vv    AMP PEAK 1(1Q31.2) MUTATED AMP PEAK 1(1Q31.2) WILD-TYPE
  NO                          26                          394
  YES                          1                           16
[1] 2 2
[1] FALSE
                              vv
clus                           MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 1(1Q31.2) MUTATED             14                       4   10
  AMP PEAK 1(1Q31.2) WILD-TYPE          118                      14  320
                              vv
clus                           VERY ADVANCED (T4B)
  AMP PEAK 1(1Q31.2) MUTATED                     1
  AMP PEAK 1(1Q31.2) WILD-TYPE                   0
D1V11, multiclass
                         clus
vv                        AMP PEAK 1(1Q31.2) MUTATED
  MINIMAL (T3)                                    14
  MODERATE/ADVANCED (T4A)                          4
  NONE                                            10
  VERY ADVANCED (T4B)                              1
                         clus
vv                        AMP PEAK 1(1Q31.2) WILD-TYPE
  MINIMAL (T3)                                     118
  MODERATE/ADVANCED (T4A)                           14
  NONE                                             320
  VERY ADVANCED (T4B)                                0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 1(1Q31.2) MUTATED    17   6   0   4
  AMP PEAK 1(1Q31.2) WILD-TYPE 366  45   4  26
D1V12, multiclass
    clus
vv   AMP PEAK 1(1Q31.2) MUTATED AMP PEAK 1(1Q31.2) WILD-TYPE
  R0                         17                          366
  R1                          6                           45
  R2                          0                            4
  RX                          4                           26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, continuous
D1V14, binary
                              cls
clus                             0   1
  AMP PEAK 1(1Q31.2) MUTATED     9  20
  AMP PEAK 1(1Q31.2) WILD-TYPE 216 244
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q31.2) MUTATED      9   20
  AMP PEAK 1(1Q31.2) WILD-TYPE  216  244
            clus
vv           AMP PEAK 1(1Q31.2) MUTATED AMP PEAK 1(1Q31.2) WILD-TYPE
  MULTIFOCAL                          9                          216
  UNIFOCAL                           20                          244
[1] 2 2
[1] FALSE
D1V15, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 1(1Q31.2) MUTATED                                  1     1
  AMP PEAK 1(1Q31.2) WILD-TYPE                                0    51
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 1(1Q31.2) MUTATED                           5    21
  AMP PEAK 1(1Q31.2) WILD-TYPE                        22   308
D1V16, multiclass
                                  clus
vv                                 AMP PEAK 1(1Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 5
  WHITE                                                    21
                                  clus
vv                                 AMP PEAK 1(1Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      51
  BLACK OR AFRICAN AMERICAN                                  22
  WHITE                                                     308
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V17, binary
                              cls
clus                             0   1
  AMP PEAK 1(1Q31.2) MUTATED     6  20
  AMP PEAK 1(1Q31.2) WILD-TYPE  32 340
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q31.2) MUTATED      6   20
  AMP PEAK 1(1Q31.2) WILD-TYPE   32  340
                        clus
vv                       AMP PEAK 1(1Q31.2) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                         20
                        clus
vv                       AMP PEAK 1(1Q31.2) WILD-TYPE
  HISPANIC OR LATINO                               32
  NOT HISPANIC OR LATINO                          340
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK 3(4Q31.21) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 3(4Q31.21) MUTATED     8   1
  AMP PEAK 3(4Q31.21) WILD-TYPE 474  15
  AMP PEAK 3(4Q31.21) MUTATED AMP PEAK 3(4Q31.21) WILD-TYPE 
                            9                           489 
  AMP PEAK 3(4Q31.21) MUTATED AMP PEAK 3(4Q31.21) WILD-TYPE 
                            1                            15 
$`AMP PEAK 3(4Q31.21) MUTATED`
TCGA-FY-A76V TCGA-DJ-A3V2 TCGA-EL-A3T1 TCGA-EM-A1YD TCGA-EM-A22N TCGA-ET-A39P 
        1.68        20.22       129.57        57.01        10.65        95.34 
TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       33.63         7.82        29.10 

$`AMP PEAK 3(4Q31.21) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET 
       50.40        75.42         1.05        17.23         2.60        21.83 
TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       23.93         4.24        24.79        13.78        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 
       25.48        15.12        42.08        51.39        41.52        20.58 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       36.99        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      142.52        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        91.17        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        72.69        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       61.02        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        78.61        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        44.52         8.35 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        27.02        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39S 
      108.46        84.89       123.32       100.57        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A 
       68.22       117.40        66.77       112.80        39.95        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       17.82        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08        23.31        21.63        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 
       23.87        22.49        19.04        13.81        14.04        21.60 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46        11.01        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
       31.10         8.22        25.64        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.24        33.40        40.37         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       30.21        12.89         3.02 

  AMP PEAK 3(4Q31.21) MUTATED AMP PEAK 3(4Q31.21) WILD-TYPE 
                         1.68                          0.20 
  AMP PEAK 3(4Q31.21) MUTATED AMP PEAK 3(4Q31.21) WILD-TYPE 
                       129.57                        178.29 
  AMP PEAK 3(4Q31.21) MUTATED AMP PEAK 3(4Q31.21) WILD-TYPE 
                        29.10                         31.27 
[1] "1.7 - 129.6 (29.1)" "0.2 - 178.3 (31.3)"
[1] "hr=" "3.3"
D2V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 3(4Q31.21) MUTATED         3        2         4        0         0
  AMP PEAK 3(4Q31.21) WILD-TYPE     279       48       107        2        46
                               vv
clus                            STAGE IVC
  AMP PEAK 3(4Q31.21) MUTATED           0
  AMP PEAK 3(4Q31.21) WILD-TYPE         6
D2V3, multiclass
           clus
vv          AMP PEAK 3(4Q31.21) MUTATED AMP PEAK 3(4Q31.21) WILD-TYPE
  STAGE I                             3                           279
  STAGE II                            2                            48
  STAGE III                           4                           107
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] 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(4Q31.21) MUTATED     1   4   4   0
  AMP PEAK 3(4Q31.21) WILD-TYPE 141 161 163  23
D2V4, multiclass
    clus
vv   AMP PEAK 3(4Q31.21) MUTATED AMP PEAK 3(4Q31.21) WILD-TYPE
  T1                           1                           141
  T2                           4                           161
  T3                           4                           163
  T4                           0                            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"
D2V5, binary
                               cls
clus                              0   1
  AMP PEAK 3(4Q31.21) MUTATED     7   1
  AMP PEAK 3(4Q31.21) WILD-TYPE 218 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(4Q31.21) MUTATED      7    1
  AMP PEAK 3(4Q31.21) WILD-TYPE  218  223
   clus
vv  AMP PEAK 3(4Q31.21) MUTATED AMP PEAK 3(4Q31.21) WILD-TYPE
  0                           7                           218
  1                           1                           223
[1] 2 2
[1] FALSE
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK 3(4Q31.21) MUTATED     2   0
  AMP PEAK 3(4Q31.21) WILD-TYPE 276   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(4Q31.21) MUTATED      2    0
  AMP PEAK 3(4Q31.21) WILD-TYPE  276    9
   clus
vv  AMP PEAK 3(4Q31.21) MUTATED AMP PEAK 3(4Q31.21) WILD-TYPE
  0                           2                           276
  1                           0                             9
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK 3(4Q31.21) MUTATED     7   2
  AMP PEAK 3(4Q31.21) WILD-TYPE 358 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(4Q31.21) MUTATED      7    2
  AMP PEAK 3(4Q31.21) WILD-TYPE  358  132
        clus
vv       AMP PEAK 3(4Q31.21) MUTATED AMP PEAK 3(4Q31.21) WILD-TYPE
  FEMALE                           7                           358
  MALE                             2                           132
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK 3(4Q31.21) MUTATED     3   3
  AMP PEAK 3(4Q31.21) WILD-TYPE 177 300
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(4Q31.21) MUTATED      3    3
  AMP PEAK 3(4Q31.21) WILD-TYPE  177  300
     clus
vv    AMP PEAK 3(4Q31.21) MUTATED AMP PEAK 3(4Q31.21) WILD-TYPE
  NO                            3                           177
  YES                           3                           300
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER, SPECIFY
  AMP PEAK 3(4Q31.21) MUTATED                0
  AMP PEAK 3(4Q31.21) WILD-TYPE              7
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 3(4Q31.21) MUTATED                                               6
  AMP PEAK 3(4Q31.21) WILD-TYPE                                           350
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 3(4Q31.21) MUTATED                                                                        3
  AMP PEAK 3(4Q31.21) WILD-TYPE                                                                     97
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 3(4Q31.21) MUTATED                                                                     0
  AMP PEAK 3(4Q31.21) WILD-TYPE                                                                  36
D2V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 3(4Q31.21) MUTATED
  OTHER, SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 3(4Q31.21) WILD-TYPE
  OTHER, SPECIFY                                                                                     7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
                               cls
clus                              0   1
  AMP PEAK 3(4Q31.21) MUTATED     8   0
  AMP PEAK 3(4Q31.21) WILD-TYPE 412  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(4Q31.21) MUTATED      8    0
  AMP PEAK 3(4Q31.21) WILD-TYPE  412   17
     clus
vv    AMP PEAK 3(4Q31.21) MUTATED AMP PEAK 3(4Q31.21) WILD-TYPE
  NO                            8                           412
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 3(4Q31.21) MUTATED              3                       0    6
  AMP PEAK 3(4Q31.21) WILD-TYPE          129                      18  324
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 3(4Q31.21) MUTATED                     0
  AMP PEAK 3(4Q31.21) WILD-TYPE                   1
D2V11, multiclass
                         clus
vv                        AMP PEAK 3(4Q31.21) MUTATED
  MINIMAL (T3)                                      3
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              6
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 3(4Q31.21) WILD-TYPE
  MINIMAL (T3)                                      129
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              324
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 3(4Q31.21) MUTATED     7   1   0   1
  AMP PEAK 3(4Q31.21) WILD-TYPE 376  50   4  29
D2V12, multiclass
    clus
vv   AMP PEAK 3(4Q31.21) MUTATED AMP PEAK 3(4Q31.21) WILD-TYPE
  R0                           7                           376
  R1                           1                            50
  R2                           0                             4
  RX                           1                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, continuous
D2V14, binary
                               cls
clus                              0   1
  AMP PEAK 3(4Q31.21) MUTATED     6   3
  AMP PEAK 3(4Q31.21) WILD-TYPE 219 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(4Q31.21) MUTATED      6    3
  AMP PEAK 3(4Q31.21) WILD-TYPE  219  261
            clus
vv           AMP PEAK 3(4Q31.21) MUTATED AMP PEAK 3(4Q31.21) WILD-TYPE
  MULTIFOCAL                           6                           219
  UNIFOCAL                             3                           261
[1] 2 2
[1] FALSE
D2V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 3(4Q31.21) MUTATED                                  0     0
  AMP PEAK 3(4Q31.21) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 3(4Q31.21) MUTATED                           3     4
  AMP PEAK 3(4Q31.21) WILD-TYPE                        24   325
D2V16, multiclass
                                  clus
vv                                 AMP PEAK 3(4Q31.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                      4
                                  clus
vv                                 AMP PEAK 3(4Q31.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   24
  WHITE                                                      325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V17, binary
                               cls
clus                              0   1
  AMP PEAK 3(4Q31.21) MUTATED     0   7
  AMP PEAK 3(4Q31.21) WILD-TYPE  38 353
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(4Q31.21) MUTATED      0    7
  AMP PEAK 3(4Q31.21) WILD-TYPE   38  353
                        clus
vv                       AMP PEAK 3(4Q31.21) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           7
                        clus
vv                       AMP PEAK 3(4Q31.21) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           353
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK 4(5Q21.1) MUTATION ANALYSIS
D3V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 4(5Q21.1) MUTATED    21   2
  AMP PEAK 4(5Q21.1) WILD-TYPE 461  14
  AMP PEAK 4(5Q21.1) MUTATED AMP PEAK 4(5Q21.1) WILD-TYPE 
                          23                          475 
  AMP PEAK 4(5Q21.1) MUTATED AMP PEAK 4(5Q21.1) WILD-TYPE 
                           2                           14 
$`AMP PEAK 4(5Q21.1) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A28X TCGA-BJ-A2N9 TCGA-DJ-A3UK TCGA-DJ-A3US TCGA-DO-A2HM 
       20.58        30.97        20.48        36.92        32.81         2.33 
TCGA-EL-A3T3 TCGA-EL-A3T9 TCGA-EL-A3ZM TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1YC 
      132.07         5.72        36.03        47.84        23.90        78.61 
TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY 
       57.01        10.65         6.05        32.32        22.52        13.51 
TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       37.25       123.32        33.63         7.82        29.10 

$`AMP PEAK 4(5Q21.1) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       11.31        11.08        18.38        16.57        18.97        12.82 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       21.63        19.43        23.47        12.30        12.79        12.46 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 
       11.38        10.68        15.02        12.43        12.66        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        27.32        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       52.27        43.17        52.37         8.32        48.07       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.99        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       35.41        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74        43.96 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UM TCGA-DJ-A3UN 
       35.90        33.53        35.18        39.95        31.04        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3UT TCGA-DJ-A3UX 
       31.46        16.41        19.56        36.33        36.33        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 
       35.87        40.96        36.99        20.22        30.61        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        40.70 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         9.60        35.67        36.43        23.44        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       30.87        30.12        33.04        34.78        27.06        26.93 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       35.54         3.12        15.81        35.38        54.90        21.53 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       31.30        30.84        25.45        30.61        31.27        31.33 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96        39.88        33.50        31.00        30.15        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 
       37.94        57.01       106.62        79.50        98.53        69.57 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        64.87        49.51       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX 
       43.36        49.71        83.57       139.00       108.66        57.63 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T6 
       52.50        29.65       142.52       129.57        32.48        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29       107.47        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       51.78        62.30        53.06        72.69        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       61.02        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       41.13        43.59        24.30        27.06        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        48.49        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        44.52         8.35 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        27.02        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.95        29.85        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       88.41        58.75        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW 
       79.10        76.64         5.79        87.62        77.82        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       66.77       112.80        39.95        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON 
       48.10       116.09         1.25        20.42        17.82        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
       21.63        17.06        17.36        15.16        23.87        22.49 
TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04        13.81        14.04        21.60        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46        11.01        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       25.64        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F 
       24.69        22.29         5.75         2.47         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV 
       40.37         9.50        36.10        32.45        30.21        12.89 
TCGA-E8-A418 
        3.02 

  AMP PEAK 4(5Q21.1) MUTATED AMP PEAK 4(5Q21.1) WILD-TYPE 
                        2.33                         0.20 
  AMP PEAK 4(5Q21.1) MUTATED AMP PEAK 4(5Q21.1) WILD-TYPE 
                      132.07                       178.29 
  AMP PEAK 4(5Q21.1) MUTATED AMP PEAK 4(5Q21.1) WILD-TYPE 
                       30.97                        31.27 
[1] "2.3 - 132.1 (31.0)" "0.2 - 178.3 (31.3)"
[1] "hr=" "3.5"
D3V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 4(5Q21.1) MUTATED         8        7         5        1         2
  AMP PEAK 4(5Q21.1) WILD-TYPE     274       43       106        1        44
                              vv
clus                           STAGE IVC
  AMP PEAK 4(5Q21.1) MUTATED           0
  AMP PEAK 4(5Q21.1) WILD-TYPE         6
D3V3, multiclass
           clus
vv          AMP PEAK 4(5Q21.1) MUTATED AMP PEAK 4(5Q21.1) WILD-TYPE
  STAGE I                            8                          274
  STAGE II                           7                           43
  STAGE III                          5                          106
  STAGE IV                           1                            1
  STAGE IVA                          2                           44
  STAGE IVC                          0                            6
[1] 6 2
[1] 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(5Q21.1) MUTATED     6   8   7   2
  AMP PEAK 4(5Q21.1) WILD-TYPE 136 157 160  21
D3V4, multiclass
    clus
vv   AMP PEAK 4(5Q21.1) MUTATED AMP PEAK 4(5Q21.1) WILD-TYPE
  T1                          6                          136
  T2                          8                          157
  T3                          7                          160
  T4                          2                           21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                              cls
clus                             0   1
  AMP PEAK 4(5Q21.1) MUTATED    15   4
  AMP PEAK 4(5Q21.1) WILD-TYPE 210 220
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q21.1) MUTATED     15    4
  AMP PEAK 4(5Q21.1) WILD-TYPE  210  220
   clus
vv  AMP PEAK 4(5Q21.1) MUTATED AMP PEAK 4(5Q21.1) WILD-TYPE
  0                         15                          210
  1                          4                          220
[1] 2 2
[1] FALSE
D3V6, binary
                              cls
clus                             0   1
  AMP PEAK 4(5Q21.1) MUTATED     7   0
  AMP PEAK 4(5Q21.1) WILD-TYPE 271   9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q21.1) MUTATED      7    0
  AMP PEAK 4(5Q21.1) WILD-TYPE  271    9
   clus
vv  AMP PEAK 4(5Q21.1) MUTATED AMP PEAK 4(5Q21.1) WILD-TYPE
  0                          7                          271
  1                          0                            9
[1] 2 2
[1] FALSE
D3V7, binary
                              cls
clus                             0   1
  AMP PEAK 4(5Q21.1) MUTATED    14   9
  AMP PEAK 4(5Q21.1) WILD-TYPE 351 125
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q21.1) MUTATED     14    9
  AMP PEAK 4(5Q21.1) WILD-TYPE  351  125
        clus
vv       AMP PEAK 4(5Q21.1) MUTATED AMP PEAK 4(5Q21.1) WILD-TYPE
  FEMALE                         14                          351
  MALE                            9                          125
[1] 2 2
[1] FALSE
D3V8, binary
                              cls
clus                             0   1
  AMP PEAK 4(5Q21.1) MUTATED     6  13
  AMP PEAK 4(5Q21.1) WILD-TYPE 174 290
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q21.1) MUTATED      6   13
  AMP PEAK 4(5Q21.1) WILD-TYPE  174  290
     clus
vv    AMP PEAK 4(5Q21.1) MUTATED AMP PEAK 4(5Q21.1) WILD-TYPE
  NO                           6                          174
  YES                         13                          290
[1] 2 2
[1] FALSE
                              vv
clus                           OTHER, SPECIFY
  AMP PEAK 4(5Q21.1) MUTATED                0
  AMP PEAK 4(5Q21.1) WILD-TYPE              7
                              vv
clus                           THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 4(5Q21.1) MUTATED                                              14
  AMP PEAK 4(5Q21.1) WILD-TYPE                                           342
                              vv
clus                           THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 4(5Q21.1) MUTATED                                                                        8
  AMP PEAK 4(5Q21.1) WILD-TYPE                                                                     92
                              vv
clus                           THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 4(5Q21.1) MUTATED                                                                     1
  AMP PEAK 4(5Q21.1) WILD-TYPE                                                                  35
D3V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 4(5Q21.1) MUTATED
  OTHER, SPECIFY                                                                                  0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  14
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             1
                                                                        clus
vv                                                                       AMP PEAK 4(5Q21.1) WILD-TYPE
  OTHER, SPECIFY                                                                                    7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   342
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           92
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
                              cls
clus                             0   1
  AMP PEAK 4(5Q21.1) MUTATED    21   0
  AMP PEAK 4(5Q21.1) WILD-TYPE 399  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q21.1) MUTATED     21    0
  AMP PEAK 4(5Q21.1) WILD-TYPE  399   17
     clus
vv    AMP PEAK 4(5Q21.1) MUTATED AMP PEAK 4(5Q21.1) WILD-TYPE
  NO                          21                          399
  YES                          0                           17
[1] 2 2
[1] FALSE
                              vv
clus                           MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 4(5Q21.1) MUTATED              4                       1   17
  AMP PEAK 4(5Q21.1) WILD-TYPE          128                      17  313
                              vv
clus                           VERY ADVANCED (T4B)
  AMP PEAK 4(5Q21.1) MUTATED                     1
  AMP PEAK 4(5Q21.1) WILD-TYPE                   0
D3V11, multiclass
                         clus
vv                        AMP PEAK 4(5Q21.1) MUTATED
  MINIMAL (T3)                                     4
  MODERATE/ADVANCED (T4A)                          1
  NONE                                            17
  VERY ADVANCED (T4B)                              1
                         clus
vv                        AMP PEAK 4(5Q21.1) WILD-TYPE
  MINIMAL (T3)                                     128
  MODERATE/ADVANCED (T4A)                           17
  NONE                                             313
  VERY ADVANCED (T4B)                                0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 4(5Q21.1) MUTATED    17   3   0   3
  AMP PEAK 4(5Q21.1) WILD-TYPE 366  48   4  27
D3V12, multiclass
    clus
vv   AMP PEAK 4(5Q21.1) MUTATED AMP PEAK 4(5Q21.1) WILD-TYPE
  R0                         17                          366
  R1                          3                           48
  R2                          0                            4
  RX                          3                           27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, continuous
D3V14, binary
                              cls
clus                             0   1
  AMP PEAK 4(5Q21.1) MUTATED    10  13
  AMP PEAK 4(5Q21.1) WILD-TYPE 215 251
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q21.1) MUTATED     10   13
  AMP PEAK 4(5Q21.1) WILD-TYPE  215  251
            clus
vv           AMP PEAK 4(5Q21.1) MUTATED AMP PEAK 4(5Q21.1) WILD-TYPE
  MULTIFOCAL                         10                          215
  UNIFOCAL                           13                          251
[1] 2 2
[1] FALSE
D3V15, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 4(5Q21.1) MUTATED                                  0     0
  AMP PEAK 4(5Q21.1) WILD-TYPE                                1    52
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 4(5Q21.1) MUTATED                           0    16
  AMP PEAK 4(5Q21.1) WILD-TYPE                        27   313
D3V16, multiclass
                                  clus
vv                                 AMP PEAK 4(5Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 0
  WHITE                                                    16
                                  clus
vv                                 AMP PEAK 4(5Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      52
  BLACK OR AFRICAN AMERICAN                                  27
  WHITE                                                     313
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V17, binary
                              cls
clus                             0   1
  AMP PEAK 4(5Q21.1) MUTATED     1  15
  AMP PEAK 4(5Q21.1) WILD-TYPE  37 345
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q21.1) MUTATED      1   15
  AMP PEAK 4(5Q21.1) WILD-TYPE   37  345
                        clus
vv                       AMP PEAK 4(5Q21.1) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         15
                        clus
vv                       AMP PEAK 4(5Q21.1) WILD-TYPE
  HISPANIC OR LATINO                               37
  NOT HISPANIC OR LATINO                          345
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK 5(5Q33.1) MUTATION ANALYSIS
D4V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 5(5Q33.1) MUTATED    19   2
  AMP PEAK 5(5Q33.1) WILD-TYPE 463  14
  AMP PEAK 5(5Q33.1) MUTATED AMP PEAK 5(5Q33.1) WILD-TYPE 
                          21                          477 
  AMP PEAK 5(5Q33.1) MUTATED AMP PEAK 5(5Q33.1) WILD-TYPE 
                           2                           14 
$`AMP PEAK 5(5Q33.1) MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-DJ-A4UW TCGA-EL-A3T9 TCGA-EL-A3ZM 
       13.78        20.58        20.48        26.93         5.72        36.03 
TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO 
       47.84        23.90        78.61        57.01        10.65         6.05 
TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
       40.34        32.32        22.52        13.51        37.25       123.32 
TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       33.63         7.82        29.10 

$`AMP PEAK 5(5Q33.1) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       21.83        23.93         4.24        24.79        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 
       25.48        15.12        42.08        51.39        41.52         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.97        11.08        18.38        16.57        18.97        12.82 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       21.63        19.43        23.47        12.30        12.79        12.46 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 
       11.38        10.68        15.02        12.43        12.66        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        27.32        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       52.27        43.17        52.37         8.32        48.07       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.99        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       35.41        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74        43.96 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        39.95        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       36.33        11.34        35.87        40.96        36.99        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       30.61        19.20        23.21        21.27        20.48        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        40.70        18.97         9.60        35.67        36.43 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       23.44        27.62        30.87        30.12        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       27.06        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       63.19        52.44        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 
       31.50        31.04        31.30        30.84        25.45        30.61 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       31.27        31.33        14.96        39.88        33.50        31.00 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       30.15        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ 
       60.95       157.15        37.94        57.01       106.62        79.50 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR 
       98.53        69.57       108.36        64.87        49.51       115.10 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       136.01        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      139.99        49.32        43.36        49.71        83.57       139.00 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 
      108.66        57.63        52.50        29.65       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       132.07        98.24        41.29       107.47        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        89.56        91.17        51.78        62.30        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       72.69        65.49        61.22        60.16         7.07        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       57.47        34.72        45.96        61.02        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KG 
       30.51        53.36        44.15        41.13        43.59        24.30 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       27.06        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.79        19.46        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       17.88        13.18        23.51         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       13.15        22.16        19.73        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        63.45        88.41        58.75        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
      108.46        84.89       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A 
       68.22       117.40        66.77       112.80        39.95        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       17.82        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08        23.31        21.63        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 
       23.87        22.49        19.04        13.81        14.04        21.60 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46        11.01        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
       31.10         8.22        25.64        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.24        33.40        40.37         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       30.21        12.89         3.02 

  AMP PEAK 5(5Q33.1) MUTATED AMP PEAK 5(5Q33.1) WILD-TYPE 
                        5.72                         0.20 
  AMP PEAK 5(5Q33.1) MUTATED AMP PEAK 5(5Q33.1) WILD-TYPE 
                      123.32                       178.29 
  AMP PEAK 5(5Q33.1) MUTATED AMP PEAK 5(5Q33.1) WILD-TYPE 
                       26.93                        31.27 
[1] "5.7 - 123.3 (26.9)" "0.2 - 178.3 (31.3)"
[1] "hr=" "4.3"
D4V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 5(5Q33.1) MUTATED         7        7         5        1         1
  AMP PEAK 5(5Q33.1) WILD-TYPE     275       43       106        1        45
                              vv
clus                           STAGE IVC
  AMP PEAK 5(5Q33.1) MUTATED           0
  AMP PEAK 5(5Q33.1) WILD-TYPE         6
D4V3, multiclass
           clus
vv          AMP PEAK 5(5Q33.1) MUTATED AMP PEAK 5(5Q33.1) WILD-TYPE
  STAGE I                            7                          275
  STAGE II                           7                           43
  STAGE III                          5                          106
  STAGE IV                           1                            1
  STAGE IVA                          1                           45
  STAGE IVC                          0                            6
[1] 6 2
[1] 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(5Q33.1) MUTATED     5   8   6   2
  AMP PEAK 5(5Q33.1) WILD-TYPE 137 157 161  21
D4V4, multiclass
    clus
vv   AMP PEAK 5(5Q33.1) MUTATED AMP PEAK 5(5Q33.1) WILD-TYPE
  T1                          5                          137
  T2                          8                          157
  T3                          6                          161
  T4                          2                           21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                              cls
clus                             0   1
  AMP PEAK 5(5Q33.1) MUTATED    13   3
  AMP PEAK 5(5Q33.1) WILD-TYPE 212 221
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(5Q33.1) MUTATED     13    3
  AMP PEAK 5(5Q33.1) WILD-TYPE  212  221
   clus
vv  AMP PEAK 5(5Q33.1) MUTATED AMP PEAK 5(5Q33.1) WILD-TYPE
  0                         13                          212
  1                          3                          221
[1] 2 2
[1] FALSE
D4V6, binary
                              cls
clus                             0   1
  AMP PEAK 5(5Q33.1) MUTATED     4   0
  AMP PEAK 5(5Q33.1) WILD-TYPE 274   9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(5Q33.1) MUTATED      4    0
  AMP PEAK 5(5Q33.1) WILD-TYPE  274    9
   clus
vv  AMP PEAK 5(5Q33.1) MUTATED AMP PEAK 5(5Q33.1) WILD-TYPE
  0                          4                          274
  1                          0                            9
[1] 2 2
[1] FALSE
D4V7, binary
                              cls
clus                             0   1
  AMP PEAK 5(5Q33.1) MUTATED    13   8
  AMP PEAK 5(5Q33.1) WILD-TYPE 352 126
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(5Q33.1) MUTATED     13    8
  AMP PEAK 5(5Q33.1) WILD-TYPE  352  126
        clus
vv       AMP PEAK 5(5Q33.1) MUTATED AMP PEAK 5(5Q33.1) WILD-TYPE
  FEMALE                         13                          352
  MALE                            8                          126
[1] 2 2
[1] FALSE
D4V8, binary
                              cls
clus                             0   1
  AMP PEAK 5(5Q33.1) MUTATED     5  13
  AMP PEAK 5(5Q33.1) WILD-TYPE 175 290
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(5Q33.1) MUTATED      5   13
  AMP PEAK 5(5Q33.1) WILD-TYPE  175  290
     clus
vv    AMP PEAK 5(5Q33.1) MUTATED AMP PEAK 5(5Q33.1) WILD-TYPE
  NO                           5                          175
  YES                         13                          290
[1] 2 2
[1] FALSE
                              vv
clus                           OTHER, SPECIFY
  AMP PEAK 5(5Q33.1) MUTATED                0
  AMP PEAK 5(5Q33.1) WILD-TYPE              7
                              vv
clus                           THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 5(5Q33.1) MUTATED                                              11
  AMP PEAK 5(5Q33.1) WILD-TYPE                                           345
                              vv
clus                           THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 5(5Q33.1) MUTATED                                                                        9
  AMP PEAK 5(5Q33.1) WILD-TYPE                                                                     91
                              vv
clus                           THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 5(5Q33.1) MUTATED                                                                     1
  AMP PEAK 5(5Q33.1) WILD-TYPE                                                                  35
D4V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 5(5Q33.1) MUTATED
  OTHER, SPECIFY                                                                                  0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  11
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             1
                                                                        clus
vv                                                                       AMP PEAK 5(5Q33.1) WILD-TYPE
  OTHER, SPECIFY                                                                                    7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   345
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           91
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
                              cls
clus                             0   1
  AMP PEAK 5(5Q33.1) MUTATED    19   0
  AMP PEAK 5(5Q33.1) WILD-TYPE 401  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(5Q33.1) MUTATED     19    0
  AMP PEAK 5(5Q33.1) WILD-TYPE  401   17
     clus
vv    AMP PEAK 5(5Q33.1) MUTATED AMP PEAK 5(5Q33.1) WILD-TYPE
  NO                          19                          401
  YES                          0                           17
[1] 2 2
[1] FALSE
                              vv
clus                           MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 5(5Q33.1) MUTATED              3                       1   16
  AMP PEAK 5(5Q33.1) WILD-TYPE          129                      17  314
                              vv
clus                           VERY ADVANCED (T4B)
  AMP PEAK 5(5Q33.1) MUTATED                     1
  AMP PEAK 5(5Q33.1) WILD-TYPE                   0
D4V11, multiclass
                         clus
vv                        AMP PEAK 5(5Q33.1) MUTATED
  MINIMAL (T3)                                     3
  MODERATE/ADVANCED (T4A)                          1
  NONE                                            16
  VERY ADVANCED (T4B)                              1
                         clus
vv                        AMP PEAK 5(5Q33.1) WILD-TYPE
  MINIMAL (T3)                                     129
  MODERATE/ADVANCED (T4A)                           17
  NONE                                             314
  VERY ADVANCED (T4B)                                0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 5(5Q33.1) MUTATED    15   4   0   2
  AMP PEAK 5(5Q33.1) WILD-TYPE 368  47   4  28
D4V12, multiclass
    clus
vv   AMP PEAK 5(5Q33.1) MUTATED AMP PEAK 5(5Q33.1) WILD-TYPE
  R0                         15                          368
  R1                          4                           47
  R2                          0                            4
  RX                          2                           28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, continuous
D4V14, binary
                              cls
clus                             0   1
  AMP PEAK 5(5Q33.1) MUTATED    10  11
  AMP PEAK 5(5Q33.1) WILD-TYPE 215 253
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(5Q33.1) MUTATED     10   11
  AMP PEAK 5(5Q33.1) WILD-TYPE  215  253
            clus
vv           AMP PEAK 5(5Q33.1) MUTATED AMP PEAK 5(5Q33.1) WILD-TYPE
  MULTIFOCAL                         10                          215
  UNIFOCAL                           11                          253
[1] 2 2
[1] FALSE
D4V15, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 5(5Q33.1) MUTATED                                  0     1
  AMP PEAK 5(5Q33.1) WILD-TYPE                                1    51
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 5(5Q33.1) MUTATED                           0    11
  AMP PEAK 5(5Q33.1) WILD-TYPE                        27   318
D4V16, multiclass
                                  clus
vv                                 AMP PEAK 5(5Q33.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 0
  WHITE                                                    11
                                  clus
vv                                 AMP PEAK 5(5Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      51
  BLACK OR AFRICAN AMERICAN                                  27
  WHITE                                                     318
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V17, binary
                              cls
clus                             0   1
  AMP PEAK 5(5Q33.1) MUTATED     0  13
  AMP PEAK 5(5Q33.1) WILD-TYPE  38 347
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(5Q33.1) MUTATED      0   13
  AMP PEAK 5(5Q33.1) WILD-TYPE   38  347
                        clus
vv                       AMP PEAK 5(5Q33.1) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         13
                        clus
vv                       AMP PEAK 5(5Q33.1) WILD-TYPE
  HISPANIC OR LATINO                               38
  NOT HISPANIC OR LATINO                          347
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK 6(13Q14.2) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 6(13Q14.2) MUTATED     6   0
  AMP PEAK 6(13Q14.2) WILD-TYPE 476  16
  AMP PEAK 6(13Q14.2) MUTATED AMP PEAK 6(13Q14.2) WILD-TYPE 
                            6                           492 
  AMP PEAK 6(13Q14.2) MUTATED AMP PEAK 6(13Q14.2) WILD-TYPE 
                            0                            16 
$`AMP PEAK 6(13Q14.2) MUTATED`
TCGA-BJ-A45E TCGA-CE-A482 TCGA-EL-A4KI TCGA-EM-A1YD TCGA-EM-A2CO TCGA-EM-A2OY 
       21.01        10.68        23.90        57.01         6.05        32.32 

$`AMP PEAK 6(13Q14.2) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         7.99        10.88         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.79        12.46        11.38        15.02        12.43        12.66 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       21.63        50.17        37.64        27.32        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        52.27        43.17        52.37         8.32        48.07 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       30.58        35.41        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        78.61        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ 
       47.57        17.88        13.18        23.51         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       48.46        13.15        22.16        40.34        19.73        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR 
       15.68        14.14        33.07        44.52         8.35        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
       12.53         9.24        27.02        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.85        13.51        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89       123.32       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        4.11        22.03         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
       20.42        17.82         7.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       13.81        14.04        21.60        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46        11.01        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
       22.29         5.75         2.47         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
        9.50        36.10        32.45        30.21        12.89         3.02 

  AMP PEAK 6(13Q14.2) MUTATED AMP PEAK 6(13Q14.2) WILD-TYPE 
                         6.05                          0.20 
  AMP PEAK 6(13Q14.2) MUTATED AMP PEAK 6(13Q14.2) WILD-TYPE 
                        57.01                        178.29 
  AMP PEAK 6(13Q14.2) MUTATED AMP PEAK 6(13Q14.2) WILD-TYPE 
                       22.455                        31.270 
[1] "6.0 - 57.0 (22.5)"  "0.2 - 178.3 (31.3)"
[1] "hr="     "3300000"
D5V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 6(13Q14.2) MUTATED         2        3         1        0         0
  AMP PEAK 6(13Q14.2) WILD-TYPE     280       47       110        2        46
                               vv
clus                            STAGE IVC
  AMP PEAK 6(13Q14.2) MUTATED           0
  AMP PEAK 6(13Q14.2) WILD-TYPE         6
D5V3, multiclass
           clus
vv          AMP PEAK 6(13Q14.2) MUTATED AMP PEAK 6(13Q14.2) WILD-TYPE
  STAGE I                             2                           280
  STAGE II                            3                            47
  STAGE III                           1                           110
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] 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(13Q14.2) MUTATED     2   3   1   0
  AMP PEAK 6(13Q14.2) WILD-TYPE 140 162 166  23
D5V4, multiclass
    clus
vv   AMP PEAK 6(13Q14.2) MUTATED AMP PEAK 6(13Q14.2) WILD-TYPE
  T1                           2                           140
  T2                           3                           162
  T3                           1                           166
  T4                           0                            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"
D5V5, binary
                               cls
clus                              0   1
  AMP PEAK 6(13Q14.2) MUTATED     4   1
  AMP PEAK 6(13Q14.2) WILD-TYPE 221 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(13Q14.2) MUTATED      4    1
  AMP PEAK 6(13Q14.2) WILD-TYPE  221  223
   clus
vv  AMP PEAK 6(13Q14.2) MUTATED AMP PEAK 6(13Q14.2) WILD-TYPE
  0                           4                           221
  1                           1                           223
[1] 2 2
[1] FALSE
D5V6, binary
                               cls
clus                              0   1
  AMP PEAK 6(13Q14.2) MUTATED     2   0
  AMP PEAK 6(13Q14.2) WILD-TYPE 276   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(13Q14.2) MUTATED      2    0
  AMP PEAK 6(13Q14.2) WILD-TYPE  276    9
   clus
vv  AMP PEAK 6(13Q14.2) MUTATED AMP PEAK 6(13Q14.2) WILD-TYPE
  0                           2                           276
  1                           0                             9
[1] 2 2
[1] FALSE
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK 6(13Q14.2) MUTATED     5   1
  AMP PEAK 6(13Q14.2) WILD-TYPE 360 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(13Q14.2) MUTATED      5    1
  AMP PEAK 6(13Q14.2) WILD-TYPE  360  133
        clus
vv       AMP PEAK 6(13Q14.2) MUTATED AMP PEAK 6(13Q14.2) WILD-TYPE
  FEMALE                           5                           360
  MALE                             1                           133
[1] 2 2
[1] FALSE
D5V8, binary
                               cls
clus                              0   1
  AMP PEAK 6(13Q14.2) MUTATED     3   3
  AMP PEAK 6(13Q14.2) WILD-TYPE 177 300
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(13Q14.2) MUTATED      3    3
  AMP PEAK 6(13Q14.2) WILD-TYPE  177  300
     clus
vv    AMP PEAK 6(13Q14.2) MUTATED AMP PEAK 6(13Q14.2) WILD-TYPE
  NO                            3                           177
  YES                           3                           300
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER, SPECIFY
  AMP PEAK 6(13Q14.2) MUTATED                0
  AMP PEAK 6(13Q14.2) WILD-TYPE              7
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 6(13Q14.2) MUTATED                                               3
  AMP PEAK 6(13Q14.2) WILD-TYPE                                           353
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 6(13Q14.2) MUTATED                                                                        3
  AMP PEAK 6(13Q14.2) WILD-TYPE                                                                     97
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 6(13Q14.2) MUTATED                                                                     0
  AMP PEAK 6(13Q14.2) WILD-TYPE                                                                  36
D5V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 6(13Q14.2) MUTATED
  OTHER, SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 6(13Q14.2) WILD-TYPE
  OTHER, SPECIFY                                                                                     7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
                               cls
clus                              0   1
  AMP PEAK 6(13Q14.2) MUTATED     5   0
  AMP PEAK 6(13Q14.2) WILD-TYPE 415  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(13Q14.2) MUTATED      5    0
  AMP PEAK 6(13Q14.2) WILD-TYPE  415   17
     clus
vv    AMP PEAK 6(13Q14.2) MUTATED AMP PEAK 6(13Q14.2) WILD-TYPE
  NO                            5                           415
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 6(13Q14.2) MUTATED              1                       0    4
  AMP PEAK 6(13Q14.2) WILD-TYPE          131                      18  326
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 6(13Q14.2) MUTATED                     0
  AMP PEAK 6(13Q14.2) WILD-TYPE                   1
D5V11, multiclass
                         clus
vv                        AMP PEAK 6(13Q14.2) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              4
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 6(13Q14.2) WILD-TYPE
  MINIMAL (T3)                                      131
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              326
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 6(13Q14.2) MUTATED     5   0   0   0
  AMP PEAK 6(13Q14.2) WILD-TYPE 378  51   4  30
D5V12, multiclass
    clus
vv   AMP PEAK 6(13Q14.2) MUTATED AMP PEAK 6(13Q14.2) WILD-TYPE
  R0                           5                           378
  R1                           0                            51
  R2                           0                             4
  RX                           0                            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"
D5V13, continuous
D5V14, binary
                               cls
clus                              0   1
  AMP PEAK 6(13Q14.2) MUTATED     3   3
  AMP PEAK 6(13Q14.2) WILD-TYPE 222 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(13Q14.2) MUTATED      3    3
  AMP PEAK 6(13Q14.2) WILD-TYPE  222  261
            clus
vv           AMP PEAK 6(13Q14.2) MUTATED AMP PEAK 6(13Q14.2) WILD-TYPE
  MULTIFOCAL                           3                           222
  UNIFOCAL                             3                           261
[1] 2 2
[1] FALSE
D5V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 6(13Q14.2) MUTATED                                  0     1
  AMP PEAK 6(13Q14.2) WILD-TYPE                                1    51
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 6(13Q14.2) MUTATED                           0     2
  AMP PEAK 6(13Q14.2) WILD-TYPE                        27   327
D5V16, multiclass
                                  clus
vv                                 AMP PEAK 6(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      2
                                  clus
vv                                 AMP PEAK 6(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V17, binary
                               cls
clus                              0   1
  AMP PEAK 6(13Q14.2) MUTATED     0   3
  AMP PEAK 6(13Q14.2) WILD-TYPE  38 357
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(13Q14.2) MUTATED      0    3
  AMP PEAK 6(13Q14.2) WILD-TYPE   38  357
                        clus
vv                       AMP PEAK 6(13Q14.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK 6(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           357
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK 7(22Q11.21) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 7(22Q11.21) MUTATED     7   0
  AMP PEAK 7(22Q11.21) WILD-TYPE 475  16
  AMP PEAK 7(22Q11.21) MUTATED AMP PEAK 7(22Q11.21) WILD-TYPE 
                             7                            491 
  AMP PEAK 7(22Q11.21) MUTATED AMP PEAK 7(22Q11.21) WILD-TYPE 
                             0                             16 
$`AMP PEAK 7(22Q11.21) MUTATED`
TCGA-BJ-A45E TCGA-DJ-A3UP TCGA-EM-A22K TCGA-EM-A22N TCGA-ET-A3DT TCGA-FY-A3W9 
       21.01        16.41        15.75        10.65        43.73        21.63 
TCGA-QD-A8IV 
       12.89 

$`AMP PEAK 7(22Q11.21) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         7.99        10.88         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       36.92        31.04        32.42        31.46        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       14.50        10.45        14.53        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        44.52 
TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
        8.35        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33        12.53         9.24        27.02        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DU TCGA-ET-A3DV 
       94.59        84.85        80.58        66.84        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25        20.42        17.82         7.82        29.10        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       13.81        14.04        21.60        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46        11.01        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
       22.29         5.75         2.47         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-E8-A418 
        9.50        36.10        32.45        30.21         3.02 

  AMP PEAK 7(22Q11.21) MUTATED AMP PEAK 7(22Q11.21) WILD-TYPE 
                         10.65                           0.20 
  AMP PEAK 7(22Q11.21) MUTATED AMP PEAK 7(22Q11.21) WILD-TYPE 
                         43.73                         178.29 
  AMP PEAK 7(22Q11.21) MUTATED AMP PEAK 7(22Q11.21) WILD-TYPE 
                         16.41                          31.30 
[1] "10.7 - 43.7 (16.4)" "0.2 - 178.3 (31.3)"
[1] "hr="     "3300000"
D6V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 7(22Q11.21) MUTATED         4        1         0        0         2
  AMP PEAK 7(22Q11.21) WILD-TYPE     278       49       111        2        44
                                vv
clus                             STAGE IVC
  AMP PEAK 7(22Q11.21) MUTATED           0
  AMP PEAK 7(22Q11.21) WILD-TYPE         6
D6V3, multiclass
           clus
vv          AMP PEAK 7(22Q11.21) MUTATED AMP PEAK 7(22Q11.21) WILD-TYPE
  STAGE I                              4                            278
  STAGE II                             1                             49
  STAGE III                            0                            111
  STAGE IV                             0                              2
  STAGE IVA                            2                             44
  STAGE IVC                            0                              6
[1] 6 2
[1] 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(22Q11.21) MUTATED     3   3   1   0
  AMP PEAK 7(22Q11.21) WILD-TYPE 139 162 166  23
D6V4, multiclass
    clus
vv   AMP PEAK 7(22Q11.21) MUTATED AMP PEAK 7(22Q11.21) WILD-TYPE
  T1                            3                            139
  T2                            3                            162
  T3                            1                            166
  T4                            0                             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"
D6V5, binary
                                cls
clus                               0   1
  AMP PEAK 7(22Q11.21) MUTATED     4   3
  AMP PEAK 7(22Q11.21) WILD-TYPE 221 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 7(22Q11.21) MUTATED      4    3
  AMP PEAK 7(22Q11.21) WILD-TYPE  221  221
   clus
vv  AMP PEAK 7(22Q11.21) MUTATED AMP PEAK 7(22Q11.21) WILD-TYPE
  0                            4                            221
  1                            3                            221
[1] 2 2
[1] FALSE
D6V6, binary
                                cls
clus                               0   1
  AMP PEAK 7(22Q11.21) MUTATED     2   0
  AMP PEAK 7(22Q11.21) WILD-TYPE 276   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 7(22Q11.21) MUTATED      2    0
  AMP PEAK 7(22Q11.21) WILD-TYPE  276    9
   clus
vv  AMP PEAK 7(22Q11.21) MUTATED AMP PEAK 7(22Q11.21) WILD-TYPE
  0                            2                            276
  1                            0                              9
[1] 2 2
[1] FALSE
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK 7(22Q11.21) MUTATED     7   0
  AMP PEAK 7(22Q11.21) WILD-TYPE 358 134
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 7(22Q11.21) MUTATED      7    0
  AMP PEAK 7(22Q11.21) WILD-TYPE  358  134
        clus
vv       AMP PEAK 7(22Q11.21) MUTATED AMP PEAK 7(22Q11.21) WILD-TYPE
  FEMALE                            7                            358
  MALE                              0                            134
[1] 2 2
[1] FALSE
D6V8, binary
                                cls
clus                               0   1
  AMP PEAK 7(22Q11.21) MUTATED     2   5
  AMP PEAK 7(22Q11.21) WILD-TYPE 178 298
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 7(22Q11.21) MUTATED      2    5
  AMP PEAK 7(22Q11.21) WILD-TYPE  178  298
     clus
vv    AMP PEAK 7(22Q11.21) MUTATED AMP PEAK 7(22Q11.21) WILD-TYPE
  NO                             2                            178
  YES                            5                            298
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER, SPECIFY
  AMP PEAK 7(22Q11.21) MUTATED                0
  AMP PEAK 7(22Q11.21) WILD-TYPE              7
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 7(22Q11.21) MUTATED                                               4
  AMP PEAK 7(22Q11.21) WILD-TYPE                                           352
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 7(22Q11.21) MUTATED                                                                        3
  AMP PEAK 7(22Q11.21) WILD-TYPE                                                                     97
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 7(22Q11.21) MUTATED                                                                     0
  AMP PEAK 7(22Q11.21) WILD-TYPE                                                                  36
D6V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 7(22Q11.21) MUTATED
  OTHER, SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 7(22Q11.21) WILD-TYPE
  OTHER, SPECIFY                                                                                      7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
                                cls
clus                               0   1
  AMP PEAK 7(22Q11.21) MUTATED     6   0
  AMP PEAK 7(22Q11.21) WILD-TYPE 414  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 7(22Q11.21) MUTATED      6    0
  AMP PEAK 7(22Q11.21) WILD-TYPE  414   17
     clus
vv    AMP PEAK 7(22Q11.21) MUTATED AMP PEAK 7(22Q11.21) WILD-TYPE
  NO                             6                            414
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 7(22Q11.21) MUTATED              1                       0    5
  AMP PEAK 7(22Q11.21) WILD-TYPE          131                      18  325
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 7(22Q11.21) MUTATED                     0
  AMP PEAK 7(22Q11.21) WILD-TYPE                   1
D6V11, multiclass
                         clus
vv                        AMP PEAK 7(22Q11.21) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               5
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 7(22Q11.21) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               325
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 7(22Q11.21) MUTATED     2   2   0   2
  AMP PEAK 7(22Q11.21) WILD-TYPE 381  49   4  28
D6V12, multiclass
    clus
vv   AMP PEAK 7(22Q11.21) MUTATED AMP PEAK 7(22Q11.21) WILD-TYPE
  R0                            2                            381
  R1                            2                             49
  R2                            0                              4
  RX                            2                             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, continuous
D6V14, binary
                                cls
clus                               0   1
  AMP PEAK 7(22Q11.21) MUTATED     3   4
  AMP PEAK 7(22Q11.21) WILD-TYPE 222 260
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 7(22Q11.21) MUTATED      3    4
  AMP PEAK 7(22Q11.21) WILD-TYPE  222  260
            clus
vv           AMP PEAK 7(22Q11.21) MUTATED AMP PEAK 7(22Q11.21) WILD-TYPE
  MULTIFOCAL                            3                            222
  UNIFOCAL                              4                            260
[1] 2 2
[1] FALSE
D6V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 7(22Q11.21) MUTATED                                  0     0
  AMP PEAK 7(22Q11.21) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 7(22Q11.21) MUTATED                           1     3
  AMP PEAK 7(22Q11.21) WILD-TYPE                        26   326
D6V16, multiclass
                                  clus
vv                                 AMP PEAK 7(22Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                       3
                                  clus
vv                                 AMP PEAK 7(22Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V17, binary
                                cls
clus                               0   1
  AMP PEAK 7(22Q11.21) MUTATED     1   4
  AMP PEAK 7(22Q11.21) WILD-TYPE  37 356
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 7(22Q11.21) MUTATED      1    4
  AMP PEAK 7(22Q11.21) WILD-TYPE   37  356
                        clus
vv                       AMP PEAK 7(22Q11.21) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            4
                        clus
vv                       AMP PEAK 7(22Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                 37
  NOT HISPANIC OR LATINO                            356
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK 8(XP11.22) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 8(XP11.22) MUTATED     7   1
  AMP PEAK 8(XP11.22) WILD-TYPE 475  15
  AMP PEAK 8(XP11.22) MUTATED AMP PEAK 8(XP11.22) WILD-TYPE 
                            8                           490 
  AMP PEAK 8(XP11.22) MUTATED AMP PEAK 8(XP11.22) WILD-TYPE 
                            1                            15 
$`AMP PEAK 8(XP11.22) MUTATED`
TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A3AI 
       20.48         5.72        78.61        57.01        10.65        22.52 
TCGA-ET-A3BS TCGA-FY-A3NM 
        5.79        29.10 

$`AMP PEAK 8(XP11.22) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29       107.47        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.79        19.46        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ 
       33.96        17.59        17.46        17.29        14.60        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR 
       15.68        14.14        33.07        44.52         8.35        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
       12.53         9.24        27.02        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.85        13.51        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89       123.32       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BT TCGA-ET-A3BU 
       98.20        28.24        79.10        76.64        87.62        77.82 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         7.82        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08        23.31        21.63        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 
       15.16        23.87        22.49        19.04        13.81        14.04 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       21.60        12.53        17.00        21.67        12.46        11.01 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 
       21.83        31.10         8.22        25.64        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.47         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 
       35.28        33.24        33.40        40.37         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       32.45        30.21        12.89         3.02 

  AMP PEAK 8(XP11.22) MUTATED AMP PEAK 8(XP11.22) WILD-TYPE 
                         5.72                          0.20 
  AMP PEAK 8(XP11.22) MUTATED AMP PEAK 8(XP11.22) WILD-TYPE 
                        78.61                        178.29 
  AMP PEAK 8(XP11.22) MUTATED AMP PEAK 8(XP11.22) WILD-TYPE 
                       21.500                        31.285 
[1] "5.7 - 78.6 (21.5)"  "0.2 - 178.3 (31.3)"
[1] "hr=" "5.7"
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 8(XP11.22) MUTATED         3        2         2        1         0
  AMP PEAK 8(XP11.22) WILD-TYPE     279       48       109        1        46
                               vv
clus                            STAGE IVC
  AMP PEAK 8(XP11.22) MUTATED           0
  AMP PEAK 8(XP11.22) WILD-TYPE         6
D7V3, multiclass
           clus
vv          AMP PEAK 8(XP11.22) MUTATED AMP PEAK 8(XP11.22) WILD-TYPE
  STAGE I                             3                           279
  STAGE II                            2                            48
  STAGE III                           2                           109
  STAGE IV                            1                             1
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] 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(XP11.22) MUTATED     1   3   3   1
  AMP PEAK 8(XP11.22) WILD-TYPE 141 162 164  22
D7V4, multiclass
    clus
vv   AMP PEAK 8(XP11.22) MUTATED AMP PEAK 8(XP11.22) WILD-TYPE
  T1                           1                           141
  T2                           3                           162
  T3                           3                           164
  T4                           1                            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                               cls
clus                              0   1
  AMP PEAK 8(XP11.22) MUTATED     5   2
  AMP PEAK 8(XP11.22) WILD-TYPE 220 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 8(XP11.22) MUTATED      5    2
  AMP PEAK 8(XP11.22) WILD-TYPE  220  222
   clus
vv  AMP PEAK 8(XP11.22) MUTATED AMP PEAK 8(XP11.22) WILD-TYPE
  0                           5                           220
  1                           2                           222
[1] 2 2
[1] FALSE
D7V6, binary
                               cls
clus                              0   1
  AMP PEAK 8(XP11.22) MUTATED     1   0
  AMP PEAK 8(XP11.22) WILD-TYPE 277   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 8(XP11.22) MUTATED      1    0
  AMP PEAK 8(XP11.22) WILD-TYPE  277    9
   clus
vv  AMP PEAK 8(XP11.22) MUTATED AMP PEAK 8(XP11.22) WILD-TYPE
  0                           1                           277
  1                           0                             9
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK 8(XP11.22) MUTATED     7   1
  AMP PEAK 8(XP11.22) WILD-TYPE 358 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 8(XP11.22) MUTATED      7    1
  AMP PEAK 8(XP11.22) WILD-TYPE  358  133
        clus
vv       AMP PEAK 8(XP11.22) MUTATED AMP PEAK 8(XP11.22) WILD-TYPE
  FEMALE                           7                           358
  MALE                             1                           133
[1] 2 2
[1] FALSE
D7V8, binary
                               cls
clus                              0   1
  AMP PEAK 8(XP11.22) MUTATED     2   4
  AMP PEAK 8(XP11.22) WILD-TYPE 178 299
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 8(XP11.22) MUTATED      2    4
  AMP PEAK 8(XP11.22) WILD-TYPE  178  299
     clus
vv    AMP PEAK 8(XP11.22) MUTATED AMP PEAK 8(XP11.22) WILD-TYPE
  NO                            2                           178
  YES                           4                           299
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER, SPECIFY
  AMP PEAK 8(XP11.22) MUTATED                0
  AMP PEAK 8(XP11.22) WILD-TYPE              7
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 8(XP11.22) MUTATED                                               4
  AMP PEAK 8(XP11.22) WILD-TYPE                                           352
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 8(XP11.22) MUTATED                                                                        4
  AMP PEAK 8(XP11.22) WILD-TYPE                                                                     96
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 8(XP11.22) MUTATED                                                                     0
  AMP PEAK 8(XP11.22) WILD-TYPE                                                                  36
D7V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 8(XP11.22) MUTATED
  OTHER, SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 8(XP11.22) WILD-TYPE
  OTHER, SPECIFY                                                                                     7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
                               cls
clus                              0   1
  AMP PEAK 8(XP11.22) MUTATED     7   1
  AMP PEAK 8(XP11.22) WILD-TYPE 413  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 8(XP11.22) MUTATED      7    1
  AMP PEAK 8(XP11.22) WILD-TYPE  413   16
     clus
vv    AMP PEAK 8(XP11.22) MUTATED AMP PEAK 8(XP11.22) WILD-TYPE
  NO                            7                           413
  YES                           1                            16
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 8(XP11.22) MUTATED              2                       0    5
  AMP PEAK 8(XP11.22) WILD-TYPE          130                      18  325
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 8(XP11.22) MUTATED                     1
  AMP PEAK 8(XP11.22) WILD-TYPE                   0
D7V11, multiclass
                         clus
vv                        AMP PEAK 8(XP11.22) MUTATED
  MINIMAL (T3)                                      2
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              5
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 8(XP11.22) WILD-TYPE
  MINIMAL (T3)                                      130
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              325
  VERY ADVANCED (T4B)                                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 8(XP11.22) MUTATED     5   2   0   1
  AMP PEAK 8(XP11.22) WILD-TYPE 378  49   4  29
D7V12, multiclass
    clus
vv   AMP PEAK 8(XP11.22) MUTATED AMP PEAK 8(XP11.22) WILD-TYPE
  R0                           5                           378
  R1                           2                            49
  R2                           0                             4
  RX                           1                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, continuous
D7V14, binary
                               cls
clus                              0   1
  AMP PEAK 8(XP11.22) MUTATED     5   3
  AMP PEAK 8(XP11.22) WILD-TYPE 220 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 8(XP11.22) MUTATED      5    3
  AMP PEAK 8(XP11.22) WILD-TYPE  220  261
            clus
vv           AMP PEAK 8(XP11.22) MUTATED AMP PEAK 8(XP11.22) WILD-TYPE
  MULTIFOCAL                           5                           220
  UNIFOCAL                             3                           261
[1] 2 2
[1] FALSE
D7V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 8(XP11.22) MUTATED                                  0     1
  AMP PEAK 8(XP11.22) WILD-TYPE                                1    51
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 8(XP11.22) MUTATED                           0     4
  AMP PEAK 8(XP11.22) WILD-TYPE                        27   325
D7V16, multiclass
                                  clus
vv                                 AMP PEAK 8(XP11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      4
                                  clus
vv                                 AMP PEAK 8(XP11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V17, binary
                               cls
clus                              0   1
  AMP PEAK 8(XP11.22) MUTATED     0   5
  AMP PEAK 8(XP11.22) WILD-TYPE  38 355
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 8(XP11.22) MUTATED      0    5
  AMP PEAK 8(XP11.22) WILD-TYPE   38  355
                        clus
vv                       AMP PEAK 8(XP11.22) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       AMP PEAK 8(XP11.22) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           355
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK 9(XQ22.3) MUTATION ANALYSIS
D8V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 9(XQ22.3) MUTATED    14   1
  AMP PEAK 9(XQ22.3) WILD-TYPE 468  15
  AMP PEAK 9(XQ22.3) MUTATED AMP PEAK 9(XQ22.3) WILD-TYPE 
                          15                          483 
  AMP PEAK 9(XQ22.3) MUTATED AMP PEAK 9(XQ22.3) WILD-TYPE 
                           1                           15 
$`AMP PEAK 9(XQ22.3) MUTATED`
TCGA-BJ-A2N9 TCGA-DJ-A4UT TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-EL-A3T9 TCGA-EL-A4K1 
       20.48        27.06         3.12        15.81         5.72        34.39 
TCGA-EL-A4KH TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A3AI TCGA-EM-A3FK 
       27.06        78.61        57.01        10.65        22.52        23.77 
TCGA-EM-A4FQ TCGA-FY-A3NM TCGA-KS-A4I5 
       22.45        29.10        18.64 

$`AMP PEAK 9(XQ22.3) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       33.04        34.78        26.93        35.54        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       63.19        52.44        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 
       31.50        31.04        31.30        30.84        25.45        30.61 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       31.27        31.33        14.96        39.88        33.50        31.00 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       30.15        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ 
       60.95       157.15        37.94        57.01       106.62        79.50 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR 
       98.53        69.57       108.36        64.87        49.51       115.10 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       136.01        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      139.99        49.32        43.36        49.71        83.57       139.00 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 
      108.66        57.63        52.50        29.65       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       132.07        98.24        41.29       107.47        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        91.17        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        72.69        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        61.02        31.04 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        53.36        44.15        41.13        47.84        43.59 
TCGA-EL-A4KG TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       24.30        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       18.05        19.79        19.46        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       15.75        10.45        14.53        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        44.52         8.35 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       37.25        27.95        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
       12.53         9.24        27.02        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.85        13.51        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
        5.33        26.37        26.37        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       13.68        81.93        81.70        77.56        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       60.20        63.39        65.29        18.38        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       58.75        37.25        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
      123.32       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       28.24        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         7.82        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08        23.31        21.63        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 
       15.16        23.87        22.49        19.04        13.81        14.04 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       21.60        12.53        17.00        21.67        12.46        11.01 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 
       21.83        31.10         8.22        25.64        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.47         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       26.70        43.69        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.24        33.40        40.37         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       30.21        12.89         3.02 

  AMP PEAK 9(XQ22.3) MUTATED AMP PEAK 9(XQ22.3) WILD-TYPE 
                        3.12                         0.20 
  AMP PEAK 9(XQ22.3) MUTATED AMP PEAK 9(XQ22.3) WILD-TYPE 
                       78.61                       178.29 
  AMP PEAK 9(XQ22.3) MUTATED AMP PEAK 9(XQ22.3) WILD-TYPE 
                       22.52                        31.40 
[1] "3.1 - 78.6 (22.5)"  "0.2 - 178.3 (31.4)"
[1] "hr=" "3.9"
D8V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 9(XQ22.3) MUTATED         8        2         3        1         1
  AMP PEAK 9(XQ22.3) WILD-TYPE     274       48       108        1        45
                              vv
clus                           STAGE IVC
  AMP PEAK 9(XQ22.3) MUTATED           0
  AMP PEAK 9(XQ22.3) WILD-TYPE         6
D8V3, multiclass
           clus
vv          AMP PEAK 9(XQ22.3) MUTATED AMP PEAK 9(XQ22.3) WILD-TYPE
  STAGE I                            8                          274
  STAGE II                           2                           48
  STAGE III                          3                          108
  STAGE IV                           1                            1
  STAGE IVA                          1                           45
  STAGE IVC                          0                            6
[1] 6 2
[1] 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(XQ22.3) MUTATED     5   6   3   1
  AMP PEAK 9(XQ22.3) WILD-TYPE 137 159 164  22
D8V4, multiclass
    clus
vv   AMP PEAK 9(XQ22.3) MUTATED AMP PEAK 9(XQ22.3) WILD-TYPE
  T1                          5                          137
  T2                          6                          159
  T3                          3                          164
  T4                          1                           22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                              cls
clus                             0   1
  AMP PEAK 9(XQ22.3) MUTATED     9   5
  AMP PEAK 9(XQ22.3) WILD-TYPE 216 219
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 9(XQ22.3) MUTATED      9    5
  AMP PEAK 9(XQ22.3) WILD-TYPE  216  219
   clus
vv  AMP PEAK 9(XQ22.3) MUTATED AMP PEAK 9(XQ22.3) WILD-TYPE
  0                          9                          216
  1                          5                          219
[1] 2 2
[1] FALSE
D8V6, binary
                              cls
clus                             0   1
  AMP PEAK 9(XQ22.3) MUTATED     7   0
  AMP PEAK 9(XQ22.3) WILD-TYPE 271   9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 9(XQ22.3) MUTATED      7    0
  AMP PEAK 9(XQ22.3) WILD-TYPE  271    9
   clus
vv  AMP PEAK 9(XQ22.3) MUTATED AMP PEAK 9(XQ22.3) WILD-TYPE
  0                          7                          271
  1                          0                            9
[1] 2 2
[1] FALSE
D8V7, binary
                              cls
clus                             0   1
  AMP PEAK 9(XQ22.3) MUTATED    15   0
  AMP PEAK 9(XQ22.3) WILD-TYPE 350 134
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 9(XQ22.3) MUTATED     15    0
  AMP PEAK 9(XQ22.3) WILD-TYPE  350  134
        clus
vv       AMP PEAK 9(XQ22.3) MUTATED AMP PEAK 9(XQ22.3) WILD-TYPE
  FEMALE                         15                          350
  MALE                            0                          134
[1] 2 2
[1] FALSE
D8V8, binary
                              cls
clus                             0   1
  AMP PEAK 9(XQ22.3) MUTATED     6   7
  AMP PEAK 9(XQ22.3) WILD-TYPE 174 296
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 9(XQ22.3) MUTATED      6    7
  AMP PEAK 9(XQ22.3) WILD-TYPE  174  296
     clus
vv    AMP PEAK 9(XQ22.3) MUTATED AMP PEAK 9(XQ22.3) WILD-TYPE
  NO                           6                          174
  YES                          7                          296
[1] 2 2
[1] FALSE
                              vv
clus                           OTHER, SPECIFY
  AMP PEAK 9(XQ22.3) MUTATED                0
  AMP PEAK 9(XQ22.3) WILD-TYPE              7
                              vv
clus                           THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 9(XQ22.3) MUTATED                                               9
  AMP PEAK 9(XQ22.3) WILD-TYPE                                           347
                              vv
clus                           THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 9(XQ22.3) MUTATED                                                                        5
  AMP PEAK 9(XQ22.3) WILD-TYPE                                                                     95
                              vv
clus                           THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 9(XQ22.3) MUTATED                                                                     1
  AMP PEAK 9(XQ22.3) WILD-TYPE                                                                  35
D8V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 9(XQ22.3) MUTATED
  OTHER, SPECIFY                                                                                  0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   9
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             1
                                                                        clus
vv                                                                       AMP PEAK 9(XQ22.3) WILD-TYPE
  OTHER, SPECIFY                                                                                    7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   347
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
                              cls
clus                             0   1
  AMP PEAK 9(XQ22.3) MUTATED    15   0
  AMP PEAK 9(XQ22.3) WILD-TYPE 405  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 9(XQ22.3) MUTATED     15    0
  AMP PEAK 9(XQ22.3) WILD-TYPE  405   17
     clus
vv    AMP PEAK 9(XQ22.3) MUTATED AMP PEAK 9(XQ22.3) WILD-TYPE
  NO                          15                          405
  YES                          0                           17
[1] 2 2
[1] FALSE
                              vv
clus                           MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 9(XQ22.3) MUTATED              1                       0   13
  AMP PEAK 9(XQ22.3) WILD-TYPE          131                      18  317
                              vv
clus                           VERY ADVANCED (T4B)
  AMP PEAK 9(XQ22.3) MUTATED                     1
  AMP PEAK 9(XQ22.3) WILD-TYPE                   0
D8V11, multiclass
                         clus
vv                        AMP PEAK 9(XQ22.3) MUTATED
  MINIMAL (T3)                                     1
  MODERATE/ADVANCED (T4A)                          0
  NONE                                            13
  VERY ADVANCED (T4B)                              1
                         clus
vv                        AMP PEAK 9(XQ22.3) WILD-TYPE
  MINIMAL (T3)                                     131
  MODERATE/ADVANCED (T4A)                           18
  NONE                                             317
  VERY ADVANCED (T4B)                                0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 9(XQ22.3) MUTATED    12   2   0   1
  AMP PEAK 9(XQ22.3) WILD-TYPE 371  49   4  29
D8V12, multiclass
    clus
vv   AMP PEAK 9(XQ22.3) MUTATED AMP PEAK 9(XQ22.3) WILD-TYPE
  R0                         12                          371
  R1                          2                           49
  R2                          0                            4
  RX                          1                           29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, continuous
D8V14, binary
                              cls
clus                             0   1
  AMP PEAK 9(XQ22.3) MUTATED     9   6
  AMP PEAK 9(XQ22.3) WILD-TYPE 216 258
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 9(XQ22.3) MUTATED      9    6
  AMP PEAK 9(XQ22.3) WILD-TYPE  216  258
            clus
vv           AMP PEAK 9(XQ22.3) MUTATED AMP PEAK 9(XQ22.3) WILD-TYPE
  MULTIFOCAL                          9                          216
  UNIFOCAL                            6                          258
[1] 2 2
[1] FALSE
D8V15, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 9(XQ22.3) MUTATED                                  0     0
  AMP PEAK 9(XQ22.3) WILD-TYPE                                1    52
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 9(XQ22.3) MUTATED                           0     9
  AMP PEAK 9(XQ22.3) WILD-TYPE                        27   320
D8V16, multiclass
                                  clus
vv                                 AMP PEAK 9(XQ22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 0
  WHITE                                                     9
                                  clus
vv                                 AMP PEAK 9(XQ22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      52
  BLACK OR AFRICAN AMERICAN                                  27
  WHITE                                                     320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V17, binary
                              cls
clus                             0   1
  AMP PEAK 9(XQ22.3) MUTATED     0   9
  AMP PEAK 9(XQ22.3) WILD-TYPE  38 351
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 9(XQ22.3) MUTATED      0    9
  AMP PEAK 9(XQ22.3) WILD-TYPE   38  351
                        clus
vv                       AMP PEAK 9(XQ22.3) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                          9
                        clus
vv                       AMP PEAK 9(XQ22.3) WILD-TYPE
  HISPANIC OR LATINO                               38
  NOT HISPANIC OR LATINO                          351
[1] 2 2
[1] FALSE

Clustering(9) Variable = DEL PEAK  1(1Q42.13) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1Q42.13) MUTATED     5   0
  DEL PEAK  1(1Q42.13) WILD-TYPE 477  16
  DEL PEAK  1(1Q42.13) MUTATED DEL PEAK  1(1Q42.13) WILD-TYPE 
                             5                            493 
  DEL PEAK  1(1Q42.13) MUTATED DEL PEAK  1(1Q42.13) WILD-TYPE 
                             0                             16 
$`DEL PEAK  1(1Q42.13) MUTATED`
TCGA-EL-A3CV TCGA-EL-A3CX TCGA-EM-A1YE TCGA-ET-A39N TCGA-FY-A3I5 
       37.94       106.62        54.08       123.32         7.82 

$`DEL PEAK  1(1Q42.13) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       31.30        30.84        25.45        30.61        31.27        31.33 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96        39.88        33.50        31.00        30.15        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CW TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
       57.01        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        78.61        57.01        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       78.77        71.08         4.11        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
      116.09         1.25        20.42        17.82        29.10        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
       21.63        17.06        17.36        15.16        23.87        22.49 
TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04        13.81        14.04        21.60        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46        11.01        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       25.64        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F 
       24.69        22.29         5.75         2.47         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV 
       40.37         9.50        36.10        32.45        30.21        12.89 
TCGA-E8-A418 
        3.02 

  DEL PEAK  1(1Q42.13) MUTATED DEL PEAK  1(1Q42.13) WILD-TYPE 
                          7.82                           0.20 
  DEL PEAK  1(1Q42.13) MUTATED DEL PEAK  1(1Q42.13) WILD-TYPE 
                        123.32                         178.29 
  DEL PEAK  1(1Q42.13) MUTATED DEL PEAK  1(1Q42.13) WILD-TYPE 
                         54.08                          31.10 
[1] "7.8 - 123.3 (54.1)" "0.2 - 178.3 (31.1)"
[1] "hr="     "9200000"
D9V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  1(1Q42.13) MUTATED         3        1         1        0         0
  DEL PEAK  1(1Q42.13) WILD-TYPE     279       49       110        2        46
                                vv
clus                             STAGE IVC
  DEL PEAK  1(1Q42.13) MUTATED           0
  DEL PEAK  1(1Q42.13) WILD-TYPE         6
D9V3, multiclass
           clus
vv          DEL PEAK  1(1Q42.13) MUTATED DEL PEAK  1(1Q42.13) WILD-TYPE
  STAGE I                              3                            279
  STAGE II                             1                             49
  STAGE III                            1                            110
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] 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(1Q42.13) MUTATED     0   2   3   0
  DEL PEAK  1(1Q42.13) WILD-TYPE 142 163 164  23
D9V4, multiclass
    clus
vv   DEL PEAK  1(1Q42.13) MUTATED DEL PEAK  1(1Q42.13) WILD-TYPE
  T1                            0                            142
  T2                            2                            163
  T3                            3                            164
  T4                            0                             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"
D9V5, binary
                                cls
clus                               0   1
  DEL PEAK  1(1Q42.13) MUTATED     3   1
  DEL PEAK  1(1Q42.13) WILD-TYPE 222 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1Q42.13) MUTATED      3    1
  DEL PEAK  1(1Q42.13) WILD-TYPE  222  223
   clus
vv  DEL PEAK  1(1Q42.13) MUTATED DEL PEAK  1(1Q42.13) WILD-TYPE
  0                            3                            222
  1                            1                            223
[1] 2 2
[1] FALSE
D9V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1Q42.13) MUTATED     2   0
  DEL PEAK  1(1Q42.13) WILD-TYPE 276   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1Q42.13) MUTATED      2    0
  DEL PEAK  1(1Q42.13) WILD-TYPE  276    9
   clus
vv  DEL PEAK  1(1Q42.13) MUTATED DEL PEAK  1(1Q42.13) WILD-TYPE
  0                            2                            276
  1                            0                              9
[1] 2 2
[1] FALSE
D9V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1Q42.13) MUTATED     4   1
  DEL PEAK  1(1Q42.13) WILD-TYPE 361 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1Q42.13) MUTATED      4    1
  DEL PEAK  1(1Q42.13) WILD-TYPE  361  133
        clus
vv       DEL PEAK  1(1Q42.13) MUTATED DEL PEAK  1(1Q42.13) WILD-TYPE
  FEMALE                            4                            361
  MALE                              1                            133
[1] 2 2
[1] FALSE
D9V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1Q42.13) MUTATED     1   3
  DEL PEAK  1(1Q42.13) WILD-TYPE 179 300
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1Q42.13) MUTATED      1    3
  DEL PEAK  1(1Q42.13) WILD-TYPE  179  300
     clus
vv    DEL PEAK  1(1Q42.13) MUTATED DEL PEAK  1(1Q42.13) WILD-TYPE
  NO                             1                            179
  YES                            3                            300
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER, SPECIFY
  DEL PEAK  1(1Q42.13) MUTATED                0
  DEL PEAK  1(1Q42.13) WILD-TYPE              7
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  1(1Q42.13) MUTATED                                               3
  DEL PEAK  1(1Q42.13) WILD-TYPE                                           353
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  1(1Q42.13) MUTATED                                                                        2
  DEL PEAK  1(1Q42.13) WILD-TYPE                                                                     98
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK  1(1Q42.13) MUTATED                                                                     0
  DEL PEAK  1(1Q42.13) WILD-TYPE                                                                  36
D9V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK  1(1Q42.13) MUTATED
  OTHER, SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK  1(1Q42.13) WILD-TYPE
  OTHER, SPECIFY                                                                                      7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
                                cls
clus                               0   1
  DEL PEAK  1(1Q42.13) MUTATED     4   0
  DEL PEAK  1(1Q42.13) WILD-TYPE 416  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1Q42.13) MUTATED      4    0
  DEL PEAK  1(1Q42.13) WILD-TYPE  416   17
     clus
vv    DEL PEAK  1(1Q42.13) MUTATED DEL PEAK  1(1Q42.13) WILD-TYPE
  NO                             4                            416
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK  1(1Q42.13) MUTATED              1                       0    4
  DEL PEAK  1(1Q42.13) WILD-TYPE          131                      18  326
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK  1(1Q42.13) MUTATED                     0
  DEL PEAK  1(1Q42.13) WILD-TYPE                   1
D9V11, multiclass
                         clus
vv                        DEL PEAK  1(1Q42.13) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               4
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK  1(1Q42.13) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               326
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1Q42.13) MUTATED     4   1   0   0
  DEL PEAK  1(1Q42.13) WILD-TYPE 379  50   4  30
D9V12, multiclass
    clus
vv   DEL PEAK  1(1Q42.13) MUTATED DEL PEAK  1(1Q42.13) WILD-TYPE
  R0                            4                            379
  R1                            1                             50
  R2                            0                              4
  RX                            0                             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"
D9V13, continuous
D9V14, binary
                                cls
clus                               0   1
  DEL PEAK  1(1Q42.13) MUTATED     2   3
  DEL PEAK  1(1Q42.13) WILD-TYPE 223 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1Q42.13) MUTATED      2    3
  DEL PEAK  1(1Q42.13) WILD-TYPE  223  261
            clus
vv           DEL PEAK  1(1Q42.13) MUTATED DEL PEAK  1(1Q42.13) WILD-TYPE
  MULTIFOCAL                            2                            223
  UNIFOCAL                              3                            261
[1] 2 2
[1] FALSE
D9V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1Q42.13) MUTATED                                  0     0
  DEL PEAK  1(1Q42.13) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1Q42.13) MUTATED                           0     4
  DEL PEAK  1(1Q42.13) WILD-TYPE                        27   325
D9V16, multiclass
                                  clus
vv                                 DEL PEAK  1(1Q42.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       4
                                  clus
vv                                 DEL PEAK  1(1Q42.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V17, binary
                                cls
clus                               0   1
  DEL PEAK  1(1Q42.13) MUTATED     2   2
  DEL PEAK  1(1Q42.13) WILD-TYPE  36 358
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1Q42.13) MUTATED      2    2
  DEL PEAK  1(1Q42.13) WILD-TYPE   36  358
                        clus
vv                       DEL PEAK  1(1Q42.13) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            2
                        clus
vv                       DEL PEAK  1(1Q42.13) WILD-TYPE
  HISPANIC OR LATINO                                 36
  NOT HISPANIC OR LATINO                            358
[1] 2 2
[1] FALSE

Clustering(10) Variable = DEL PEAK  2(2P23.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(2P23.1) MUTATED    12   0
  DEL PEAK  2(2P23.1) WILD-TYPE 470  16
  DEL PEAK  2(2P23.1) MUTATED DEL PEAK  2(2P23.1) WILD-TYPE 
                           12                           486 
  DEL PEAK  2(2P23.1) MUTATED DEL PEAK  2(2P23.1) WILD-TYPE 
                            0                            16 
$`DEL PEAK  2(2P23.1) MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-DJ-A3US TCGA-EM-A1YE TCGA-EM-A22N TCGA-EM-A2CO 
       20.58        34.36        32.81        54.08        10.65         6.05 
TCGA-EM-A2OY TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-EM-A4FR TCGA-ET-A3DS TCGA-FY-A3I5 
       32.32         9.24        13.51        21.53        66.84         7.82 

$`DEL PEAK  2(2P23.1) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       36.33        11.34        35.87        40.96        36.99        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       30.61        19.20        23.21        21.27        20.48        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        40.70        18.97         9.60        35.67        36.43 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       23.44        27.62        30.87        30.12        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       80.52        63.19        52.44        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 
       29.98        31.50        31.04        31.30        30.84        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       30.61        31.27        31.33        14.96        39.88        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       31.00        30.15        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
      158.83        60.95       157.15        37.94        57.01       106.62 
TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       79.50        98.53        69.57       108.36        64.87        49.51 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      101.13       139.99        49.32        43.36        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 
      139.00       108.66        57.63        52.50        29.65       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        91.17        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        72.69        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       61.02        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        78.61        57.01        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       17.88        13.18        23.51         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        40.34        19.73        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        33.07        44.52         8.35        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33        12.53 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       27.02        38.66        38.86        29.95        29.85        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       22.45        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       94.59        84.85        80.58        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       13.81        14.04        21.60        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46        11.01        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
       22.29         5.75         2.47         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
        9.50        36.10        32.45        30.21        12.89         3.02 

  DEL PEAK  2(2P23.1) MUTATED DEL PEAK  2(2P23.1) WILD-TYPE 
                         6.05                          0.20 
  DEL PEAK  2(2P23.1) MUTATED DEL PEAK  2(2P23.1) WILD-TYPE 
                        66.84                        178.29 
  DEL PEAK  2(2P23.1) MUTATED DEL PEAK  2(2P23.1) WILD-TYPE 
                       21.055                        31.270 
[1] "6.0 - 66.8 (21.1)"  "0.2 - 178.3 (31.3)"
[1] "hr="     "9100000"
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  2(2P23.1) MUTATED         6        5         1        0         0
  DEL PEAK  2(2P23.1) WILD-TYPE     276       45       110        2        46
                               vv
clus                            STAGE IVC
  DEL PEAK  2(2P23.1) MUTATED           0
  DEL PEAK  2(2P23.1) WILD-TYPE         6
D10V3, multiclass
           clus
vv          DEL PEAK  2(2P23.1) MUTATED DEL PEAK  2(2P23.1) WILD-TYPE
  STAGE I                             6                           276
  STAGE II                            5                            45
  STAGE III                           1                           110
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] 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(2P23.1) MUTATED     4   5   3   0
  DEL PEAK  2(2P23.1) WILD-TYPE 138 160 164  23
D10V4, multiclass
    clus
vv   DEL PEAK  2(2P23.1) MUTATED DEL PEAK  2(2P23.1) WILD-TYPE
  T1                           4                           138
  T2                           5                           160
  T3                           3                           164
  T4                           0                            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"
D10V5, binary
                               cls
clus                              0   1
  DEL PEAK  2(2P23.1) MUTATED     9   1
  DEL PEAK  2(2P23.1) WILD-TYPE 216 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2P23.1) MUTATED      9    1
  DEL PEAK  2(2P23.1) WILD-TYPE  216  223
   clus
vv  DEL PEAK  2(2P23.1) MUTATED DEL PEAK  2(2P23.1) WILD-TYPE
  0                           9                           216
  1                           1                           223
[1] 2 2
[1] FALSE
D10V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(2P23.1) MUTATED     2   0
  DEL PEAK  2(2P23.1) WILD-TYPE 276   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2P23.1) MUTATED      2    0
  DEL PEAK  2(2P23.1) WILD-TYPE  276    9
   clus
vv  DEL PEAK  2(2P23.1) MUTATED DEL PEAK  2(2P23.1) WILD-TYPE
  0                           2                           276
  1                           0                             9
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(2P23.1) MUTATED     8   4
  DEL PEAK  2(2P23.1) WILD-TYPE 357 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2P23.1) MUTATED      8    4
  DEL PEAK  2(2P23.1) WILD-TYPE  357  130
        clus
vv       DEL PEAK  2(2P23.1) MUTATED DEL PEAK  2(2P23.1) WILD-TYPE
  FEMALE                           8                           357
  MALE                             4                           130
[1] 2 2
[1] FALSE
D10V8, binary
                               cls
clus                              0   1
  DEL PEAK  2(2P23.1) MUTATED     4   7
  DEL PEAK  2(2P23.1) WILD-TYPE 176 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2P23.1) MUTATED      4    7
  DEL PEAK  2(2P23.1) WILD-TYPE  176  296
     clus
vv    DEL PEAK  2(2P23.1) MUTATED DEL PEAK  2(2P23.1) WILD-TYPE
  NO                            4                           176
  YES                           7                           296
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER, SPECIFY
  DEL PEAK  2(2P23.1) MUTATED                1
  DEL PEAK  2(2P23.1) WILD-TYPE              6
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  2(2P23.1) MUTATED                                               4
  DEL PEAK  2(2P23.1) WILD-TYPE                                           352
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  2(2P23.1) MUTATED                                                                        7
  DEL PEAK  2(2P23.1) WILD-TYPE                                                                     93
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK  2(2P23.1) MUTATED                                                                     0
  DEL PEAK  2(2P23.1) WILD-TYPE                                                                  36
D10V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK  2(2P23.1) MUTATED
  OTHER, SPECIFY                                                                                   1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       DEL PEAK  2(2P23.1) WILD-TYPE
  OTHER, SPECIFY                                                                                     6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            93
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
                               cls
clus                              0   1
  DEL PEAK  2(2P23.1) MUTATED    11   0
  DEL PEAK  2(2P23.1) WILD-TYPE 409  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2P23.1) MUTATED     11    0
  DEL PEAK  2(2P23.1) WILD-TYPE  409   17
     clus
vv    DEL PEAK  2(2P23.1) MUTATED DEL PEAK  2(2P23.1) WILD-TYPE
  NO                           11                           409
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK  2(2P23.1) MUTATED              0                       0   12
  DEL PEAK  2(2P23.1) WILD-TYPE          132                      18  318
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  2(2P23.1) MUTATED                     0
  DEL PEAK  2(2P23.1) WILD-TYPE                   1
D10V11, multiclass
                         clus
vv                        DEL PEAK  2(2P23.1) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           0
  NONE                                             12
  VERY ADVANCED (T4B)                               0
                         clus
vv                        DEL PEAK  2(2P23.1) WILD-TYPE
  MINIMAL (T3)                                      132
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              318
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  2(2P23.1) MUTATED    11   0   0   1
  DEL PEAK  2(2P23.1) WILD-TYPE 372  51   4  29
D10V12, multiclass
    clus
vv   DEL PEAK  2(2P23.1) MUTATED DEL PEAK  2(2P23.1) WILD-TYPE
  R0                          11                           372
  R1                           0                            51
  R2                           0                             4
  RX                           1                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, continuous
D10V14, binary
                               cls
clus                              0   1
  DEL PEAK  2(2P23.1) MUTATED     6   6
  DEL PEAK  2(2P23.1) WILD-TYPE 219 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2P23.1) MUTATED      6    6
  DEL PEAK  2(2P23.1) WILD-TYPE  219  258
            clus
vv           DEL PEAK  2(2P23.1) MUTATED DEL PEAK  2(2P23.1) WILD-TYPE
  MULTIFOCAL                           6                           219
  UNIFOCAL                             6                           258
[1] 2 2
[1] FALSE
D10V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(2P23.1) MUTATED                                  0     0
  DEL PEAK  2(2P23.1) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(2P23.1) MUTATED                           0     5
  DEL PEAK  2(2P23.1) WILD-TYPE                        27   324
D10V16, multiclass
                                  clus
vv                                 DEL PEAK  2(2P23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      5
                                  clus
vv                                 DEL PEAK  2(2P23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V17, binary
                               cls
clus                              0   1
  DEL PEAK  2(2P23.1) MUTATED     0   5
  DEL PEAK  2(2P23.1) WILD-TYPE  38 355
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2P23.1) MUTATED      0    5
  DEL PEAK  2(2P23.1) WILD-TYPE   38  355
                        clus
vv                       DEL PEAK  2(2P23.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       DEL PEAK  2(2P23.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           355
[1] 2 2
[1] FALSE

Clustering(11) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED    10   0
  DEL PEAK  3(2Q22.1) WILD-TYPE 472  16
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           10                           488 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            0                            16 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A1YE TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY 
       20.58        34.36        54.08        10.65         6.05        32.32 
TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A39N TCGA-FY-A3I5 
        9.24        13.51       123.32         7.82 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        78.61        57.01        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       15.75        10.45        14.53        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ 
       47.57        17.88        13.18        23.51         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       48.46        13.15        22.16        40.34        19.73        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR 
       15.68        14.14        33.07        44.52         8.35        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
       12.53        27.02        38.66        38.86        29.95        29.85 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       33.24       106.09       107.41       108.46        84.89       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP 
       95.34        94.13        55.10        98.20        28.24        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
       76.64         5.79        87.62        77.82        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10       116.09         1.25        20.42        17.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                         6.05                          0.20 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       123.32                        178.29 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       17.045                        31.270 
[1] "6.0 - 123.3 (17.0)" "0.2 - 178.3 (31.3)"
[1] "hr="     "9100000"
D11V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  3(2Q22.1) MUTATED         4        5         1        0         0
  DEL PEAK  3(2Q22.1) WILD-TYPE     278       45       110        2        46
                               vv
clus                            STAGE IVC
  DEL PEAK  3(2Q22.1) MUTATED           0
  DEL PEAK  3(2Q22.1) WILD-TYPE         6
D11V3, multiclass
           clus
vv          DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE I                             4                           278
  STAGE II                            5                            45
  STAGE III                           1                           110
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  3(2Q22.1) MUTATED     2   5   3   0
  DEL PEAK  3(2Q22.1) WILD-TYPE 140 160 164  23
D11V4, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1                           2                           140
  T2                           5                           160
  T3                           3                           164
  T4                           0                            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"
D11V5, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     7   0
  DEL PEAK  3(2Q22.1) WILD-TYPE 218 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      7    0
  DEL PEAK  3(2Q22.1) WILD-TYPE  218  224
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                           7                           218
  1                           0                           224
[1] 2 2
[1] FALSE
D11V6, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     1   0
  DEL PEAK  3(2Q22.1) WILD-TYPE 277   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      1    0
  DEL PEAK  3(2Q22.1) WILD-TYPE  277    9
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                           1                           277
  1                           0                             9
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     7   3
  DEL PEAK  3(2Q22.1) WILD-TYPE 358 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      7    3
  DEL PEAK  3(2Q22.1) WILD-TYPE  358  131
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                           7                           358
  MALE                             3                           131
[1] 2 2
[1] FALSE
D11V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     2   7
  DEL PEAK  3(2Q22.1) WILD-TYPE 178 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      2    7
  DEL PEAK  3(2Q22.1) WILD-TYPE  178  296
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  NO                            2                           178
  YES                           7                           296
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER, SPECIFY
  DEL PEAK  3(2Q22.1) MUTATED                0
  DEL PEAK  3(2Q22.1) WILD-TYPE              7
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  3(2Q22.1) MUTATED                                               3
  DEL PEAK  3(2Q22.1) WILD-TYPE                                           353
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  3(2Q22.1) MUTATED                                                                        7
  DEL PEAK  3(2Q22.1) WILD-TYPE                                                                     93
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK  3(2Q22.1) MUTATED                                                                     0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                                                  36
D11V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK  3(2Q22.1) MUTATED
  OTHER, SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       DEL PEAK  3(2Q22.1) WILD-TYPE
  OTHER, SPECIFY                                                                                     7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            93
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     9   0
  DEL PEAK  3(2Q22.1) WILD-TYPE 411  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      9    0
  DEL PEAK  3(2Q22.1) WILD-TYPE  411   17
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  NO                            9                           411
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK  3(2Q22.1) MUTATED              0                       0   10
  DEL PEAK  3(2Q22.1) WILD-TYPE          132                      18  320
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  3(2Q22.1) MUTATED                     0
  DEL PEAK  3(2Q22.1) WILD-TYPE                   1
D11V11, multiclass
                         clus
vv                        DEL PEAK  3(2Q22.1) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           0
  NONE                                             10
  VERY ADVANCED (T4B)                               0
                         clus
vv                        DEL PEAK  3(2Q22.1) WILD-TYPE
  MINIMAL (T3)                                      132
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              320
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(2Q22.1) MUTATED     9   0   0   1
  DEL PEAK  3(2Q22.1) WILD-TYPE 374  51   4  29
D11V12, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  R0                           9                           374
  R1                           0                            51
  R2                           0                             4
  RX                           1                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, continuous
D11V14, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     5   5
  DEL PEAK  3(2Q22.1) WILD-TYPE 220 259
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      5    5
  DEL PEAK  3(2Q22.1) WILD-TYPE  220  259
            clus
vv           DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  MULTIFOCAL                           5                           220
  UNIFOCAL                             5                           259
[1] 2 2
[1] FALSE
D11V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(2Q22.1) MUTATED                                  0     0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q22.1) MUTATED                           0     4
  DEL PEAK  3(2Q22.1) WILD-TYPE                        27   325
D11V16, multiclass
                                  clus
vv                                 DEL PEAK  3(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      4
                                  clus
vv                                 DEL PEAK  3(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V17, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     0   4
  DEL PEAK  3(2Q22.1) WILD-TYPE  38 356
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      0    4
  DEL PEAK  3(2Q22.1) WILD-TYPE   38  356
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           356
[1] 2 2
[1] FALSE

Clustering(12) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.3) MUTATED    12   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 470  15
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           13                           485 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            1                            15 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-EL-A3H2 TCGA-BJ-A190 TCGA-BJ-A192 TCGA-DJ-A2Q0 TCGA-DJ-A2Q5 TCGA-EM-A1YE 
       33.50        20.58        44.35        34.36        37.48        54.08 
TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A39N 
       10.65         6.05        32.32         9.24        13.51       123.32 
TCGA-FY-A3I5 
        7.82 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO 
       50.24       150.48        17.52       178.29        29.72        50.40 
TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET 
       75.42         1.05         1.68        17.23         2.60        21.83 
TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       23.93         4.24        24.79        13.78        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 
       25.48        15.12        42.08        51.39        41.52         4.83 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       11.08        18.38        16.57        20.48        18.97        12.82 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       21.63        19.43        23.47        12.30        12.79        12.46 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 
       11.38        10.68        15.02        12.43        12.66        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        27.32        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       52.27        43.17        52.37         8.32        48.07       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.99        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       35.41        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
       28.96         8.78         8.42        37.74        43.96        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       33.93        36.46        35.11        39.09        35.90        33.53 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       35.18        39.95        36.92        31.04        32.42        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX 
       16.41        19.56        36.33        32.81        36.33        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 
       35.87        40.96        36.99        20.22        30.61        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        40.70 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         9.60        35.67        36.43        23.44        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       30.87        30.12        33.04        34.78        27.06        26.93 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       35.54         3.12        15.81        35.38        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        92.55        47.21        66.38        80.52        63.19 
TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       52.44        31.23        35.67        31.27        29.98        31.50 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 
       31.04        31.30        30.84        25.45        30.61        31.27 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       31.33        14.96        39.88        33.50        31.00        30.15 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT 
       31.66        26.73       155.54        97.74       158.83        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 
      157.15        37.94        57.01       106.62        79.50        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS 
       69.57       108.36        64.87        49.51       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      136.01        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW 
       49.32        43.36        49.71        83.57       139.00       108.66 
TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       57.63        52.50        29.65       142.52       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        91.17        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        72.69        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        61.02        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       57.01        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
       23.51         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       40.34        19.73        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       14.50        15.06         7.33        12.53        27.02        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       38.86        29.95        29.85        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
      108.46        84.89       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        4.11        22.03         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82        29.10        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08        23.31        21.63        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 
       17.36        15.16        23.87        22.49        19.04        13.81 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       14.04        21.60        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
       11.01        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 
       16.90        21.83        31.10         8.22        25.64        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        5.75         2.47         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU 
       84.72        35.28        33.24        33.40        40.37         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       36.10        32.45        30.21        12.89         3.02 

  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         6.05                          0.20 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       123.32                        178.29 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                        32.32                         31.23 
[1] "6.0 - 123.3 (32.3)" "0.2 - 178.3 (31.2)"
[1] "hr=" "3.2"
D12V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  4(2Q37.3) MUTATED         4        6         2        0         1
  DEL PEAK  4(2Q37.3) WILD-TYPE     278       44       109        2        45
                               vv
clus                            STAGE IVC
  DEL PEAK  4(2Q37.3) MUTATED           0
  DEL PEAK  4(2Q37.3) WILD-TYPE         6
D12V3, multiclass
           clus
vv          DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  STAGE I                             4                           278
  STAGE II                            6                            44
  STAGE III                           2                           109
  STAGE IV                            0                             2
  STAGE IVA                           1                            45
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  4(2Q37.3) MUTATED     2   7   4   0
  DEL PEAK  4(2Q37.3) WILD-TYPE 140 158 163  23
D12V4, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  T1                           2                           140
  T2                           7                           158
  T3                           4                           163
  T4                           0                            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"
D12V5, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     8   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 217 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      8    1
  DEL PEAK  4(2Q37.3) WILD-TYPE  217  223
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                           8                           217
  1                           1                           223
[1] 2 2
[1] FALSE
D12V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     3   0
  DEL PEAK  4(2Q37.3) WILD-TYPE 275   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      3    0
  DEL PEAK  4(2Q37.3) WILD-TYPE  275    9
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                           3                           275
  1                           0                             9
[1] 2 2
[1] FALSE
D12V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     8   5
  DEL PEAK  4(2Q37.3) WILD-TYPE 357 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      8    5
  DEL PEAK  4(2Q37.3) WILD-TYPE  357  129
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                           8                           357
  MALE                             5                           129
[1] 2 2
[1] FALSE
D12V8, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     3   9
  DEL PEAK  4(2Q37.3) WILD-TYPE 177 294
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      3    9
  DEL PEAK  4(2Q37.3) WILD-TYPE  177  294
     clus
vv    DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  NO                            3                           177
  YES                           9                           294
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER, SPECIFY
  DEL PEAK  4(2Q37.3) MUTATED                0
  DEL PEAK  4(2Q37.3) WILD-TYPE              7
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  4(2Q37.3) MUTATED                                               6
  DEL PEAK  4(2Q37.3) WILD-TYPE                                           350
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  4(2Q37.3) MUTATED                                                                        7
  DEL PEAK  4(2Q37.3) WILD-TYPE                                                                     93
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK  4(2Q37.3) MUTATED                                                                     0
  DEL PEAK  4(2Q37.3) WILD-TYPE                                                                  36
D12V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK  4(2Q37.3) MUTATED
  OTHER, SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       DEL PEAK  4(2Q37.3) WILD-TYPE
  OTHER, SPECIFY                                                                                     7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            93
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    11   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 409  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     11    1
  DEL PEAK  4(2Q37.3) WILD-TYPE  409   16
     clus
vv    DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  NO                           11                           409
  YES                           1                            16
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK  4(2Q37.3) MUTATED              1                       0   12
  DEL PEAK  4(2Q37.3) WILD-TYPE          131                      18  318
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  4(2Q37.3) MUTATED                     0
  DEL PEAK  4(2Q37.3) WILD-TYPE                   1
D12V11, multiclass
                         clus
vv                        DEL PEAK  4(2Q37.3) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           0
  NONE                                             12
  VERY ADVANCED (T4B)                               0
                         clus
vv                        DEL PEAK  4(2Q37.3) WILD-TYPE
  MINIMAL (T3)                                      131
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              318
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  4(2Q37.3) MUTATED    11   0   0   2
  DEL PEAK  4(2Q37.3) WILD-TYPE 372  51   4  28
D12V12, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  R0                          11                           372
  R1                           0                            51
  R2                           0                             4
  RX                           2                            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, continuous
D12V14, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     5   8
  DEL PEAK  4(2Q37.3) WILD-TYPE 220 256
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      5    8
  DEL PEAK  4(2Q37.3) WILD-TYPE  220  256
            clus
vv           DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  MULTIFOCAL                           5                           220
  UNIFOCAL                             8                           256
[1] 2 2
[1] FALSE
D12V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2Q37.3) MUTATED                                  0     0
  DEL PEAK  4(2Q37.3) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED                           0     7
  DEL PEAK  4(2Q37.3) WILD-TYPE                        27   322
D12V16, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      7
                                  clus
vv                                 DEL PEAK  4(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V17, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     0   6
  DEL PEAK  4(2Q37.3) WILD-TYPE  38 354
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      0    6
  DEL PEAK  4(2Q37.3) WILD-TYPE   38  354
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           6
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           354
[1] 2 2
[1] FALSE

Clustering(13) Variable = DEL PEAK  5(4Q34.3) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(4Q34.3) MUTATED     5   0
  DEL PEAK  5(4Q34.3) WILD-TYPE 477  16
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                            5                           493 
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                            0                            16 
$`DEL PEAK  5(4Q34.3) MUTATED`
TCGA-BJ-A190 TCGA-E8-A414 TCGA-EM-A1YE TCGA-ET-A39N TCGA-FE-A22Z 
       20.58        31.50        54.08       123.32        73.74 

$`DEL PEAK  5(4Q34.3) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       35.67        31.27        29.98        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        78.61        57.01        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       37.48        33.17        31.40        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25        20.42        17.82         7.82        29.10        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
       21.63        17.06        17.36        15.16        23.87        22.49 
TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04        13.81        14.04        21.60        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46        11.01        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       25.64        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F 
       24.69        22.29         5.75         2.47         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV 
       40.37         9.50        36.10        32.45        30.21        12.89 
TCGA-E8-A418 
        3.02 

  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                        20.58                          0.20 
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                       123.32                        178.29 
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                        54.08                         31.10 
[1] "20.6 - 123.3 (54.1)" "0.2 - 178.3 (31.1)" 
[1] "hr="     "9200000"
D13V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  5(4Q34.3) MUTATED         1        2         1        0         1
  DEL PEAK  5(4Q34.3) WILD-TYPE     281       48       110        2        45
                               vv
clus                            STAGE IVC
  DEL PEAK  5(4Q34.3) MUTATED           0
  DEL PEAK  5(4Q34.3) WILD-TYPE         6
D13V3, multiclass
           clus
vv          DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  STAGE I                             1                           281
  STAGE II                            2                            48
  STAGE III                           1                           110
  STAGE IV                            0                             2
  STAGE IVA                           1                            45
  STAGE IVC                           0                             6
[1] 6 2
[1] 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(4Q34.3) MUTATED     0   2   2   1
  DEL PEAK  5(4Q34.3) WILD-TYPE 142 163 165  22
D13V4, multiclass
    clus
vv   DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  T1                           0                           142
  T2                           2                           163
  T3                           2                           165
  T4                           1                            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                               cls
clus                              0   1
  DEL PEAK  5(4Q34.3) MUTATED     3   1
  DEL PEAK  5(4Q34.3) WILD-TYPE 222 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q34.3) MUTATED      3    1
  DEL PEAK  5(4Q34.3) WILD-TYPE  222  223
   clus
vv  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  0                           3                           222
  1                           1                           223
[1] 2 2
[1] FALSE
D13V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(4Q34.3) MUTATED     1   0
  DEL PEAK  5(4Q34.3) WILD-TYPE 277   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q34.3) MUTATED      1    0
  DEL PEAK  5(4Q34.3) WILD-TYPE  277    9
   clus
vv  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  0                           1                           277
  1                           0                             9
[1] 2 2
[1] FALSE
D13V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(4Q34.3) MUTATED     4   1
  DEL PEAK  5(4Q34.3) WILD-TYPE 361 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q34.3) MUTATED      4    1
  DEL PEAK  5(4Q34.3) WILD-TYPE  361  133
        clus
vv       DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  FEMALE                           4                           361
  MALE                             1                           133
[1] 2 2
[1] FALSE
D13V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(4Q34.3) MUTATED     2   3
  DEL PEAK  5(4Q34.3) WILD-TYPE 178 300
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q34.3) MUTATED      2    3
  DEL PEAK  5(4Q34.3) WILD-TYPE  178  300
     clus
vv    DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  NO                            2                           178
  YES                           3                           300
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER, SPECIFY
  DEL PEAK  5(4Q34.3) MUTATED                0
  DEL PEAK  5(4Q34.3) WILD-TYPE              7
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  5(4Q34.3) MUTATED                                               3
  DEL PEAK  5(4Q34.3) WILD-TYPE                                           353
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  5(4Q34.3) MUTATED                                                                        2
  DEL PEAK  5(4Q34.3) WILD-TYPE                                                                     98
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK  5(4Q34.3) MUTATED                                                                     0
  DEL PEAK  5(4Q34.3) WILD-TYPE                                                                  36
D13V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK  5(4Q34.3) MUTATED
  OTHER, SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       DEL PEAK  5(4Q34.3) WILD-TYPE
  OTHER, SPECIFY                                                                                     7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, binary
                               cls
clus                              0   1
  DEL PEAK  5(4Q34.3) MUTATED     5   0
  DEL PEAK  5(4Q34.3) WILD-TYPE 415  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q34.3) MUTATED      5    0
  DEL PEAK  5(4Q34.3) WILD-TYPE  415   17
     clus
vv    DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  NO                            5                           415
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK  5(4Q34.3) MUTATED              0                       1    4
  DEL PEAK  5(4Q34.3) WILD-TYPE          132                      17  326
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  5(4Q34.3) MUTATED                     0
  DEL PEAK  5(4Q34.3) WILD-TYPE                   1
D13V11, multiclass
                         clus
vv                        DEL PEAK  5(4Q34.3) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           1
  NONE                                              4
  VERY ADVANCED (T4B)                               0
                         clus
vv                        DEL PEAK  5(4Q34.3) WILD-TYPE
  MINIMAL (T3)                                      132
  MODERATE/ADVANCED (T4A)                            17
  NONE                                              326
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(4Q34.3) MUTATED     5   0   0   0
  DEL PEAK  5(4Q34.3) WILD-TYPE 378  51   4  30
D13V12, multiclass
    clus
vv   DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  R0                           5                           378
  R1                           0                            51
  R2                           0                             4
  RX                           0                            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"
D13V13, continuous
D13V14, binary
                               cls
clus                              0   1
  DEL PEAK  5(4Q34.3) MUTATED     1   4
  DEL PEAK  5(4Q34.3) WILD-TYPE 224 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q34.3) MUTATED      1    4
  DEL PEAK  5(4Q34.3) WILD-TYPE  224  260
            clus
vv           DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  MULTIFOCAL                           1                           224
  UNIFOCAL                             4                           260
[1] 2 2
[1] FALSE
D13V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(4Q34.3) MUTATED                                  0     1
  DEL PEAK  5(4Q34.3) WILD-TYPE                                1    51
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(4Q34.3) MUTATED                           0     3
  DEL PEAK  5(4Q34.3) WILD-TYPE                        27   326
D13V16, multiclass
                                  clus
vv                                 DEL PEAK  5(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      3
                                  clus
vv                                 DEL PEAK  5(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V17, binary
                               cls
clus                              0   1
  DEL PEAK  5(4Q34.3) MUTATED     0   4
  DEL PEAK  5(4Q34.3) WILD-TYPE  38 356
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q34.3) MUTATED      0    4
  DEL PEAK  5(4Q34.3) WILD-TYPE   38  356
                        clus
vv                       DEL PEAK  5(4Q34.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       DEL PEAK  5(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           356
[1] 2 2
[1] FALSE

Clustering(14) Variable = DEL PEAK  6(5P15.2) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(5P15.2) MUTATED     4   0
  DEL PEAK  6(5P15.2) WILD-TYPE 478  16
  DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE 
                            4                           494 
  DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE 
                            0                            16 
$`DEL PEAK  6(5P15.2) MUTATED`
TCGA-BJ-A4O9 TCGA-DE-A4MB TCGA-DJ-A3V2 TCGA-L6-A4EU 
       23.47        11.57        20.22         9.50 

$`DEL PEAK  6(5P15.2) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-CE-A27D 
       23.84        28.44        15.45        21.63        19.43        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       18.84        30.12        30.02        25.12        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        52.27        43.17        52.37         8.32        48.07 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       30.58        35.41        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       30.61        19.20        23.21        21.27        20.48        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        40.70        18.97         9.60        35.67        36.43 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       23.44        27.62        30.87        30.12        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       80.52        63.19        52.44        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 
       29.98        31.50        31.04        31.30        30.84        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       30.61        31.27        31.33        14.96        39.88        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       31.00        30.15        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
      158.83        60.95       157.15        37.94        57.01       106.62 
TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       79.50        98.53        69.57       108.36        64.87        49.51 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      101.13       139.99        49.32        43.36        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 
      139.00       108.66        57.63        52.50        29.65       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        91.17        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        72.69        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       61.02        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.46        78.61        57.01        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP 
       95.34        94.13        55.10        98.20        28.24        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
       76.64         5.79        87.62        77.82        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10       116.09         1.25        20.42        17.82         7.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       29.10        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08        23.31        21.63        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 
       23.87        22.49        19.04        13.81        14.04        21.60 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46        11.01        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
       31.10         8.22        25.64        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.24        33.40        40.37        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE 
                          9.5                           0.2 
  DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE 
                        23.47                        178.29 
  DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE 
                       15.895                        31.285 
[1] "9.5 - 23.5 (15.9)"  "0.2 - 178.3 (31.3)"
[1] "hr="     "1200000"
D14V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  6(5P15.2) MUTATED         1        1         1        0         1
  DEL PEAK  6(5P15.2) WILD-TYPE     281       49       110        2        45
                               vv
clus                            STAGE IVC
  DEL PEAK  6(5P15.2) MUTATED           0
  DEL PEAK  6(5P15.2) WILD-TYPE         6
D14V3, multiclass
           clus
vv          DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE
  STAGE I                             1                           281
  STAGE II                            1                            49
  STAGE III                           1                           110
  STAGE IV                            0                             2
  STAGE IVA                           1                            45
  STAGE IVC                           0                             6
[1] 6 2
[1] 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(5P15.2) MUTATED     0   2   2   0
  DEL PEAK  6(5P15.2) WILD-TYPE 142 163 165  23
D14V4, multiclass
    clus
vv   DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE
  T1                           0                           142
  T2                           2                           163
  T3                           2                           165
  T4                           0                            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"
D14V5, binary
                               cls
clus                              0   1
  DEL PEAK  6(5P15.2) MUTATED     1   3
  DEL PEAK  6(5P15.2) WILD-TYPE 224 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(5P15.2) MUTATED      1    3
  DEL PEAK  6(5P15.2) WILD-TYPE  224  221
   clus
vv  DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE
  0                           1                           224
  1                           3                           221
[1] 2 2
[1] FALSE
D14V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(5P15.2) MUTATED     4   0
  DEL PEAK  6(5P15.2) WILD-TYPE 274   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(5P15.2) MUTATED      4    0
  DEL PEAK  6(5P15.2) WILD-TYPE  274    9
   clus
vv  DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE
  0                           4                           274
  1                           0                             9
[1] 2 2
[1] FALSE
D14V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(5P15.2) MUTATED     4   0
  DEL PEAK  6(5P15.2) WILD-TYPE 361 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(5P15.2) MUTATED      4    0
  DEL PEAK  6(5P15.2) WILD-TYPE  361  134
        clus
vv       DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE
  FEMALE                           4                           361
  MALE                             0                           134
[1] 2 2
[1] FALSE
D14V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(5P15.2) MUTATED     2   2
  DEL PEAK  6(5P15.2) WILD-TYPE 178 301
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(5P15.2) MUTATED      2    2
  DEL PEAK  6(5P15.2) WILD-TYPE  178  301
     clus
vv    DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE
  NO                            2                           178
  YES                           2                           301
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER, SPECIFY
  DEL PEAK  6(5P15.2) MUTATED                0
  DEL PEAK  6(5P15.2) WILD-TYPE              7
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  6(5P15.2) MUTATED                                               2
  DEL PEAK  6(5P15.2) WILD-TYPE                                           354
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  6(5P15.2) MUTATED                                                                        1
  DEL PEAK  6(5P15.2) WILD-TYPE                                                                     99
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK  6(5P15.2) MUTATED                                                                     1
  DEL PEAK  6(5P15.2) WILD-TYPE                                                                  35
D14V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK  6(5P15.2) MUTATED
  OTHER, SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              1
                                                                        clus
vv                                                                       DEL PEAK  6(5P15.2) WILD-TYPE
  OTHER, SPECIFY                                                                                     7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, binary
                               cls
clus                              0   1
  DEL PEAK  6(5P15.2) MUTATED     3   0
  DEL PEAK  6(5P15.2) WILD-TYPE 417  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(5P15.2) MUTATED      3    0
  DEL PEAK  6(5P15.2) WILD-TYPE  417   17
     clus
vv    DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE
  NO                            3                           417
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK  6(5P15.2) MUTATED              2                       0    2
  DEL PEAK  6(5P15.2) WILD-TYPE          130                      18  328
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  6(5P15.2) MUTATED                     0
  DEL PEAK  6(5P15.2) WILD-TYPE                   1
D14V11, multiclass
                         clus
vv                        DEL PEAK  6(5P15.2) MUTATED
  MINIMAL (T3)                                      2
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              2
  VERY ADVANCED (T4B)                               0
                         clus
vv                        DEL PEAK  6(5P15.2) WILD-TYPE
  MINIMAL (T3)                                      130
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              328
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(5P15.2) MUTATED     1   2   0   0
  DEL PEAK  6(5P15.2) WILD-TYPE 382  49   4  30
D14V12, multiclass
    clus
vv   DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE
  R0                           1                           382
  R1                           2                            49
  R2                           0                             4
  RX                           0                            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"
D14V13, continuous
D14V14, binary
                               cls
clus                              0   1
  DEL PEAK  6(5P15.2) MUTATED     3   1
  DEL PEAK  6(5P15.2) WILD-TYPE 222 263
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(5P15.2) MUTATED      3    1
  DEL PEAK  6(5P15.2) WILD-TYPE  222  263
            clus
vv           DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE
  MULTIFOCAL                           3                           222
  UNIFOCAL                             1                           263
[1] 2 2
[1] FALSE
D14V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(5P15.2) MUTATED                                  0     0
  DEL PEAK  6(5P15.2) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(5P15.2) MUTATED                           1     3
  DEL PEAK  6(5P15.2) WILD-TYPE                        26   326
D14V16, multiclass
                                  clus
vv                                 DEL PEAK  6(5P15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                      3
                                  clus
vv                                 DEL PEAK  6(5P15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V17, binary
                               cls
clus                              0   1
  DEL PEAK  6(5P15.2) MUTATED     1   3
  DEL PEAK  6(5P15.2) WILD-TYPE  37 357
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(5P15.2) MUTATED      1    3
  DEL PEAK  6(5P15.2) WILD-TYPE   37  357
                        clus
vv                       DEL PEAK  6(5P15.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       DEL PEAK  6(5P15.2) WILD-TYPE
  HISPANIC OR LATINO                                37
  NOT HISPANIC OR LATINO                           357
[1] 2 2
[1] FALSE

Clustering(15) Variable = DEL PEAK 10(7Q34) MUTATION ANALYSIS
D15V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 10(7Q34) MUTATED     4   0
  DEL PEAK 10(7Q34) WILD-TYPE 478  16
  DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE 
                          4                         494 
  DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE 
                          0                          16 
$`DEL PEAK 10(7Q34) MUTATED`
TCGA-DJ-A2Q8 TCGA-DJ-A3VM TCGA-ET-A2MX TCGA-FY-A40N 
       39.09        27.62        88.41        19.04 

$`DEL PEAK 10(7Q34) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       36.46        35.11        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       35.67        36.43        23.44        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       27.02        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ 
       63.39        65.29        18.38        63.45        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP 
       95.34        94.13        55.10        98.20        28.24        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
       76.64         5.79        87.62        77.82        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10       116.09         1.25        20.42        17.82         7.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       29.10        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08        23.31        21.63        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       23.87        22.49        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE 
                      19.04                        0.20 
  DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE 
                      88.41                      178.29 
  DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE 
                     33.355                      31.250 
[1] "19.0 - 88.4 (33.4)" "0.2 - 178.3 (31.2)"
[1] "hr="     "3300000"
D15V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 10(7Q34) MUTATED         3        1         0        0         0
  DEL PEAK 10(7Q34) WILD-TYPE     279       49       111        2        46
                             vv
clus                          STAGE IVC
  DEL PEAK 10(7Q34) MUTATED           0
  DEL PEAK 10(7Q34) WILD-TYPE         6
D15V3, multiclass
           clus
vv          DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE
  STAGE I                           3                         279
  STAGE II                          1                          49
  STAGE III                         0                         111
  STAGE IV                          0                           2
  STAGE IVA                         0                          46
  STAGE IVC                         0                           6
[1] 6 2
[1] 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(7Q34) MUTATED     2   2   0   0
  DEL PEAK 10(7Q34) WILD-TYPE 140 163 167  23
D15V4, multiclass
    clus
vv   DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE
  T1                         2                         140
  T2                         2                         163
  T3                         0                         167
  T4                         0                          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"
D15V5, binary
                             cls
clus                            0   1
  DEL PEAK 10(7Q34) MUTATED     3   1
  DEL PEAK 10(7Q34) WILD-TYPE 222 223
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(7Q34) MUTATED      3    1
  DEL PEAK 10(7Q34) WILD-TYPE  222  223
   clus
vv  DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE
  0                         3                         222
  1                         1                         223
[1] 2 2
[1] FALSE
D15V6, binary
                             cls
clus                            0   1
  DEL PEAK 10(7Q34) MUTATED     2   0
  DEL PEAK 10(7Q34) WILD-TYPE 276   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(7Q34) MUTATED      2    0
  DEL PEAK 10(7Q34) WILD-TYPE  276    9
   clus
vv  DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE
  0                         2                         276
  1                         0                           9
[1] 2 2
[1] FALSE
D15V7, binary
                             cls
clus                            0   1
  DEL PEAK 10(7Q34) MUTATED     3   1
  DEL PEAK 10(7Q34) WILD-TYPE 362 133
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(7Q34) MUTATED      3    1
  DEL PEAK 10(7Q34) WILD-TYPE  362  133
        clus
vv       DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE
  FEMALE                         3                         362
  MALE                           1                         133
[1] 2 2
[1] FALSE
D15V8, binary
                             cls
clus                            0   1
  DEL PEAK 10(7Q34) MUTATED     2   2
  DEL PEAK 10(7Q34) WILD-TYPE 178 301
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(7Q34) MUTATED      2    2
  DEL PEAK 10(7Q34) WILD-TYPE  178  301
     clus
vv    DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE
  NO                          2                         178
  YES                         2                         301
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER, SPECIFY
  DEL PEAK 10(7Q34) MUTATED                0
  DEL PEAK 10(7Q34) WILD-TYPE              7
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 10(7Q34) MUTATED                                               1
  DEL PEAK 10(7Q34) WILD-TYPE                                           355
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 10(7Q34) MUTATED                                                                        2
  DEL PEAK 10(7Q34) WILD-TYPE                                                                     98
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 10(7Q34) MUTATED                                                                     1
  DEL PEAK 10(7Q34) WILD-TYPE                                                                  35
D15V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 10(7Q34) MUTATED
  OTHER, SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  1
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            1
                                                                        clus
vv                                                                       DEL PEAK 10(7Q34) WILD-TYPE
  OTHER, SPECIFY                                                                                   7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  355
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, binary
                             cls
clus                            0   1
  DEL PEAK 10(7Q34) MUTATED     3   0
  DEL PEAK 10(7Q34) WILD-TYPE 417  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(7Q34) MUTATED      3    0
  DEL PEAK 10(7Q34) WILD-TYPE  417   17
     clus
vv    DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE
  NO                          3                         417
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 10(7Q34) MUTATED              0                       0    4
  DEL PEAK 10(7Q34) WILD-TYPE          132                      18  326
                             vv
clus                          VERY ADVANCED (T4B)
  DEL PEAK 10(7Q34) MUTATED                     0
  DEL PEAK 10(7Q34) WILD-TYPE                   1
D15V11, multiclass
                         clus
vv                        DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE
  MINIMAL (T3)                                    0                         132
  MODERATE/ADVANCED (T4A)                         0                          18
  NONE                                            4                         326
  VERY ADVANCED (T4B)                             0                           1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 10(7Q34) MUTATED     4   0   0   0
  DEL PEAK 10(7Q34) WILD-TYPE 379  51   4  30
D15V12, multiclass
    clus
vv   DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE
  R0                         4                         379
  R1                         0                          51
  R2                         0                           4
  RX                         0                          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"
D15V13, continuous
D15V14, binary
                             cls
clus                            0   1
  DEL PEAK 10(7Q34) MUTATED     1   3
  DEL PEAK 10(7Q34) WILD-TYPE 224 261
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(7Q34) MUTATED      1    3
  DEL PEAK 10(7Q34) WILD-TYPE  224  261
            clus
vv           DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE
  MULTIFOCAL                         1                         224
  UNIFOCAL                           3                         261
[1] 2 2
[1] FALSE
D15V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(7Q34) MUTATED                                  0     0
  DEL PEAK 10(7Q34) WILD-TYPE                                1    52
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(7Q34) MUTATED                           0     3
  DEL PEAK 10(7Q34) WILD-TYPE                        27   326
D15V16, multiclass
                                  clus
vv                                 DEL PEAK 10(7Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                    3
                                  clus
vv                                 DEL PEAK 10(7Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     52
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V17, binary
                             cls
clus                            0   1
  DEL PEAK 10(7Q34) MUTATED     0   4
  DEL PEAK 10(7Q34) WILD-TYPE  38 356
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(7Q34) MUTATED      0    4
  DEL PEAK 10(7Q34) WILD-TYPE   38  356
                        clus
vv                       DEL PEAK 10(7Q34) MUTATED DEL PEAK 10(7Q34) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         4                         356
[1] 2 2
[1] FALSE

Clustering(16) Variable = DEL PEAK 11(8P23.2) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(8P23.2) MUTATED     4   0
  DEL PEAK 11(8P23.2) WILD-TYPE 478  16
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                            4                           494 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                            0                            16 
$`DEL PEAK 11(8P23.2) MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A3O9 TCGA-EM-A3SY 
       20.58        34.36         9.24        13.51 

$`DEL PEAK 11(8P23.2) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       15.02        14.50        15.06         7.33        12.53        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       78.77        71.08         4.11        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
      116.09         1.25        20.42        17.82         7.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                         9.24                          0.20 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                        34.36                        178.29 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                       17.045                        31.270 
[1] "9.2 - 34.4 (17.0)"  "0.2 - 178.3 (31.3)"
[1] "hr="     "1200000"
D16V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 11(8P23.2) MUTATED         2        2         0        0         0
  DEL PEAK 11(8P23.2) WILD-TYPE     280       48       111        2        46
                               vv
clus                            STAGE IVC
  DEL PEAK 11(8P23.2) MUTATED           0
  DEL PEAK 11(8P23.2) WILD-TYPE         6
D16V3, multiclass
           clus
vv          DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  STAGE I                             2                           280
  STAGE II                            2                            48
  STAGE III                           0                           111
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] 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(8P23.2) MUTATED     1   2   1   0
  DEL PEAK 11(8P23.2) WILD-TYPE 141 163 166  23
D16V4, multiclass
    clus
vv   DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  T1                           1                           141
  T2                           2                           163
  T3                           1                           166
  T4                           0                            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"
D16V5, binary
                               cls
clus                              0   1
  DEL PEAK 11(8P23.2) MUTATED     3   0
  DEL PEAK 11(8P23.2) WILD-TYPE 222 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED      3    0
  DEL PEAK 11(8P23.2) WILD-TYPE  222  224
   clus
vv  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  0                           3                           222
  1                           0                           224
[1] 2 2
[1] FALSE
D16V6, binary
                               cls
clus                              0   1
  DEL PEAK 11(8P23.2) MUTATED     1   0
  DEL PEAK 11(8P23.2) WILD-TYPE 277   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED      1    0
  DEL PEAK 11(8P23.2) WILD-TYPE  277    9
   clus
vv  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  0                           1                           277
  1                           0                             9
[1] 2 2
[1] FALSE
D16V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(8P23.2) MUTATED     1   3
  DEL PEAK 11(8P23.2) WILD-TYPE 364 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED      1    3
  DEL PEAK 11(8P23.2) WILD-TYPE  364  131
        clus
vv       DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  FEMALE                           1                           364
  MALE                             3                           131
[1] 2 2
[1] FALSE
D16V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(8P23.2) MUTATED     2   2
  DEL PEAK 11(8P23.2) WILD-TYPE 178 301
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED      2    2
  DEL PEAK 11(8P23.2) WILD-TYPE  178  301
     clus
vv    DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  NO                            2                           178
  YES                           2                           301
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER, SPECIFY
  DEL PEAK 11(8P23.2) MUTATED                0
  DEL PEAK 11(8P23.2) WILD-TYPE              7
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 11(8P23.2) MUTATED                                               2
  DEL PEAK 11(8P23.2) WILD-TYPE                                           354
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 11(8P23.2) MUTATED                                                                        2
  DEL PEAK 11(8P23.2) WILD-TYPE                                                                     98
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 11(8P23.2) MUTATED                                                                     0
  DEL PEAK 11(8P23.2) WILD-TYPE                                                                  36
D16V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 11(8P23.2) MUTATED
  OTHER, SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       DEL PEAK 11(8P23.2) WILD-TYPE
  OTHER, SPECIFY                                                                                     7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, binary
                               cls
clus                              0   1
  DEL PEAK 11(8P23.2) MUTATED     4   0
  DEL PEAK 11(8P23.2) WILD-TYPE 416  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED      4    0
  DEL PEAK 11(8P23.2) WILD-TYPE  416   17
     clus
vv    DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  NO                            4                           416
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 11(8P23.2) MUTATED              0                       0    4
  DEL PEAK 11(8P23.2) WILD-TYPE          132                      18  326
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK 11(8P23.2) MUTATED                     0
  DEL PEAK 11(8P23.2) WILD-TYPE                   1
D16V11, multiclass
                         clus
vv                        DEL PEAK 11(8P23.2) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              4
  VERY ADVANCED (T4B)                               0
                         clus
vv                        DEL PEAK 11(8P23.2) WILD-TYPE
  MINIMAL (T3)                                      132
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              326
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(8P23.2) MUTATED     4   0   0   0
  DEL PEAK 11(8P23.2) WILD-TYPE 379  51   4  30
D16V12, multiclass
    clus
vv   DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  R0                           4                           379
  R1                           0                            51
  R2                           0                             4
  RX                           0                            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"
D16V13, continuous
D16V14, binary
                               cls
clus                              0   1
  DEL PEAK 11(8P23.2) MUTATED     2   2
  DEL PEAK 11(8P23.2) WILD-TYPE 223 262
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED      2    2
  DEL PEAK 11(8P23.2) WILD-TYPE  223  262
            clus
vv           DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  MULTIFOCAL                           2                           223
  UNIFOCAL                             2                           262
[1] 2 2
[1] FALSE
D16V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(8P23.2) MUTATED                                  0     0
  DEL PEAK 11(8P23.2) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(8P23.2) MUTATED                           0     2
  DEL PEAK 11(8P23.2) WILD-TYPE                        27   327
D16V16, multiclass
[1] "Remove cluster labels:"      "DEL PEAK 11(8P23.2) MUTATED"
clus
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                            2                           407 
                   TCGA-BJ-A290                    TCGA-BJ-A291 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A45K                    TCGA-CE-A13K 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DE-A0XZ                    TCGA-DJ-A13L 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2PR                    TCGA-DJ-A3UU 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UW                    TCGA-DJ-A3V4 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3VI                    TCGA-DJ-A3VK 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-E3-A3E5                    TCGA-EL-A3CR 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CS                    TCGA-EL-A3CY 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3D0                    TCGA-EL-A3D5 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GQ                    TCGA-EL-A3H2 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3H8                    TCGA-EL-A3MY 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3N3                    TCGA-ET-A3BO 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3BV                    TCGA-FK-A3SD 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FY-A76V                    TCGA-J8-A3NZ 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-J8-A4HW                    TCGA-L6-A4ET 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-MK-A84Z                    TCGA-4C-A93U 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0YZ                    TCGA-BJ-A0Z2 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0Z3                    TCGA-BJ-A0Z5 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0Z9                    TCGA-BJ-A0ZA 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0ZB                    TCGA-BJ-A0ZC 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0ZE                    TCGA-BJ-A0ZG 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0ZH                    TCGA-BJ-A0ZJ 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A18Y                    TCGA-BJ-A18Z 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A191                    TCGA-BJ-A192 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A28R                    TCGA-BJ-A28S 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A28T                    TCGA-BJ-A28V 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A28W                    TCGA-BJ-A28X 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A28Z                    TCGA-BJ-A2N7 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A2N8                    TCGA-BJ-A2N9 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A2NA                    TCGA-BJ-A2P4 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A3EZ                    TCGA-BJ-A3F0 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A3PR                    TCGA-BJ-A3PT 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A3PU                    TCGA-BJ-A45C 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A45D                    TCGA-BJ-A45E 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A45F                    TCGA-BJ-A45G 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A45H                    TCGA-BJ-A45I 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A45J                    TCGA-BJ-A4O8 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A4O9                    TCGA-CE-A27D 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-CE-A3MD                    TCGA-CE-A3ME 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-CE-A481                    TCGA-CE-A482 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-CE-A483                    TCGA-CE-A484 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-CE-A485                    TCGA-DE-A0Y2 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DE-A0Y3                    TCGA-DE-A2OL 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DE-A3KN                    TCGA-DE-A4M8 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DE-A4M9                    TCGA-DE-A4MA 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DE-A4MB                    TCGA-DE-A4MC 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DE-A4MD                    TCGA-DE-A69J 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DE-A69K                    TCGA-DE-A7U5 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A13M                    TCGA-DJ-A13O 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A13P                    TCGA-DJ-A13R 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A13S                    TCGA-DJ-A13T 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A13U                    TCGA-DJ-A13W 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A1QD                    TCGA-DJ-A1QE 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A1QF                    TCGA-DJ-A1QG 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A1QH                    TCGA-DJ-A1QI 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A1QM                    TCGA-DJ-A1QO 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A1QQ                    TCGA-DJ-A2PN 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2PO                    TCGA-DJ-A2PQ 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2PS                    TCGA-DJ-A2PT 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2PU                    TCGA-DJ-A2PV 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2PW                    TCGA-DJ-A2PX 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2Q1                    TCGA-DJ-A2Q2 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2Q3                    TCGA-DJ-A2Q4 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2Q5                    TCGA-DJ-A2Q6 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2Q7                    TCGA-DJ-A2Q9 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2QA                    TCGA-DJ-A2QB 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UK                    TCGA-DJ-A3UM 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UN                    TCGA-DJ-A3UO 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UQ                    TCGA-DJ-A3UR 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3US                    TCGA-DJ-A3UT 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UX                    TCGA-DJ-A3UY 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UZ                    TCGA-DJ-A3V2 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3V3                    TCGA-DJ-A3V5 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3V7                    TCGA-DJ-A3V8 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3V9                    TCGA-DJ-A3VD 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3VE                    TCGA-DJ-A3VF 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3VG                    TCGA-DJ-A3VJ 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3VL                    TCGA-DJ-A3VM 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A4UL                    TCGA-DJ-A4UP 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A4UQ                    TCGA-DJ-A4UR 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A4UT                    TCGA-DJ-A4UW 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A4V0                    TCGA-DJ-A4V4 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A4V5                    TCGA-DO-A1JZ 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-DO-A1K0                    TCGA-DO-A2HM 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-E3-A3DY                    TCGA-E3-A3DZ 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-E3-A3E0                    TCGA-E3-A3E1 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-E3-A3E2                    TCGA-E3-A3E3 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-E8-A242                    TCGA-E8-A2EA 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-E8-A3X7                    TCGA-E8-A413 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-E8-A414                    TCGA-E8-A415 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-E8-A416                    TCGA-E8-A417 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-E8-A419                    TCGA-E8-A432 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-E8-A433                    TCGA-E8-A434 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-E8-A436                    TCGA-E8-A437 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-E8-A438                    TCGA-E8-A44K 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-E8-A44M                    TCGA-EL-A3CL 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CM                    TCGA-EL-A3CN 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CO                    TCGA-EL-A3CP 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CT                    TCGA-EL-A3CU 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CV                    TCGA-EL-A3CW 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CX                    TCGA-EL-A3CZ 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3D1                    TCGA-EL-A3D4 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3D6                    TCGA-EL-A3GO 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GP                    TCGA-EL-A3GR 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GS                    TCGA-EL-A3GU 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GV                    TCGA-EL-A3GW 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GX                    TCGA-EL-A3GY 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GZ                    TCGA-EL-A3H1 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3H3                    TCGA-EL-A3H4 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3H5                    TCGA-EL-A3H7 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3MW                    TCGA-EL-A3MX 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3MZ                    TCGA-EL-A3N2 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3T0                    TCGA-EL-A3T1 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3T2                    TCGA-EL-A3T3 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3T6                    TCGA-EL-A3T7 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3T8                    TCGA-EL-A3T9 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3TA                    TCGA-EL-A3TB 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZG                    TCGA-EL-A3ZH 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZK                    TCGA-EL-A3ZL 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZN                    TCGA-EL-A3ZO 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZP                    TCGA-EL-A3ZQ 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZR                    TCGA-EL-A3ZS 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZT                    TCGA-EL-A4JV 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4JW                    TCGA-EL-A4JX 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4JZ                    TCGA-EL-A4K0 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4K1                    TCGA-EL-A4K2 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4K4                    TCGA-EL-A4K6 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4K7                    TCGA-EL-A4K9 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4KD                    TCGA-EL-A4KG 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4KH                    TCGA-EL-A4KI 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EM-A22M                    TCGA-EM-A22O 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-EM-A2OV                    TCGA-EM-A3AI 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A25G                    TCGA-ET-A25I 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A25J                    TCGA-ET-A25K 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A25L                    TCGA-ET-A25M 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A25N                    TCGA-ET-A25O 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A25P                    TCGA-ET-A25R 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A2MX                    TCGA-ET-A2MY 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A2MZ                    TCGA-ET-A2N0 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A2N1                    TCGA-ET-A2N3 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A2N4                    TCGA-ET-A2N5 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A39I                    TCGA-ET-A39J 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A39K                    TCGA-ET-A39M 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A39N                    TCGA-ET-A39O 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A39P                    TCGA-ET-A39R 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A39S                    TCGA-ET-A39T 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3BN                    TCGA-ET-A3BP 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3BQ                    TCGA-ET-A3BS 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3BT                    TCGA-ET-A3BU 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3BW                    TCGA-ET-A3BX 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3DO                    TCGA-ET-A3DP 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3DQ                    TCGA-ET-A3DR 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3DS                    TCGA-ET-A3DT 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3DU                    TCGA-ET-A3DV 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3DW                    TCGA-ET-A40P 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A40Q                    TCGA-ET-A40R 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A40S                    TCGA-ET-A40T 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-ET-A4KN                    TCGA-ET-A4KQ 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FE-A22Z                    TCGA-FE-A230 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FE-A231                    TCGA-FE-A232 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FE-A233                    TCGA-FE-A234 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FE-A235                    TCGA-FE-A236 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FE-A237                    TCGA-FE-A238 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FE-A239                    TCGA-FE-A23A 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FE-A3PA                    TCGA-FE-A3PB 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FE-A3PC                    TCGA-FE-A3PD 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FK-A3S3                    TCGA-FK-A3SB 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FK-A3SE                    TCGA-FK-A3SG 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FK-A3SH                    TCGA-FK-A4UB 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FY-A2QD                    TCGA-FY-A3BL 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3I4                    TCGA-FY-A3I5 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3NM                    TCGA-FY-A3ON 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3R6                    TCGA-FY-A3R7 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3R8                    TCGA-FY-A3R9 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3RA                    TCGA-FY-A3TY 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3W9                    TCGA-FY-A3WA 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3YR                    TCGA-FY-A40K 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FY-A40L                    TCGA-FY-A40M 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FY-A40N                    TCGA-FY-A4B0 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-FY-A4B3                    TCGA-FY-A4B4 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-GE-A2C6                    TCGA-H2-A26U 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-H2-A2K9                    TCGA-H2-A3RH 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-H2-A3RI                    TCGA-H2-A421 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-H2-A422                    TCGA-IM-A3EB 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-IM-A3ED                    TCGA-IM-A3U2 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-IM-A3U3                    TCGA-IM-A41Y 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-IM-A41Z                    TCGA-IM-A420 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-IM-A4EB                    TCGA-J8-A3O0 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-J8-A3O1                    TCGA-J8-A3O2 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-J8-A3YD                    TCGA-J8-A3YE 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-J8-A3YF                    TCGA-J8-A3YG 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-J8-A3YH                    TCGA-J8-A42S 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-J8-A4HY                    TCGA-KS-A41F 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-KS-A41I                    TCGA-KS-A41J 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-KS-A41L                    TCGA-KS-A4I1 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-KS-A4I3                    TCGA-KS-A4I5 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-KS-A4I7                    TCGA-KS-A4I9 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-KS-A4IB                    TCGA-KS-A4IC 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-KS-A4ID                    TCGA-L6-A4EP 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-L6-A4EQ                    TCGA-L6-A4EU 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-MK-A4N6                    TCGA-MK-A4N7 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-MK-A4N9                    TCGA-QD-A8IV 
"DEL PEAK 11(8P23.2) WILD-TYPE" "DEL PEAK 11(8P23.2) WILD-TYPE" 
                   TCGA-E8-A418 
"DEL PEAK 11(8P23.2) WILD-TYPE" 
D16V17, binary
                               cls
clus                              0   1
  DEL PEAK 11(8P23.2) MUTATED     0   2
  DEL PEAK 11(8P23.2) WILD-TYPE  38 358
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED      0    2
  DEL PEAK 11(8P23.2) WILD-TYPE   38  358
                        clus
vv                       DEL PEAK 11(8P23.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           2
                        clus
vv                       DEL PEAK 11(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           358
[1] 2 2
[1] FALSE

Clustering(17) Variable = DEL PEAK 12(8P22) MUTATION ANALYSIS
D17V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 12(8P22) MUTATED     4   0
  DEL PEAK 12(8P22) WILD-TYPE 478  16
  DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE 
                          4                         494 
  DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE 
                          0                          16 
$`DEL PEAK 12(8P22) MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A3O9 TCGA-EM-A3SY 
       20.58        34.36         9.24        13.51 

$`DEL PEAK 12(8P22) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       15.02        14.50        15.06         7.33        12.53        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       78.77        71.08         4.11        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
      116.09         1.25        20.42        17.82         7.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE 
                       9.24                        0.20 
  DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE 
                      34.36                      178.29 
  DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE 
                     17.045                      31.270 
[1] "9.2 - 34.4 (17.0)"  "0.2 - 178.3 (31.3)"
[1] "hr="     "1200000"
D17V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 12(8P22) MUTATED         2        2         0        0         0
  DEL PEAK 12(8P22) WILD-TYPE     280       48       111        2        46
                             vv
clus                          STAGE IVC
  DEL PEAK 12(8P22) MUTATED           0
  DEL PEAK 12(8P22) WILD-TYPE         6
D17V3, multiclass
           clus
vv          DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE
  STAGE I                           2                         280
  STAGE II                          2                          48
  STAGE III                         0                         111
  STAGE IV                          0                           2
  STAGE IVA                         0                          46
  STAGE IVC                         0                           6
[1] 6 2
[1] 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(8P22) MUTATED     1   2   1   0
  DEL PEAK 12(8P22) WILD-TYPE 141 163 166  23
D17V4, multiclass
    clus
vv   DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE
  T1                         1                         141
  T2                         2                         163
  T3                         1                         166
  T4                         0                          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"
D17V5, binary
                             cls
clus                            0   1
  DEL PEAK 12(8P22) MUTATED     3   0
  DEL PEAK 12(8P22) WILD-TYPE 222 224
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P22) MUTATED      3    0
  DEL PEAK 12(8P22) WILD-TYPE  222  224
   clus
vv  DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE
  0                         3                         222
  1                         0                         224
[1] 2 2
[1] FALSE
D17V6, binary
                             cls
clus                            0   1
  DEL PEAK 12(8P22) MUTATED     1   0
  DEL PEAK 12(8P22) WILD-TYPE 277   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P22) MUTATED      1    0
  DEL PEAK 12(8P22) WILD-TYPE  277    9
   clus
vv  DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE
  0                         1                         277
  1                         0                           9
[1] 2 2
[1] FALSE
D17V7, binary
                             cls
clus                            0   1
  DEL PEAK 12(8P22) MUTATED     1   3
  DEL PEAK 12(8P22) WILD-TYPE 364 131
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P22) MUTATED      1    3
  DEL PEAK 12(8P22) WILD-TYPE  364  131
        clus
vv       DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE
  FEMALE                         1                         364
  MALE                           3                         131
[1] 2 2
[1] FALSE
D17V8, binary
                             cls
clus                            0   1
  DEL PEAK 12(8P22) MUTATED     2   2
  DEL PEAK 12(8P22) WILD-TYPE 178 301
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P22) MUTATED      2    2
  DEL PEAK 12(8P22) WILD-TYPE  178  301
     clus
vv    DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE
  NO                          2                         178
  YES                         2                         301
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER, SPECIFY
  DEL PEAK 12(8P22) MUTATED                0
  DEL PEAK 12(8P22) WILD-TYPE              7
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 12(8P22) MUTATED                                               2
  DEL PEAK 12(8P22) WILD-TYPE                                           354
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 12(8P22) MUTATED                                                                        2
  DEL PEAK 12(8P22) WILD-TYPE                                                                     98
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 12(8P22) MUTATED                                                                     0
  DEL PEAK 12(8P22) WILD-TYPE                                                                  36
D17V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 12(8P22) MUTATED
  OTHER, SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            0
                                                                        clus
vv                                                                       DEL PEAK 12(8P22) WILD-TYPE
  OTHER, SPECIFY                                                                                   7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, binary
                             cls
clus                            0   1
  DEL PEAK 12(8P22) MUTATED     4   0
  DEL PEAK 12(8P22) WILD-TYPE 416  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P22) MUTATED      4    0
  DEL PEAK 12(8P22) WILD-TYPE  416   17
     clus
vv    DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE
  NO                          4                         416
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 12(8P22) MUTATED              0                       0    4
  DEL PEAK 12(8P22) WILD-TYPE          132                      18  326
                             vv
clus                          VERY ADVANCED (T4B)
  DEL PEAK 12(8P22) MUTATED                     0
  DEL PEAK 12(8P22) WILD-TYPE                   1
D17V11, multiclass
                         clus
vv                        DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE
  MINIMAL (T3)                                    0                         132
  MODERATE/ADVANCED (T4A)                         0                          18
  NONE                                            4                         326
  VERY ADVANCED (T4B)                             0                           1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 12(8P22) MUTATED     4   0   0   0
  DEL PEAK 12(8P22) WILD-TYPE 379  51   4  30
D17V12, multiclass
    clus
vv   DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE
  R0                         4                         379
  R1                         0                          51
  R2                         0                           4
  RX                         0                          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"
D17V13, continuous
D17V14, binary
                             cls
clus                            0   1
  DEL PEAK 12(8P22) MUTATED     2   2
  DEL PEAK 12(8P22) WILD-TYPE 223 262
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P22) MUTATED      2    2
  DEL PEAK 12(8P22) WILD-TYPE  223  262
            clus
vv           DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE
  MULTIFOCAL                         2                         223
  UNIFOCAL                           2                         262
[1] 2 2
[1] FALSE
D17V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(8P22) MUTATED                                  0     0
  DEL PEAK 12(8P22) WILD-TYPE                                1    52
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(8P22) MUTATED                           0     2
  DEL PEAK 12(8P22) WILD-TYPE                        27   327
D17V16, multiclass
[1] "Remove cluster labels:"    "DEL PEAK 12(8P22) MUTATED"
clus
  DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE 
                          2                         407 
                 TCGA-BJ-A290                  TCGA-BJ-A291 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A45K                  TCGA-CE-A13K 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DE-A0XZ                  TCGA-DJ-A13L 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A2PR                  TCGA-DJ-A3UU 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UW                  TCGA-DJ-A3V4 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A3VI                  TCGA-DJ-A3VK 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-E3-A3E5                  TCGA-EL-A3CR 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3CS                  TCGA-EL-A3CY 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3D0                  TCGA-EL-A3D5 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3GQ                  TCGA-EL-A3H2 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3H8                  TCGA-EL-A3MY 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3N3                  TCGA-ET-A3BO 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A3BV                  TCGA-FK-A3SD 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FY-A76V                  TCGA-J8-A3NZ 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-J8-A4HW                  TCGA-L6-A4ET 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-MK-A84Z                  TCGA-4C-A93U 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A0YZ                  TCGA-BJ-A0Z2 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A0Z3                  TCGA-BJ-A0Z5 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A0Z9                  TCGA-BJ-A0ZA 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A0ZB                  TCGA-BJ-A0ZC 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A0ZE                  TCGA-BJ-A0ZG 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A0ZH                  TCGA-BJ-A0ZJ 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A18Y                  TCGA-BJ-A18Z 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A191                  TCGA-BJ-A192 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A28R                  TCGA-BJ-A28S 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A28T                  TCGA-BJ-A28V 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A28W                  TCGA-BJ-A28X 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A28Z                  TCGA-BJ-A2N7 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A2N8                  TCGA-BJ-A2N9 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A2NA                  TCGA-BJ-A2P4 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A3EZ                  TCGA-BJ-A3F0 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A3PR                  TCGA-BJ-A3PT 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A3PU                  TCGA-BJ-A45C 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A45D                  TCGA-BJ-A45E 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A45F                  TCGA-BJ-A45G 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A45H                  TCGA-BJ-A45I 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A45J                  TCGA-BJ-A4O8 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-BJ-A4O9                  TCGA-CE-A27D 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-CE-A3MD                  TCGA-CE-A3ME 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-CE-A481                  TCGA-CE-A482 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-CE-A483                  TCGA-CE-A484 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-CE-A485                  TCGA-DE-A0Y2 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DE-A0Y3                  TCGA-DE-A2OL 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DE-A3KN                  TCGA-DE-A4M8 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DE-A4M9                  TCGA-DE-A4MA 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DE-A4MB                  TCGA-DE-A4MC 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DE-A4MD                  TCGA-DE-A69J 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DE-A69K                  TCGA-DE-A7U5 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A13M                  TCGA-DJ-A13O 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A13P                  TCGA-DJ-A13R 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A13S                  TCGA-DJ-A13T 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A13U                  TCGA-DJ-A13W 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A1QD                  TCGA-DJ-A1QE 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A1QF                  TCGA-DJ-A1QG 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A1QH                  TCGA-DJ-A1QI 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A1QM                  TCGA-DJ-A1QO 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A1QQ                  TCGA-DJ-A2PN 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A2PO                  TCGA-DJ-A2PQ 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A2PS                  TCGA-DJ-A2PT 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A2PU                  TCGA-DJ-A2PV 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A2PW                  TCGA-DJ-A2PX 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A2PY                  TCGA-DJ-A2PZ 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A2Q1                  TCGA-DJ-A2Q2 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A2Q3                  TCGA-DJ-A2Q4 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A2Q5                  TCGA-DJ-A2Q6 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A2Q7                  TCGA-DJ-A2Q9 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A2QA                  TCGA-DJ-A2QB 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UK                  TCGA-DJ-A3UM 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UN                  TCGA-DJ-A3UO 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UQ                  TCGA-DJ-A3UR 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A3US                  TCGA-DJ-A3UT 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UX                  TCGA-DJ-A3UY 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UZ                  TCGA-DJ-A3V2 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A3V3                  TCGA-DJ-A3V5 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A3V7                  TCGA-DJ-A3V8 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A3V9                  TCGA-DJ-A3VD 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A3VE                  TCGA-DJ-A3VF 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A3VG                  TCGA-DJ-A3VJ 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A3VL                  TCGA-DJ-A3VM 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A4UL                  TCGA-DJ-A4UP 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A4UQ                  TCGA-DJ-A4UR 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A4UT                  TCGA-DJ-A4UW 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A4V0                  TCGA-DJ-A4V4 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DJ-A4V5                  TCGA-DO-A1JZ 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-DO-A1K0                  TCGA-DO-A2HM 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-E3-A3DY                  TCGA-E3-A3DZ 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-E3-A3E0                  TCGA-E3-A3E1 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-E3-A3E2                  TCGA-E3-A3E3 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-E8-A242                  TCGA-E8-A2EA 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-E8-A3X7                  TCGA-E8-A413 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-E8-A414                  TCGA-E8-A415 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-E8-A416                  TCGA-E8-A417 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-E8-A419                  TCGA-E8-A432 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-E8-A433                  TCGA-E8-A434 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-E8-A436                  TCGA-E8-A437 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-E8-A438                  TCGA-E8-A44K 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-E8-A44M                  TCGA-EL-A3CL 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3CM                  TCGA-EL-A3CN 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3CO                  TCGA-EL-A3CP 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3CT                  TCGA-EL-A3CU 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3CV                  TCGA-EL-A3CW 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3CX                  TCGA-EL-A3CZ 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3D1                  TCGA-EL-A3D4 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3D6                  TCGA-EL-A3GO 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3GP                  TCGA-EL-A3GR 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3GS                  TCGA-EL-A3GU 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3GV                  TCGA-EL-A3GW 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3GX                  TCGA-EL-A3GY 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3GZ                  TCGA-EL-A3H1 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3H3                  TCGA-EL-A3H4 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3H5                  TCGA-EL-A3H7 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3MW                  TCGA-EL-A3MX 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3MZ                  TCGA-EL-A3N2 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3T0                  TCGA-EL-A3T1 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3T2                  TCGA-EL-A3T3 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3T6                  TCGA-EL-A3T7 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3T8                  TCGA-EL-A3T9 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3TA                  TCGA-EL-A3TB 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZG                  TCGA-EL-A3ZH 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZK                  TCGA-EL-A3ZL 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZN                  TCGA-EL-A3ZO 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZP                  TCGA-EL-A3ZQ 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZR                  TCGA-EL-A3ZS 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZT                  TCGA-EL-A4JV 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A4JW                  TCGA-EL-A4JX 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A4JZ                  TCGA-EL-A4K0 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A4K1                  TCGA-EL-A4K2 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A4K4                  TCGA-EL-A4K6 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A4K7                  TCGA-EL-A4K9 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A4KD                  TCGA-EL-A4KG 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EL-A4KH                  TCGA-EL-A4KI 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EM-A22M                  TCGA-EM-A22O 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-EM-A2OV                  TCGA-EM-A3AI 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A25G                  TCGA-ET-A25I 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A25J                  TCGA-ET-A25K 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A25L                  TCGA-ET-A25M 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A25N                  TCGA-ET-A25O 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A25P                  TCGA-ET-A25R 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A2MX                  TCGA-ET-A2MY 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A2MZ                  TCGA-ET-A2N0 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A2N1                  TCGA-ET-A2N3 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A2N4                  TCGA-ET-A2N5 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A39I                  TCGA-ET-A39J 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A39K                  TCGA-ET-A39M 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A39N                  TCGA-ET-A39O 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A39P                  TCGA-ET-A39R 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A39S                  TCGA-ET-A39T 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A3BN                  TCGA-ET-A3BP 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A3BQ                  TCGA-ET-A3BS 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A3BT                  TCGA-ET-A3BU 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A3BW                  TCGA-ET-A3BX 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A3DO                  TCGA-ET-A3DP 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A3DQ                  TCGA-ET-A3DR 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A3DS                  TCGA-ET-A3DT 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A3DU                  TCGA-ET-A3DV 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A3DW                  TCGA-ET-A40P 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A40Q                  TCGA-ET-A40R 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A40S                  TCGA-ET-A40T 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-ET-A4KN                  TCGA-ET-A4KQ 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FE-A22Z                  TCGA-FE-A230 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FE-A231                  TCGA-FE-A232 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FE-A233                  TCGA-FE-A234 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FE-A235                  TCGA-FE-A236 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FE-A237                  TCGA-FE-A238 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FE-A239                  TCGA-FE-A23A 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FE-A3PA                  TCGA-FE-A3PB 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FE-A3PC                  TCGA-FE-A3PD 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FK-A3S3                  TCGA-FK-A3SB 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FK-A3SE                  TCGA-FK-A3SG 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FK-A3SH                  TCGA-FK-A4UB 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FY-A2QD                  TCGA-FY-A3BL 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FY-A3I4                  TCGA-FY-A3I5 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FY-A3NM                  TCGA-FY-A3ON 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FY-A3R6                  TCGA-FY-A3R7 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FY-A3R8                  TCGA-FY-A3R9 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FY-A3RA                  TCGA-FY-A3TY 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FY-A3W9                  TCGA-FY-A3WA 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FY-A3YR                  TCGA-FY-A40K 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FY-A40L                  TCGA-FY-A40M 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FY-A40N                  TCGA-FY-A4B0 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-FY-A4B3                  TCGA-FY-A4B4 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-GE-A2C6                  TCGA-H2-A26U 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-H2-A2K9                  TCGA-H2-A3RH 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-H2-A3RI                  TCGA-H2-A421 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-H2-A422                  TCGA-IM-A3EB 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-IM-A3ED                  TCGA-IM-A3U2 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-IM-A3U3                  TCGA-IM-A41Y 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-IM-A41Z                  TCGA-IM-A420 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-IM-A4EB                  TCGA-J8-A3O0 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-J8-A3O1                  TCGA-J8-A3O2 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-J8-A3YD                  TCGA-J8-A3YE 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-J8-A3YF                  TCGA-J8-A3YG 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-J8-A3YH                  TCGA-J8-A42S 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-J8-A4HY                  TCGA-KS-A41F 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-KS-A41I                  TCGA-KS-A41J 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-KS-A41L                  TCGA-KS-A4I1 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-KS-A4I3                  TCGA-KS-A4I5 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-KS-A4I7                  TCGA-KS-A4I9 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-KS-A4IB                  TCGA-KS-A4IC 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-KS-A4ID                  TCGA-L6-A4EP 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-L6-A4EQ                  TCGA-L6-A4EU 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-MK-A4N6                  TCGA-MK-A4N7 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-MK-A4N9                  TCGA-QD-A8IV 
"DEL PEAK 12(8P22) WILD-TYPE" "DEL PEAK 12(8P22) WILD-TYPE" 
                 TCGA-E8-A418 
"DEL PEAK 12(8P22) WILD-TYPE" 
D17V17, binary
                             cls
clus                            0   1
  DEL PEAK 12(8P22) MUTATED     0   2
  DEL PEAK 12(8P22) WILD-TYPE  38 358
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P22) MUTATED      0    2
  DEL PEAK 12(8P22) WILD-TYPE   38  358
                        clus
vv                       DEL PEAK 12(8P22) MUTATED DEL PEAK 12(8P22) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         2                         358
[1] 2 2
[1] FALSE

Clustering(18) Variable = DEL PEAK 13(8P12) MUTATION ANALYSIS
D18V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 13(8P12) MUTATED     4   0
  DEL PEAK 13(8P12) WILD-TYPE 478  16
  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE 
                          4                         494 
  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE 
                          0                          16 
$`DEL PEAK 13(8P12) MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A3O9 TCGA-EM-A3SY 
       20.58        34.36         9.24        13.51 

$`DEL PEAK 13(8P12) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       15.02        14.50        15.06         7.33        12.53        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       78.77        71.08         4.11        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
      116.09         1.25        20.42        17.82         7.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE 
                       9.24                        0.20 
  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE 
                      34.36                      178.29 
  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE 
                     17.045                      31.270 
[1] "9.2 - 34.4 (17.0)"  "0.2 - 178.3 (31.3)"
[1] "hr="     "1200000"
D18V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 13(8P12) MUTATED         2        2         0        0         0
  DEL PEAK 13(8P12) WILD-TYPE     280       48       111        2        46
                             vv
clus                          STAGE IVC
  DEL PEAK 13(8P12) MUTATED           0
  DEL PEAK 13(8P12) WILD-TYPE         6
D18V3, multiclass
           clus
vv          DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  STAGE I                           2                         280
  STAGE II                          2                          48
  STAGE III                         0                         111
  STAGE IV                          0                           2
  STAGE IVA                         0                          46
  STAGE IVC                         0                           6
[1] 6 2
[1] 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(8P12) MUTATED     1   2   1   0
  DEL PEAK 13(8P12) WILD-TYPE 141 163 166  23
D18V4, multiclass
    clus
vv   DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  T1                         1                         141
  T2                         2                         163
  T3                         1                         166
  T4                         0                          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"
D18V5, binary
                             cls
clus                            0   1
  DEL PEAK 13(8P12) MUTATED     3   0
  DEL PEAK 13(8P12) WILD-TYPE 222 224
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(8P12) MUTATED      3    0
  DEL PEAK 13(8P12) WILD-TYPE  222  224
   clus
vv  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  0                         3                         222
  1                         0                         224
[1] 2 2
[1] FALSE
D18V6, binary
                             cls
clus                            0   1
  DEL PEAK 13(8P12) MUTATED     1   0
  DEL PEAK 13(8P12) WILD-TYPE 277   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(8P12) MUTATED      1    0
  DEL PEAK 13(8P12) WILD-TYPE  277    9
   clus
vv  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  0                         1                         277
  1                         0                           9
[1] 2 2
[1] FALSE
D18V7, binary
                             cls
clus                            0   1
  DEL PEAK 13(8P12) MUTATED     1   3
  DEL PEAK 13(8P12) WILD-TYPE 364 131
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(8P12) MUTATED      1    3
  DEL PEAK 13(8P12) WILD-TYPE  364  131
        clus
vv       DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  FEMALE                         1                         364
  MALE                           3                         131
[1] 2 2
[1] FALSE
D18V8, binary
                             cls
clus                            0   1
  DEL PEAK 13(8P12) MUTATED     2   2
  DEL PEAK 13(8P12) WILD-TYPE 178 301
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(8P12) MUTATED      2    2
  DEL PEAK 13(8P12) WILD-TYPE  178  301
     clus
vv    DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  NO                          2                         178
  YES                         2                         301
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER, SPECIFY
  DEL PEAK 13(8P12) MUTATED                0
  DEL PEAK 13(8P12) WILD-TYPE              7
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 13(8P12) MUTATED                                               2
  DEL PEAK 13(8P12) WILD-TYPE                                           354
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 13(8P12) MUTATED                                                                        2
  DEL PEAK 13(8P12) WILD-TYPE                                                                     98
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 13(8P12) MUTATED                                                                     0
  DEL PEAK 13(8P12) WILD-TYPE                                                                  36
D18V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 13(8P12) MUTATED
  OTHER, SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            0
                                                                        clus
vv                                                                       DEL PEAK 13(8P12) WILD-TYPE
  OTHER, SPECIFY                                                                                   7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, binary
                             cls
clus                            0   1
  DEL PEAK 13(8P12) MUTATED     4   0
  DEL PEAK 13(8P12) WILD-TYPE 416  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(8P12) MUTATED      4    0
  DEL PEAK 13(8P12) WILD-TYPE  416   17
     clus
vv    DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  NO                          4                         416
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 13(8P12) MUTATED              0                       0    4
  DEL PEAK 13(8P12) WILD-TYPE          132                      18  326
                             vv
clus                          VERY ADVANCED (T4B)
  DEL PEAK 13(8P12) MUTATED                     0
  DEL PEAK 13(8P12) WILD-TYPE                   1
D18V11, multiclass
                         clus
vv                        DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  MINIMAL (T3)                                    0                         132
  MODERATE/ADVANCED (T4A)                         0                          18
  NONE                                            4                         326
  VERY ADVANCED (T4B)                             0                           1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 13(8P12) MUTATED     4   0   0   0
  DEL PEAK 13(8P12) WILD-TYPE 379  51   4  30
D18V12, multiclass
    clus
vv   DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  R0                         4                         379
  R1                         0                          51
  R2                         0                           4
  RX                         0                          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"
D18V13, continuous
D18V14, binary
                             cls
clus                            0   1
  DEL PEAK 13(8P12) MUTATED     2   2
  DEL PEAK 13(8P12) WILD-TYPE 223 262
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(8P12) MUTATED      2    2
  DEL PEAK 13(8P12) WILD-TYPE  223  262
            clus
vv           DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  MULTIFOCAL                         2                         223
  UNIFOCAL                           2                         262
[1] 2 2
[1] FALSE
D18V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(8P12) MUTATED                                  0     0
  DEL PEAK 13(8P12) WILD-TYPE                                1    52
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(8P12) MUTATED                           0     2
  DEL PEAK 13(8P12) WILD-TYPE                        27   327
D18V16, multiclass
[1] "Remove cluster labels:"    "DEL PEAK 13(8P12) MUTATED"
clus
  DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE 
                          2                         407 
                 TCGA-BJ-A290                  TCGA-BJ-A291 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A45K                  TCGA-CE-A13K 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DE-A0XZ                  TCGA-DJ-A13L 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A2PR                  TCGA-DJ-A3UU 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UW                  TCGA-DJ-A3V4 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A3VI                  TCGA-DJ-A3VK 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-E3-A3E5                  TCGA-EL-A3CR 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3CS                  TCGA-EL-A3CY 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3D0                  TCGA-EL-A3D5 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3GQ                  TCGA-EL-A3H2 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3H8                  TCGA-EL-A3MY 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3N3                  TCGA-ET-A3BO 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A3BV                  TCGA-FK-A3SD 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FY-A76V                  TCGA-J8-A3NZ 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-J8-A4HW                  TCGA-L6-A4ET 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-MK-A84Z                  TCGA-4C-A93U 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A0YZ                  TCGA-BJ-A0Z2 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A0Z3                  TCGA-BJ-A0Z5 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A0Z9                  TCGA-BJ-A0ZA 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A0ZB                  TCGA-BJ-A0ZC 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A0ZE                  TCGA-BJ-A0ZG 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A0ZH                  TCGA-BJ-A0ZJ 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A18Y                  TCGA-BJ-A18Z 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A191                  TCGA-BJ-A192 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A28R                  TCGA-BJ-A28S 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A28T                  TCGA-BJ-A28V 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A28W                  TCGA-BJ-A28X 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A28Z                  TCGA-BJ-A2N7 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A2N8                  TCGA-BJ-A2N9 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A2NA                  TCGA-BJ-A2P4 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A3EZ                  TCGA-BJ-A3F0 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A3PR                  TCGA-BJ-A3PT 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A3PU                  TCGA-BJ-A45C 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A45D                  TCGA-BJ-A45E 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A45F                  TCGA-BJ-A45G 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A45H                  TCGA-BJ-A45I 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A45J                  TCGA-BJ-A4O8 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-BJ-A4O9                  TCGA-CE-A27D 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-CE-A3MD                  TCGA-CE-A3ME 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-CE-A481                  TCGA-CE-A482 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-CE-A483                  TCGA-CE-A484 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-CE-A485                  TCGA-DE-A0Y2 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DE-A0Y3                  TCGA-DE-A2OL 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DE-A3KN                  TCGA-DE-A4M8 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DE-A4M9                  TCGA-DE-A4MA 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DE-A4MB                  TCGA-DE-A4MC 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DE-A4MD                  TCGA-DE-A69J 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DE-A69K                  TCGA-DE-A7U5 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A13M                  TCGA-DJ-A13O 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A13P                  TCGA-DJ-A13R 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A13S                  TCGA-DJ-A13T 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A13U                  TCGA-DJ-A13W 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A1QD                  TCGA-DJ-A1QE 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A1QF                  TCGA-DJ-A1QG 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A1QH                  TCGA-DJ-A1QI 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A1QM                  TCGA-DJ-A1QO 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A1QQ                  TCGA-DJ-A2PN 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A2PO                  TCGA-DJ-A2PQ 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A2PS                  TCGA-DJ-A2PT 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A2PU                  TCGA-DJ-A2PV 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A2PW                  TCGA-DJ-A2PX 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A2PY                  TCGA-DJ-A2PZ 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A2Q1                  TCGA-DJ-A2Q2 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A2Q3                  TCGA-DJ-A2Q4 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A2Q5                  TCGA-DJ-A2Q6 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A2Q7                  TCGA-DJ-A2Q9 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A2QA                  TCGA-DJ-A2QB 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UK                  TCGA-DJ-A3UM 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UN                  TCGA-DJ-A3UO 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UQ                  TCGA-DJ-A3UR 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A3US                  TCGA-DJ-A3UT 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UX                  TCGA-DJ-A3UY 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UZ                  TCGA-DJ-A3V2 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A3V3                  TCGA-DJ-A3V5 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A3V7                  TCGA-DJ-A3V8 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A3V9                  TCGA-DJ-A3VD 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A3VE                  TCGA-DJ-A3VF 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A3VG                  TCGA-DJ-A3VJ 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A3VL                  TCGA-DJ-A3VM 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A4UL                  TCGA-DJ-A4UP 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A4UQ                  TCGA-DJ-A4UR 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A4UT                  TCGA-DJ-A4UW 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A4V0                  TCGA-DJ-A4V4 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DJ-A4V5                  TCGA-DO-A1JZ 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-DO-A1K0                  TCGA-DO-A2HM 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-E3-A3DY                  TCGA-E3-A3DZ 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-E3-A3E0                  TCGA-E3-A3E1 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-E3-A3E2                  TCGA-E3-A3E3 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-E8-A242                  TCGA-E8-A2EA 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-E8-A3X7                  TCGA-E8-A413 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-E8-A414                  TCGA-E8-A415 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-E8-A416                  TCGA-E8-A417 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-E8-A419                  TCGA-E8-A432 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-E8-A433                  TCGA-E8-A434 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-E8-A436                  TCGA-E8-A437 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-E8-A438                  TCGA-E8-A44K 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-E8-A44M                  TCGA-EL-A3CL 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3CM                  TCGA-EL-A3CN 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3CO                  TCGA-EL-A3CP 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3CT                  TCGA-EL-A3CU 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3CV                  TCGA-EL-A3CW 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3CX                  TCGA-EL-A3CZ 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3D1                  TCGA-EL-A3D4 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3D6                  TCGA-EL-A3GO 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3GP                  TCGA-EL-A3GR 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3GS                  TCGA-EL-A3GU 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3GV                  TCGA-EL-A3GW 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3GX                  TCGA-EL-A3GY 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3GZ                  TCGA-EL-A3H1 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3H3                  TCGA-EL-A3H4 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3H5                  TCGA-EL-A3H7 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3MW                  TCGA-EL-A3MX 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3MZ                  TCGA-EL-A3N2 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3T0                  TCGA-EL-A3T1 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3T2                  TCGA-EL-A3T3 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3T6                  TCGA-EL-A3T7 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3T8                  TCGA-EL-A3T9 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3TA                  TCGA-EL-A3TB 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZG                  TCGA-EL-A3ZH 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZK                  TCGA-EL-A3ZL 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZN                  TCGA-EL-A3ZO 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZP                  TCGA-EL-A3ZQ 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZR                  TCGA-EL-A3ZS 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZT                  TCGA-EL-A4JV 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A4JW                  TCGA-EL-A4JX 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A4JZ                  TCGA-EL-A4K0 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A4K1                  TCGA-EL-A4K2 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A4K4                  TCGA-EL-A4K6 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A4K7                  TCGA-EL-A4K9 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A4KD                  TCGA-EL-A4KG 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EL-A4KH                  TCGA-EL-A4KI 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EM-A22M                  TCGA-EM-A22O 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-EM-A2OV                  TCGA-EM-A3AI 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A25G                  TCGA-ET-A25I 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A25J                  TCGA-ET-A25K 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A25L                  TCGA-ET-A25M 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A25N                  TCGA-ET-A25O 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A25P                  TCGA-ET-A25R 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A2MX                  TCGA-ET-A2MY 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A2MZ                  TCGA-ET-A2N0 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A2N1                  TCGA-ET-A2N3 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A2N4                  TCGA-ET-A2N5 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A39I                  TCGA-ET-A39J 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A39K                  TCGA-ET-A39M 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A39N                  TCGA-ET-A39O 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A39P                  TCGA-ET-A39R 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A39S                  TCGA-ET-A39T 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A3BN                  TCGA-ET-A3BP 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A3BQ                  TCGA-ET-A3BS 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A3BT                  TCGA-ET-A3BU 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A3BW                  TCGA-ET-A3BX 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A3DO                  TCGA-ET-A3DP 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A3DQ                  TCGA-ET-A3DR 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A3DS                  TCGA-ET-A3DT 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A3DU                  TCGA-ET-A3DV 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A3DW                  TCGA-ET-A40P 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A40Q                  TCGA-ET-A40R 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A40S                  TCGA-ET-A40T 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-ET-A4KN                  TCGA-ET-A4KQ 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FE-A22Z                  TCGA-FE-A230 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FE-A231                  TCGA-FE-A232 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FE-A233                  TCGA-FE-A234 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FE-A235                  TCGA-FE-A236 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FE-A237                  TCGA-FE-A238 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FE-A239                  TCGA-FE-A23A 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FE-A3PA                  TCGA-FE-A3PB 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FE-A3PC                  TCGA-FE-A3PD 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FK-A3S3                  TCGA-FK-A3SB 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FK-A3SE                  TCGA-FK-A3SG 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FK-A3SH                  TCGA-FK-A4UB 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FY-A2QD                  TCGA-FY-A3BL 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FY-A3I4                  TCGA-FY-A3I5 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FY-A3NM                  TCGA-FY-A3ON 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FY-A3R6                  TCGA-FY-A3R7 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FY-A3R8                  TCGA-FY-A3R9 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FY-A3RA                  TCGA-FY-A3TY 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FY-A3W9                  TCGA-FY-A3WA 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FY-A3YR                  TCGA-FY-A40K 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FY-A40L                  TCGA-FY-A40M 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FY-A40N                  TCGA-FY-A4B0 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-FY-A4B3                  TCGA-FY-A4B4 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-GE-A2C6                  TCGA-H2-A26U 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-H2-A2K9                  TCGA-H2-A3RH 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-H2-A3RI                  TCGA-H2-A421 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-H2-A422                  TCGA-IM-A3EB 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-IM-A3ED                  TCGA-IM-A3U2 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-IM-A3U3                  TCGA-IM-A41Y 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-IM-A41Z                  TCGA-IM-A420 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-IM-A4EB                  TCGA-J8-A3O0 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-J8-A3O1                  TCGA-J8-A3O2 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-J8-A3YD                  TCGA-J8-A3YE 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-J8-A3YF                  TCGA-J8-A3YG 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-J8-A3YH                  TCGA-J8-A42S 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-J8-A4HY                  TCGA-KS-A41F 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-KS-A41I                  TCGA-KS-A41J 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-KS-A41L                  TCGA-KS-A4I1 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-KS-A4I3                  TCGA-KS-A4I5 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-KS-A4I7                  TCGA-KS-A4I9 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-KS-A4IB                  TCGA-KS-A4IC 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-KS-A4ID                  TCGA-L6-A4EP 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-L6-A4EQ                  TCGA-L6-A4EU 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-MK-A4N6                  TCGA-MK-A4N7 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-MK-A4N9                  TCGA-QD-A8IV 
"DEL PEAK 13(8P12) WILD-TYPE" "DEL PEAK 13(8P12) WILD-TYPE" 
                 TCGA-E8-A418 
"DEL PEAK 13(8P12) WILD-TYPE" 
D18V17, binary
                             cls
clus                            0   1
  DEL PEAK 13(8P12) MUTATED     0   2
  DEL PEAK 13(8P12) WILD-TYPE  38 358
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(8P12) MUTATED      0    2
  DEL PEAK 13(8P12) WILD-TYPE   38  358
                        clus
vv                       DEL PEAK 13(8P12) MUTATED DEL PEAK 13(8P12) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         2                         358
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEL PEAK 14(8Q24.22) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 14(8Q24.22) MUTATED     7   0
  DEL PEAK 14(8Q24.22) WILD-TYPE 475  16
  DEL PEAK 14(8Q24.22) MUTATED DEL PEAK 14(8Q24.22) WILD-TYPE 
                             7                            491 
  DEL PEAK 14(8Q24.22) MUTATED DEL PEAK 14(8Q24.22) WILD-TYPE 
                             0                             16 
$`DEL PEAK 14(8Q24.22) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A192 TCGA-DJ-A1QL TCGA-DJ-A2Q0 TCGA-EM-A2P2 TCGA-EM-A3O9 
       20.58        44.35        17.59        34.36        17.29         9.24 
TCGA-EM-A3SY 
       13.51 

$`DEL PEAK 14(8Q24.22) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
        4.83        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.97        11.08        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       12.82        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD 
       15.45        21.63        19.43        23.47        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.46        11.38        10.68        15.02        12.43        12.66 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       21.63        50.17        37.64        27.32        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        52.27        43.17        52.37         8.32        48.07 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QM 
      135.91        30.61        44.98        42.51        14.96         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.99        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       35.41        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
       28.96         8.78         8.42        37.74        43.96        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       33.93        37.48        36.46        35.11        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       33.53        35.18        39.95        36.92        31.04        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        36.33 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        35.87        40.96        36.99        20.22        30.61 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       40.70        18.97         9.60        35.67        36.43        23.44 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        30.12        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       63.19        52.44        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 
       31.50        31.04        31.30        30.84        25.45        30.61 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       31.27        31.33        14.96        39.88        33.50        31.00 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       30.15        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ 
       60.95       157.15        37.94        57.01       106.62        79.50 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR 
       98.53        69.57       108.36        64.87        49.51       115.10 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       136.01        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      139.99        49.32        43.36        49.71        83.57       139.00 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 
      108.66        57.63        52.50        29.65       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        91.17        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        72.69        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        61.02 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AI 
       32.32        33.96        17.59        17.46        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        44.52         8.35 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
        7.33        12.53        27.02        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       29.85        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       13.68        81.93        81.70        77.56        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       60.20        63.39        65.29        18.38        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       58.75        37.25        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
      123.32       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       28.24        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         7.82        29.10        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08        23.31        21.63        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 
       17.36        15.16        23.87        22.49        19.04        13.81 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       14.04        21.60        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
       11.01        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 
       16.90        21.83        31.10         8.22        25.64        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        5.75         2.47         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU 
       84.72        35.28        33.24        33.40        40.37         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       36.10        32.45        30.21        12.89         3.02 

  DEL PEAK 14(8Q24.22) MUTATED DEL PEAK 14(8Q24.22) WILD-TYPE 
                          9.24                           0.20 
  DEL PEAK 14(8Q24.22) MUTATED DEL PEAK 14(8Q24.22) WILD-TYPE 
                         44.35                         178.29 
  DEL PEAK 14(8Q24.22) MUTATED DEL PEAK 14(8Q24.22) WILD-TYPE 
                         17.59                          31.27 
[1] "9.2 - 44.4 (17.6)"  "0.2 - 178.3 (31.3)"
[1] "hr="     "3300000"
D19V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 14(8Q24.22) MUTATED         2        3         2        0         0
  DEL PEAK 14(8Q24.22) WILD-TYPE     280       47       109        2        46
                                vv
clus                             STAGE IVC
  DEL PEAK 14(8Q24.22) MUTATED           0
  DEL PEAK 14(8Q24.22) WILD-TYPE         6
D19V3, multiclass
           clus
vv          DEL PEAK 14(8Q24.22) MUTATED DEL PEAK 14(8Q24.22) WILD-TYPE
  STAGE I                              2                            280
  STAGE II                             3                             47
  STAGE III                            2                            109
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] 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(8Q24.22) MUTATED     1   3   3   0
  DEL PEAK 14(8Q24.22) WILD-TYPE 141 162 164  23
D19V4, multiclass
    clus
vv   DEL PEAK 14(8Q24.22) MUTATED DEL PEAK 14(8Q24.22) WILD-TYPE
  T1                            1                            141
  T2                            3                            162
  T3                            3                            164
  T4                            0                             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"
D19V5, binary
                                cls
clus                               0   1
  DEL PEAK 14(8Q24.22) MUTATED     5   0
  DEL PEAK 14(8Q24.22) WILD-TYPE 220 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(8Q24.22) MUTATED      5    0
  DEL PEAK 14(8Q24.22) WILD-TYPE  220  224
   clus
vv  DEL PEAK 14(8Q24.22) MUTATED DEL PEAK 14(8Q24.22) WILD-TYPE
  0                            5                            220
  1                            0                            224
[1] 2 2
[1] FALSE
D19V6, binary
                                cls
clus                               0   1
  DEL PEAK 14(8Q24.22) MUTATED     3   0
  DEL PEAK 14(8Q24.22) WILD-TYPE 275   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(8Q24.22) MUTATED      3    0
  DEL PEAK 14(8Q24.22) WILD-TYPE  275    9
   clus
vv  DEL PEAK 14(8Q24.22) MUTATED DEL PEAK 14(8Q24.22) WILD-TYPE
  0                            3                            275
  1                            0                              9
[1] 2 2
[1] FALSE
D19V7, binary
                                cls
clus                               0   1
  DEL PEAK 14(8Q24.22) MUTATED     2   5
  DEL PEAK 14(8Q24.22) WILD-TYPE 363 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(8Q24.22) MUTATED      2    5
  DEL PEAK 14(8Q24.22) WILD-TYPE  363  129
        clus
vv       DEL PEAK 14(8Q24.22) MUTATED DEL PEAK 14(8Q24.22) WILD-TYPE
  FEMALE                            2                            363
  MALE                              5                            129
[1] 2 2
[1] FALSE
D19V8, binary
                                cls
clus                               0   1
  DEL PEAK 14(8Q24.22) MUTATED     4   3
  DEL PEAK 14(8Q24.22) WILD-TYPE 176 300
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(8Q24.22) MUTATED      4    3
  DEL PEAK 14(8Q24.22) WILD-TYPE  176  300
     clus
vv    DEL PEAK 14(8Q24.22) MUTATED DEL PEAK 14(8Q24.22) WILD-TYPE
  NO                             4                            176
  YES                            3                            300
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER, SPECIFY
  DEL PEAK 14(8Q24.22) MUTATED                0
  DEL PEAK 14(8Q24.22) WILD-TYPE              7
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 14(8Q24.22) MUTATED                                               3
  DEL PEAK 14(8Q24.22) WILD-TYPE                                           353
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 14(8Q24.22) MUTATED                                                                        4
  DEL PEAK 14(8Q24.22) WILD-TYPE                                                                     96
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 14(8Q24.22) MUTATED                                                                     0
  DEL PEAK 14(8Q24.22) WILD-TYPE                                                                  36
D19V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 14(8Q24.22) MUTATED
  OTHER, SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK 14(8Q24.22) WILD-TYPE
  OTHER, SPECIFY                                                                                      7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, binary
                                cls
clus                               0   1
  DEL PEAK 14(8Q24.22) MUTATED     7   0
  DEL PEAK 14(8Q24.22) WILD-TYPE 413  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(8Q24.22) MUTATED      7    0
  DEL PEAK 14(8Q24.22) WILD-TYPE  413   17
     clus
vv    DEL PEAK 14(8Q24.22) MUTATED DEL PEAK 14(8Q24.22) WILD-TYPE
  NO                             7                            413
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 14(8Q24.22) MUTATED              1                       0    6
  DEL PEAK 14(8Q24.22) WILD-TYPE          131                      18  324
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 14(8Q24.22) MUTATED                     0
  DEL PEAK 14(8Q24.22) WILD-TYPE                   1
D19V11, multiclass
                         clus
vv                        DEL PEAK 14(8Q24.22) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               6
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 14(8Q24.22) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               324
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 14(8Q24.22) MUTATED     6   0   0   1
  DEL PEAK 14(8Q24.22) WILD-TYPE 377  51   4  29
D19V12, multiclass
    clus
vv   DEL PEAK 14(8Q24.22) MUTATED DEL PEAK 14(8Q24.22) WILD-TYPE
  R0                            6                            377
  R1                            0                             51
  R2                            0                              4
  RX                            1                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, continuous
D19V14, binary
                                cls
clus                               0   1
  DEL PEAK 14(8Q24.22) MUTATED     3   4
  DEL PEAK 14(8Q24.22) WILD-TYPE 222 260
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(8Q24.22) MUTATED      3    4
  DEL PEAK 14(8Q24.22) WILD-TYPE  222  260
            clus
vv           DEL PEAK 14(8Q24.22) MUTATED DEL PEAK 14(8Q24.22) WILD-TYPE
  MULTIFOCAL                            3                            222
  UNIFOCAL                              4                            260
[1] 2 2
[1] FALSE
D19V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(8Q24.22) MUTATED                                  0     0
  DEL PEAK 14(8Q24.22) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(8Q24.22) MUTATED                           0     3
  DEL PEAK 14(8Q24.22) WILD-TYPE                        27   326
D19V16, multiclass
                                  clus
vv                                 DEL PEAK 14(8Q24.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       3
                                  clus
vv                                 DEL PEAK 14(8Q24.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V17, binary
                                cls
clus                               0   1
  DEL PEAK 14(8Q24.22) MUTATED     0   3
  DEL PEAK 14(8Q24.22) WILD-TYPE  38 357
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(8Q24.22) MUTATED      0    3
  DEL PEAK 14(8Q24.22) WILD-TYPE   38  357
                        clus
vv                       DEL PEAK 14(8Q24.22) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       DEL PEAK 14(8Q24.22) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            357
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK 15(9P21.3) MUTATION ANALYSIS
D20V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(9P21.3) MUTATED    18   2
  DEL PEAK 15(9P21.3) WILD-TYPE 464  14
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                           20                           478 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                            2                            14 
$`DEL PEAK 15(9P21.3) MUTATED`
TCGA-BJ-A2N8 TCGA-DJ-A2Q0 TCGA-DO-A2HM TCGA-E8-A432 TCGA-EL-A3GP TCGA-EL-A3MX 
       16.57        34.36         2.33        30.61        49.51        57.63 
TCGA-EL-A3T9 TCGA-EL-A3ZK TCGA-EL-A3ZO TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1YE 
        5.72        51.78        72.69        44.15        23.90        54.08 
TCGA-EM-A2OY TCGA-EM-A3O3 TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A39N TCGA-FY-A3W9 
       32.32        14.50         9.24        13.51       123.32        21.63 
TCGA-FY-A40M TCGA-FY-A4B0 
       22.49        13.81 

$`DEL PEAK 15(9P21.3) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N9 
       32.45        11.31        30.97        11.08        18.38        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       35.38        54.90        21.53        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       80.52        63.19        52.44        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 
       29.98        31.50        31.04        31.30        30.84        25.45 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       31.27        31.33        14.96        39.88        33.50        31.00 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       30.15        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ 
       60.95       157.15        37.94        57.01       106.62        79.50 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GR TCGA-EL-A3GS 
       98.53        69.57       108.36        64.87       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      136.01        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW 
       49.32        43.36        49.71        83.57       139.00       108.66 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       52.50        29.65       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       98.24        41.29       107.47        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       91.17        62.30        36.03        53.06        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 
       61.02        31.04        34.39        30.51        53.36        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       47.84        43.59        24.30        27.06        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       57.01        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        40.34        19.73        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        33.07        44.52         8.35        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       16.18        15.02        15.06         7.33        12.53        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25        20.42        17.82         7.82        29.10        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40N TCGA-FY-A4B3 
       17.06        17.36        15.16        23.87        19.04        14.04 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       21.60        12.53        17.00        21.67        12.46        11.01 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 
       21.83        31.10         8.22        25.64        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.47         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 
       35.28        33.24        33.40        40.37         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       32.45        30.21        12.89         3.02 

  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                         2.33                          0.20 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                       123.32                        178.29 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                       27.255                        31.270 
[1] "2.3 - 123.3 (27.3)" "0.2 - 178.3 (31.3)"
[1] "hr=" "4"  
D20V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 15(9P21.3) MUTATED         7        5         4        2         1
  DEL PEAK 15(9P21.3) WILD-TYPE     275       45       107        0        45
                               vv
clus                            STAGE IVC
  DEL PEAK 15(9P21.3) MUTATED           1
  DEL PEAK 15(9P21.3) WILD-TYPE         5
D20V3, multiclass
           clus
vv          DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  STAGE I                             7                           275
  STAGE II                            5                            45
  STAGE III                           4                           107
  STAGE IV                            2                             0
  STAGE IVA                           1                            45
  STAGE IVC                           1                             5
[1] 6 2
[1] 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(9P21.3) MUTATED     5   7   5   3
  DEL PEAK 15(9P21.3) WILD-TYPE 137 158 162  20
D20V4, multiclass
    clus
vv   DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  T1                           5                           137
  T2                           7                           158
  T3                           5                           162
  T4                           3                            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V5, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED     9   8
  DEL PEAK 15(9P21.3) WILD-TYPE 216 216
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED      9    8
  DEL PEAK 15(9P21.3) WILD-TYPE  216  216
   clus
vv  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  0                           9                           216
  1                           8                           216
[1] 2 2
[1] FALSE
D20V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED     6   1
  DEL PEAK 15(9P21.3) WILD-TYPE 272   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED      6    1
  DEL PEAK 15(9P21.3) WILD-TYPE  272    8
   clus
vv  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  0                           6                           272
  1                           1                             8
[1] 2 2
[1] FALSE
D20V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED    13   7
  DEL PEAK 15(9P21.3) WILD-TYPE 352 127
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED     13    7
  DEL PEAK 15(9P21.3) WILD-TYPE  352  127
        clus
vv       DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  FEMALE                          13                           352
  MALE                             7                           127
[1] 2 2
[1] FALSE
D20V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED     5  13
  DEL PEAK 15(9P21.3) WILD-TYPE 175 290
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED      5   13
  DEL PEAK 15(9P21.3) WILD-TYPE  175  290
     clus
vv    DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  NO                            5                           175
  YES                          13                           290
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER, SPECIFY
  DEL PEAK 15(9P21.3) MUTATED                0
  DEL PEAK 15(9P21.3) WILD-TYPE              7
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 15(9P21.3) MUTATED                                              15
  DEL PEAK 15(9P21.3) WILD-TYPE                                           341
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 15(9P21.3) MUTATED                                                                        5
  DEL PEAK 15(9P21.3) WILD-TYPE                                                                     95
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 15(9P21.3) MUTATED                                                                     0
  DEL PEAK 15(9P21.3) WILD-TYPE                                                                  36
D20V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 15(9P21.3) MUTATED
  OTHER, SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   15
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       DEL PEAK 15(9P21.3) WILD-TYPE
  OTHER, SPECIFY                                                                                     7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    341
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED    19   0
  DEL PEAK 15(9P21.3) WILD-TYPE 401  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED     19    0
  DEL PEAK 15(9P21.3) WILD-TYPE  401   17
     clus
vv    DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  NO                           19                           401
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 15(9P21.3) MUTATED              4                       0   14
  DEL PEAK 15(9P21.3) WILD-TYPE          128                      18  316
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK 15(9P21.3) MUTATED                     1
  DEL PEAK 15(9P21.3) WILD-TYPE                   0
D20V11, multiclass
                         clus
vv                        DEL PEAK 15(9P21.3) MUTATED
  MINIMAL (T3)                                      4
  MODERATE/ADVANCED (T4A)                           0
  NONE                                             14
  VERY ADVANCED (T4B)                               1
                         clus
vv                        DEL PEAK 15(9P21.3) WILD-TYPE
  MINIMAL (T3)                                      128
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              316
  VERY ADVANCED (T4B)                                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(9P21.3) MUTATED    14   3   0   2
  DEL PEAK 15(9P21.3) WILD-TYPE 369  48   4  28
D20V12, multiclass
    clus
vv   DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  R0                          14                           369
  R1                           3                            48
  R2                           0                             4
  RX                           2                            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, continuous
D20V14, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED     6  14
  DEL PEAK 15(9P21.3) WILD-TYPE 219 250
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED      6   14
  DEL PEAK 15(9P21.3) WILD-TYPE  219  250
            clus
vv           DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  MULTIFOCAL                           6                           219
  UNIFOCAL                            14                           250
[1] 2 2
[1] FALSE
D20V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(9P21.3) MUTATED                                  0     1
  DEL PEAK 15(9P21.3) WILD-TYPE                                1    51
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(9P21.3) MUTATED                           1    13
  DEL PEAK 15(9P21.3) WILD-TYPE                        26   316
D20V16, multiclass
                                  clus
vv                                 DEL PEAK 15(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     13
                                  clus
vv                                 DEL PEAK 15(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      316
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V17, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED     0  15
  DEL PEAK 15(9P21.3) WILD-TYPE  38 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED      0   15
  DEL PEAK 15(9P21.3) WILD-TYPE   38  345
                        clus
vv                       DEL PEAK 15(9P21.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          15
                        clus
vv                       DEL PEAK 15(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           345
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK 16(9Q22.33) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 16(9Q22.33) MUTATED    25   2
  DEL PEAK 16(9Q22.33) WILD-TYPE 457  14
  DEL PEAK 16(9Q22.33) MUTATED DEL PEAK 16(9Q22.33) WILD-TYPE 
                            27                            471 
  DEL PEAK 16(9Q22.33) MUTATED DEL PEAK 16(9Q22.33) WILD-TYPE 
                             2                             14 
$`DEL PEAK 16(9Q22.33) MUTATED`
TCGA-DJ-A13L TCGA-4C-A93U TCGA-BJ-A2N8 TCGA-CE-A484 TCGA-DE-A4MB TCGA-DJ-A2Q0 
        9.96         4.24        16.57        12.43        11.57        34.36 
TCGA-DO-A2HM TCGA-E8-A432 TCGA-EL-A3GP TCGA-EL-A3MX TCGA-EL-A3T9 TCGA-EL-A3ZK 
        2.33        30.61        49.51        57.63         5.72        51.78 
TCGA-EL-A3ZO TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A2OY 
       72.69        44.15        23.90        19.46        54.08        32.32 
TCGA-EM-A3O3 TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A39N TCGA-FE-A231 TCGA-FK-A3SG 
       14.50         9.24        13.51       123.32        31.59         0.92 
TCGA-FY-A40M TCGA-FY-A4B0 TCGA-IM-A3U2 
       22.49        13.81        18.51 

$`DEL PEAK 16(9Q22.33) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A2PR 
       30.21        22.88        23.18        12.66        35.84        27.45 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK TCGA-E3-A3E5 
       23.44        59.57        42.54         3.12        24.76        39.95 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 TCGA-EL-A3GQ 
        7.66        45.53         4.18       139.86        57.11        50.24 
TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO 
       33.50       150.48        17.52       178.29        29.72        50.40 
TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET 
       75.42         1.05         1.68        17.23         2.60        21.83 
TCGA-MK-A84Z TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
       23.93        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.97        11.08        18.38        20.48        18.97        12.82 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       21.63        19.43        23.47        12.30        12.79        12.46 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       11.38        10.68        15.02        12.66        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MC 
       37.64        27.32        18.54        18.84        30.12        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12        14.70        14.27         2.76        48.79        38.17 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      169.32        18.58         8.71        56.19        52.27        43.17 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       52.37         8.32        48.07       135.91        30.61        44.98 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
       42.51        14.96        17.59         6.02        42.58        47.41 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS 
       17.56        10.09         7.99        30.58        35.41        26.20 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
       38.83        33.96        31.99        34.85        28.96         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.42        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        9.60        35.67        36.43        23.44        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       30.12        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY 
        3.12        15.81        35.38        54.90        21.53        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       30.84        25.45        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      101.13       139.99        49.32        43.36        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 
      139.00       108.66        52.50        29.65       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       132.07        98.24        41.29       107.47        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       82.82        89.56        91.17        62.30        36.03        53.06 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       53.36        41.13        47.84        43.59        24.30        27.06 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       78.61        57.01        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       48.46        13.15        22.16        40.34        19.73        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR 
       15.68        14.14        33.07        44.52         8.35        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       17.39        16.18        15.02        15.06         7.33        12.53 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       27.02        38.66        38.86        29.95        29.85        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A232 
       37.48        33.17        31.40        73.74        71.44        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
       71.08         4.11        22.03        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
       20.42        17.82         7.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40N TCGA-FY-A4B3 
       17.06        17.36        15.16        23.87        19.04        14.04 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       21.60        12.53        17.00        21.67        12.46        11.01 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U3 TCGA-IM-A41Y 
       20.05        18.61        48.92        47.41        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
       31.10         8.22        25.64        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.24        33.40        40.37         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       30.21        12.89         3.02 

  DEL PEAK 16(9Q22.33) MUTATED DEL PEAK 16(9Q22.33) WILD-TYPE 
                          0.92                           0.20 
  DEL PEAK 16(9Q22.33) MUTATED DEL PEAK 16(9Q22.33) WILD-TYPE 
                        123.32                         178.29 
  DEL PEAK 16(9Q22.33) MUTATED DEL PEAK 16(9Q22.33) WILD-TYPE 
                         19.46                          31.33 
[1] "0.9 - 123.3 (19.5)" "0.2 - 178.3 (31.3)"
[1] "hr=" "3.7"
D21V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 16(9Q22.33) MUTATED        10        5         4        2         5
  DEL PEAK 16(9Q22.33) WILD-TYPE     272       45       107        0        41
                                vv
clus                             STAGE IVC
  DEL PEAK 16(9Q22.33) MUTATED           1
  DEL PEAK 16(9Q22.33) WILD-TYPE         5
D21V3, multiclass
           clus
vv          DEL PEAK 16(9Q22.33) MUTATED DEL PEAK 16(9Q22.33) WILD-TYPE
  STAGE I                             10                            272
  STAGE II                             5                             45
  STAGE III                            4                            107
  STAGE IV                             2                              0
  STAGE IVA                            5                             41
  STAGE IVC                            1                              5
[1] 6 2
[1] 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(9Q22.33) MUTATED     6   9   8   4
  DEL PEAK 16(9Q22.33) WILD-TYPE 136 156 159  19
D21V4, multiclass
    clus
vv   DEL PEAK 16(9Q22.33) MUTATED DEL PEAK 16(9Q22.33) WILD-TYPE
  T1                            6                            136
  T2                            9                            156
  T3                            8                            159
  T4                            4                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                                cls
clus                               0   1
  DEL PEAK 16(9Q22.33) MUTATED     9  14
  DEL PEAK 16(9Q22.33) WILD-TYPE 216 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(9Q22.33) MUTATED      9   14
  DEL PEAK 16(9Q22.33) WILD-TYPE  216  210
   clus
vv  DEL PEAK 16(9Q22.33) MUTATED DEL PEAK 16(9Q22.33) WILD-TYPE
  0                            9                            216
  1                           14                            210
[1] 2 2
[1] FALSE
D21V6, binary
                                cls
clus                               0   1
  DEL PEAK 16(9Q22.33) MUTATED    10   1
  DEL PEAK 16(9Q22.33) WILD-TYPE 268   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(9Q22.33) MUTATED     10    1
  DEL PEAK 16(9Q22.33) WILD-TYPE  268    8
   clus
vv  DEL PEAK 16(9Q22.33) MUTATED DEL PEAK 16(9Q22.33) WILD-TYPE
  0                           10                            268
  1                            1                              8
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                               0   1
  DEL PEAK 16(9Q22.33) MUTATED    18   9
  DEL PEAK 16(9Q22.33) WILD-TYPE 347 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(9Q22.33) MUTATED     18    9
  DEL PEAK 16(9Q22.33) WILD-TYPE  347  125
        clus
vv       DEL PEAK 16(9Q22.33) MUTATED DEL PEAK 16(9Q22.33) WILD-TYPE
  FEMALE                           18                            347
  MALE                              9                            125
[1] 2 2
[1] FALSE
D21V8, binary
                                cls
clus                               0   1
  DEL PEAK 16(9Q22.33) MUTATED    10  14
  DEL PEAK 16(9Q22.33) WILD-TYPE 170 289
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(9Q22.33) MUTATED     10   14
  DEL PEAK 16(9Q22.33) WILD-TYPE  170  289
     clus
vv    DEL PEAK 16(9Q22.33) MUTATED DEL PEAK 16(9Q22.33) WILD-TYPE
  NO                            10                            170
  YES                           14                            289
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER, SPECIFY
  DEL PEAK 16(9Q22.33) MUTATED                0
  DEL PEAK 16(9Q22.33) WILD-TYPE              7
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 16(9Q22.33) MUTATED                                              20
  DEL PEAK 16(9Q22.33) WILD-TYPE                                           336
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 16(9Q22.33) MUTATED                                                                        5
  DEL PEAK 16(9Q22.33) WILD-TYPE                                                                     95
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 16(9Q22.33) MUTATED                                                                     2
  DEL PEAK 16(9Q22.33) WILD-TYPE                                                                  34
D21V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 16(9Q22.33) MUTATED
  OTHER, SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    20
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               2
                                                                        clus
vv                                                                       DEL PEAK 16(9Q22.33) WILD-TYPE
  OTHER, SPECIFY                                                                                      7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     336
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, binary
                                cls
clus                               0   1
  DEL PEAK 16(9Q22.33) MUTATED    25   1
  DEL PEAK 16(9Q22.33) WILD-TYPE 395  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(9Q22.33) MUTATED     25    1
  DEL PEAK 16(9Q22.33) WILD-TYPE  395   16
     clus
vv    DEL PEAK 16(9Q22.33) MUTATED DEL PEAK 16(9Q22.33) WILD-TYPE
  NO                            25                            395
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 16(9Q22.33) MUTATED              6                       1   18
  DEL PEAK 16(9Q22.33) WILD-TYPE          126                      17  312
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 16(9Q22.33) MUTATED                     1
  DEL PEAK 16(9Q22.33) WILD-TYPE                   0
D21V11, multiclass
                         clus
vv                        DEL PEAK 16(9Q22.33) MUTATED
  MINIMAL (T3)                                       6
  MODERATE/ADVANCED (T4A)                            1
  NONE                                              18
  VERY ADVANCED (T4B)                                1
                         clus
vv                        DEL PEAK 16(9Q22.33) WILD-TYPE
  MINIMAL (T3)                                       126
  MODERATE/ADVANCED (T4A)                             17
  NONE                                               312
  VERY ADVANCED (T4B)                                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 16(9Q22.33) MUTATED    21   3   0   2
  DEL PEAK 16(9Q22.33) WILD-TYPE 362  48   4  28
D21V12, multiclass
    clus
vv   DEL PEAK 16(9Q22.33) MUTATED DEL PEAK 16(9Q22.33) WILD-TYPE
  R0                           21                            362
  R1                            3                             48
  R2                            0                              4
  RX                            2                             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, continuous
D21V14, binary
                                cls
clus                               0   1
  DEL PEAK 16(9Q22.33) MUTATED    11  16
  DEL PEAK 16(9Q22.33) WILD-TYPE 214 248
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(9Q22.33) MUTATED     11   16
  DEL PEAK 16(9Q22.33) WILD-TYPE  214  248
            clus
vv           DEL PEAK 16(9Q22.33) MUTATED DEL PEAK 16(9Q22.33) WILD-TYPE
  MULTIFOCAL                           11                            214
  UNIFOCAL                             16                            248
[1] 2 2
[1] FALSE
D21V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(9Q22.33) MUTATED                                  0     2
  DEL PEAK 16(9Q22.33) WILD-TYPE                                1    50
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(9Q22.33) MUTATED                           2    17
  DEL PEAK 16(9Q22.33) WILD-TYPE                        25   312
D21V16, multiclass
                                  clus
vv                                 DEL PEAK 16(9Q22.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      17
                                  clus
vv                                 DEL PEAK 16(9Q22.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        50
  BLACK OR AFRICAN AMERICAN                                    25
  WHITE                                                       312
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V17, binary
                                cls
clus                               0   1
  DEL PEAK 16(9Q22.33) MUTATED     2  19
  DEL PEAK 16(9Q22.33) WILD-TYPE  36 341
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(9Q22.33) MUTATED      2   19
  DEL PEAK 16(9Q22.33) WILD-TYPE   36  341
                        clus
vv                       DEL PEAK 16(9Q22.33) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           19
                        clus
vv                       DEL PEAK 16(9Q22.33) WILD-TYPE
  HISPANIC OR LATINO                                 36
  NOT HISPANIC OR LATINO                            341
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK 17(10P12.31) MUTATION ANALYSIS
D22V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 17(10P12.31) MUTATED     7   0
  DEL PEAK 17(10P12.31) WILD-TYPE 475  16
  DEL PEAK 17(10P12.31) MUTATED DEL PEAK 17(10P12.31) WILD-TYPE 
                              7                             491 
  DEL PEAK 17(10P12.31) MUTATED DEL PEAK 17(10P12.31) WILD-TYPE 
                              0                              16 
$`DEL PEAK 17(10P12.31) MUTATED`
TCGA-BJ-A190 TCGA-E8-A432 TCGA-EL-A4KI TCGA-EM-A3O9 TCGA-ET-A39N TCGA-ET-A3DS 
       20.58        30.61        23.90         9.24       123.32        66.84 
TCGA-FY-A3I5 
        7.82 

$`DEL PEAK 17(10P12.31) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       30.84        25.45        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.46        78.61        57.01        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       14.50        15.06         7.33        12.53        27.02        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       84.85        80.58        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        4.11        22.03         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82        29.10        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08        23.31        21.63        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 
       17.36        15.16        23.87        22.49        19.04        13.81 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       14.04        21.60        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
       11.01        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 
       16.90        21.83        31.10         8.22        25.64        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        5.75         2.47         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU 
       84.72        35.28        33.24        33.40        40.37         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       36.10        32.45        30.21        12.89         3.02 

  DEL PEAK 17(10P12.31) MUTATED DEL PEAK 17(10P12.31) WILD-TYPE 
                           7.82                            0.20 
  DEL PEAK 17(10P12.31) MUTATED DEL PEAK 17(10P12.31) WILD-TYPE 
                         123.32                          178.29 
  DEL PEAK 17(10P12.31) MUTATED DEL PEAK 17(10P12.31) WILD-TYPE 
                          23.90                           31.27 
[1] "7.8 - 123.3 (23.9)" "0.2 - 178.3 (31.3)"
[1] "hr="     "9100000"
D22V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 17(10P12.31) MUTATED         3        2         2        0         0
  DEL PEAK 17(10P12.31) WILD-TYPE     279       48       109        2        46
                                 vv
clus                              STAGE IVC
  DEL PEAK 17(10P12.31) MUTATED           0
  DEL PEAK 17(10P12.31) WILD-TYPE         6
D22V3, multiclass
           clus
vv          DEL PEAK 17(10P12.31) MUTATED DEL PEAK 17(10P12.31) WILD-TYPE
  STAGE I                               3                             279
  STAGE II                              2                              48
  STAGE III                             2                             109
  STAGE IV                              0                               2
  STAGE IVA                             0                              46
  STAGE IVC                             0                               6
[1] 6 2
[1] 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(10P12.31) MUTATED     1   2   4   0
  DEL PEAK 17(10P12.31) WILD-TYPE 141 163 163  23
D22V4, multiclass
    clus
vv   DEL PEAK 17(10P12.31) MUTATED DEL PEAK 17(10P12.31) WILD-TYPE
  T1                             1                             141
  T2                             2                             163
  T3                             4                             163
  T4                             0                              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"
D22V5, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10P12.31) MUTATED     6   0
  DEL PEAK 17(10P12.31) WILD-TYPE 219 224
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10P12.31) MUTATED      6    0
  DEL PEAK 17(10P12.31) WILD-TYPE  219  224
   clus
vv  DEL PEAK 17(10P12.31) MUTATED DEL PEAK 17(10P12.31) WILD-TYPE
  0                             6                             219
  1                             0                             224
[1] 2 2
[1] FALSE
D22V6, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10P12.31) MUTATED     1   0
  DEL PEAK 17(10P12.31) WILD-TYPE 277   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10P12.31) MUTATED      1    0
  DEL PEAK 17(10P12.31) WILD-TYPE  277    9
   clus
vv  DEL PEAK 17(10P12.31) MUTATED DEL PEAK 17(10P12.31) WILD-TYPE
  0                             1                             277
  1                             0                               9
[1] 2 2
[1] FALSE
D22V7, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10P12.31) MUTATED     4   3
  DEL PEAK 17(10P12.31) WILD-TYPE 361 131
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10P12.31) MUTATED      4    3
  DEL PEAK 17(10P12.31) WILD-TYPE  361  131
        clus
vv       DEL PEAK 17(10P12.31) MUTATED DEL PEAK 17(10P12.31) WILD-TYPE
  FEMALE                             4                             361
  MALE                               3                             131
[1] 2 2
[1] FALSE
D22V8, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10P12.31) MUTATED     2   4
  DEL PEAK 17(10P12.31) WILD-TYPE 178 299
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10P12.31) MUTATED      2    4
  DEL PEAK 17(10P12.31) WILD-TYPE  178  299
     clus
vv    DEL PEAK 17(10P12.31) MUTATED DEL PEAK 17(10P12.31) WILD-TYPE
  NO                              2                             178
  YES                             4                             299
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER, SPECIFY
  DEL PEAK 17(10P12.31) MUTATED                0
  DEL PEAK 17(10P12.31) WILD-TYPE              7
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 17(10P12.31) MUTATED                                               5
  DEL PEAK 17(10P12.31) WILD-TYPE                                           351
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 17(10P12.31) MUTATED                                                                        2
  DEL PEAK 17(10P12.31) WILD-TYPE                                                                     98
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 17(10P12.31) MUTATED                                                                     0
  DEL PEAK 17(10P12.31) WILD-TYPE                                                                  36
D22V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 17(10P12.31) MUTATED
  OTHER, SPECIFY                                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                0
                                                                        clus
vv                                                                       DEL PEAK 17(10P12.31) WILD-TYPE
  OTHER, SPECIFY                                                                                       7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10P12.31) MUTATED     6   0
  DEL PEAK 17(10P12.31) WILD-TYPE 414  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10P12.31) MUTATED      6    0
  DEL PEAK 17(10P12.31) WILD-TYPE  414   17
     clus
vv    DEL PEAK 17(10P12.31) MUTATED DEL PEAK 17(10P12.31) WILD-TYPE
  NO                              6                             414
  YES                             0                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 17(10P12.31) MUTATED              1                       0    6
  DEL PEAK 17(10P12.31) WILD-TYPE          131                      18  324
                                 vv
clus                              VERY ADVANCED (T4B)
  DEL PEAK 17(10P12.31) MUTATED                     0
  DEL PEAK 17(10P12.31) WILD-TYPE                   1
D22V11, multiclass
                         clus
vv                        DEL PEAK 17(10P12.31) MUTATED
  MINIMAL (T3)                                        1
  MODERATE/ADVANCED (T4A)                             0
  NONE                                                6
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        DEL PEAK 17(10P12.31) WILD-TYPE
  MINIMAL (T3)                                        131
  MODERATE/ADVANCED (T4A)                              18
  NONE                                                324
  VERY ADVANCED (T4B)                                   1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 17(10P12.31) MUTATED     7   0   0   0
  DEL PEAK 17(10P12.31) WILD-TYPE 376  51   4  30
D22V12, multiclass
    clus
vv   DEL PEAK 17(10P12.31) MUTATED DEL PEAK 17(10P12.31) WILD-TYPE
  R0                             7                             376
  R1                             0                              51
  R2                             0                               4
  RX                             0                              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"
D22V13, continuous
D22V14, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10P12.31) MUTATED     4   3
  DEL PEAK 17(10P12.31) WILD-TYPE 221 261
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10P12.31) MUTATED      4    3
  DEL PEAK 17(10P12.31) WILD-TYPE  221  261
            clus
vv           DEL PEAK 17(10P12.31) MUTATED DEL PEAK 17(10P12.31) WILD-TYPE
  MULTIFOCAL                             4                             221
  UNIFOCAL                               3                             261
[1] 2 2
[1] FALSE
D22V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(10P12.31) MUTATED                                  0     1
  DEL PEAK 17(10P12.31) WILD-TYPE                                1    51
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(10P12.31) MUTATED                           0     5
  DEL PEAK 17(10P12.31) WILD-TYPE                        27   324
D22V16, multiclass
                                  clus
vv                                 DEL PEAK 17(10P12.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    0
  WHITE                                                        5
                                  clus
vv                                 DEL PEAK 17(10P12.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         51
  BLACK OR AFRICAN AMERICAN                                     27
  WHITE                                                        324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V17, binary
                                 cls
clus                                0   1
  DEL PEAK 17(10P12.31) MUTATED     0   6
  DEL PEAK 17(10P12.31) WILD-TYPE  38 354
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(10P12.31) MUTATED      0    6
  DEL PEAK 17(10P12.31) WILD-TYPE   38  354
                        clus
vv                       DEL PEAK 17(10P12.31) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                             6
                        clus
vv                       DEL PEAK 17(10P12.31) WILD-TYPE
  HISPANIC OR LATINO                                  38
  NOT HISPANIC OR LATINO                             354
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK 18(10Q21.2) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(10Q21.2) MUTATED    12   0
  DEL PEAK 18(10Q21.2) WILD-TYPE 470  16
  DEL PEAK 18(10Q21.2) MUTATED DEL PEAK 18(10Q21.2) WILD-TYPE 
                            12                            486 
  DEL PEAK 18(10Q21.2) MUTATED DEL PEAK 18(10Q21.2) WILD-TYPE 
                             0                             16 
$`DEL PEAK 18(10Q21.2) MUTATED`
TCGA-BJ-A0ZC TCGA-BJ-A190 TCGA-BJ-A28Z TCGA-DE-A3KN TCGA-DO-A1JZ TCGA-E8-A432 
       11.57        20.58        11.08        27.32        54.90        30.61 
TCGA-EL-A3ZS TCGA-EL-A4KI TCGA-EM-A3O9 TCGA-ET-A39N TCGA-ET-A3DQ TCGA-FY-A3I5 
        7.07        23.90         9.24       123.32        84.85         7.82 

$`DEL PEAK 18(10Q21.2) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZE 
       16.34        14.73        41.33        18.87         4.01        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 
       25.48        15.12        42.08        51.39        41.52         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.97        18.38        16.57        20.48        18.97        12.82 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       21.63        19.43        23.47        12.30        12.79        12.46 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 
       11.38        10.68        15.02        12.43        12.66        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       50.17        37.64        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12        14.70        14.27         2.76        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        52.27 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        48.07       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.99        30.58        35.41 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42        34.36        37.74        43.96        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       33.93        37.48        36.46        35.11        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       33.53        35.18        39.95        36.92        31.04        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        36.33 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        35.87        40.96        36.99        20.22        30.61 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       40.70        18.97         9.60        35.67        36.43        23.44 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        30.12        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1K0 
       26.93        35.54         3.12        15.81        35.38        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        92.55        47.21        66.38        80.52        63.19 
TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       52.44        31.23        35.67        31.27        29.98        31.50 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 
       31.04        31.30        30.84        25.45        31.27        31.33 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96        39.88        33.50        31.00        30.15        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 
       37.94        57.01       106.62        79.50        98.53        69.57 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        64.87        49.51       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX 
       43.36        49.71        83.57       139.00       108.66        57.63 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       52.50        29.65       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       89.56        91.17        51.78        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV 
       72.69        65.49        61.22        60.16        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       27.06        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        44.52         8.35        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       15.02        14.50        15.06         7.33        12.53        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       94.59        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       13.81        14.04        21.60        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46        11.01        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
       22.29         5.75         2.47         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
        9.50        36.10        32.45        30.21        12.89         3.02 

  DEL PEAK 18(10Q21.2) MUTATED DEL PEAK 18(10Q21.2) WILD-TYPE 
                          7.07                           0.20 
  DEL PEAK 18(10Q21.2) MUTATED DEL PEAK 18(10Q21.2) WILD-TYPE 
                        123.32                         178.29 
  DEL PEAK 18(10Q21.2) MUTATED DEL PEAK 18(10Q21.2) WILD-TYPE 
                        22.240                         31.315 
[1] "7.1 - 123.3 (22.2)" "0.2 - 178.3 (31.3)"
[1] "hr="     "9200000"
D23V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 18(10Q21.2) MUTATED         6        2         3        0         1
  DEL PEAK 18(10Q21.2) WILD-TYPE     276       48       108        2        45
                                vv
clus                             STAGE IVC
  DEL PEAK 18(10Q21.2) MUTATED           0
  DEL PEAK 18(10Q21.2) WILD-TYPE         6
D23V3, multiclass
           clus
vv          DEL PEAK 18(10Q21.2) MUTATED DEL PEAK 18(10Q21.2) WILD-TYPE
  STAGE I                              6                            276
  STAGE II                             2                             48
  STAGE III                            3                            108
  STAGE IV                             0                              2
  STAGE IVA                            1                             45
  STAGE IVC                            0                              6
[1] 6 2
[1] 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(10Q21.2) MUTATED     3   3   6   0
  DEL PEAK 18(10Q21.2) WILD-TYPE 139 162 161  23
D23V4, multiclass
    clus
vv   DEL PEAK 18(10Q21.2) MUTATED DEL PEAK 18(10Q21.2) WILD-TYPE
  T1                            3                            139
  T2                            3                            162
  T3                            6                            161
  T4                            0                             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"
D23V5, binary
                                cls
clus                               0   1
  DEL PEAK 18(10Q21.2) MUTATED     7   3
  DEL PEAK 18(10Q21.2) WILD-TYPE 218 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q21.2) MUTATED      7    3
  DEL PEAK 18(10Q21.2) WILD-TYPE  218  221
   clus
vv  DEL PEAK 18(10Q21.2) MUTATED DEL PEAK 18(10Q21.2) WILD-TYPE
  0                            7                            218
  1                            3                            221
[1] 2 2
[1] FALSE
D23V6, binary
                                cls
clus                               0   1
  DEL PEAK 18(10Q21.2) MUTATED     5   0
  DEL PEAK 18(10Q21.2) WILD-TYPE 273   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q21.2) MUTATED      5    0
  DEL PEAK 18(10Q21.2) WILD-TYPE  273    9
   clus
vv  DEL PEAK 18(10Q21.2) MUTATED DEL PEAK 18(10Q21.2) WILD-TYPE
  0                            5                            273
  1                            0                              9
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                               0   1
  DEL PEAK 18(10Q21.2) MUTATED     8   4
  DEL PEAK 18(10Q21.2) WILD-TYPE 357 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q21.2) MUTATED      8    4
  DEL PEAK 18(10Q21.2) WILD-TYPE  357  130
        clus
vv       DEL PEAK 18(10Q21.2) MUTATED DEL PEAK 18(10Q21.2) WILD-TYPE
  FEMALE                            8                            357
  MALE                              4                            130
[1] 2 2
[1] FALSE
D23V8, binary
                                cls
clus                               0   1
  DEL PEAK 18(10Q21.2) MUTATED     3   8
  DEL PEAK 18(10Q21.2) WILD-TYPE 177 295
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q21.2) MUTATED      3    8
  DEL PEAK 18(10Q21.2) WILD-TYPE  177  295
     clus
vv    DEL PEAK 18(10Q21.2) MUTATED DEL PEAK 18(10Q21.2) WILD-TYPE
  NO                             3                            177
  YES                            8                            295
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER, SPECIFY
  DEL PEAK 18(10Q21.2) MUTATED                0
  DEL PEAK 18(10Q21.2) WILD-TYPE              7
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 18(10Q21.2) MUTATED                                               8
  DEL PEAK 18(10Q21.2) WILD-TYPE                                           348
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 18(10Q21.2) MUTATED                                                                        4
  DEL PEAK 18(10Q21.2) WILD-TYPE                                                                     96
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 18(10Q21.2) MUTATED                                                                     0
  DEL PEAK 18(10Q21.2) WILD-TYPE                                                                  36
D23V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 18(10Q21.2) MUTATED
  OTHER, SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     8
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK 18(10Q21.2) WILD-TYPE
  OTHER, SPECIFY                                                                                      7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, binary
                                cls
clus                               0   1
  DEL PEAK 18(10Q21.2) MUTATED    10   0
  DEL PEAK 18(10Q21.2) WILD-TYPE 410  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q21.2) MUTATED     10    0
  DEL PEAK 18(10Q21.2) WILD-TYPE  410   17
     clus
vv    DEL PEAK 18(10Q21.2) MUTATED DEL PEAK 18(10Q21.2) WILD-TYPE
  NO                            10                            410
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 18(10Q21.2) MUTATED              3                       0    9
  DEL PEAK 18(10Q21.2) WILD-TYPE          129                      18  321
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 18(10Q21.2) MUTATED                     0
  DEL PEAK 18(10Q21.2) WILD-TYPE                   1
D23V11, multiclass
                         clus
vv                        DEL PEAK 18(10Q21.2) MUTATED
  MINIMAL (T3)                                       3
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               9
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 18(10Q21.2) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               321
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 18(10Q21.2) MUTATED    10   1   0   0
  DEL PEAK 18(10Q21.2) WILD-TYPE 373  50   4  30
D23V12, multiclass
    clus
vv   DEL PEAK 18(10Q21.2) MUTATED DEL PEAK 18(10Q21.2) WILD-TYPE
  R0                           10                            373
  R1                            1                             50
  R2                            0                              4
  RX                            0                             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"
D23V13, continuous
D23V14, binary
                                cls
clus                               0   1
  DEL PEAK 18(10Q21.2) MUTATED     6   5
  DEL PEAK 18(10Q21.2) WILD-TYPE 219 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q21.2) MUTATED      6    5
  DEL PEAK 18(10Q21.2) WILD-TYPE  219  259
            clus
vv           DEL PEAK 18(10Q21.2) MUTATED DEL PEAK 18(10Q21.2) WILD-TYPE
  MULTIFOCAL                            6                            219
  UNIFOCAL                              5                            259
[1] 2 2
[1] FALSE
D23V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(10Q21.2) MUTATED                                  0     1
  DEL PEAK 18(10Q21.2) WILD-TYPE                                1    51
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(10Q21.2) MUTATED                           1     9
  DEL PEAK 18(10Q21.2) WILD-TYPE                        26   320
D23V16, multiclass
                                  clus
vv                                 DEL PEAK 18(10Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                       9
                                  clus
vv                                 DEL PEAK 18(10Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        51
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V17, binary
                                cls
clus                               0   1
  DEL PEAK 18(10Q21.2) MUTATED     0  11
  DEL PEAK 18(10Q21.2) WILD-TYPE  38 349
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q21.2) MUTATED      0   11
  DEL PEAK 18(10Q21.2) WILD-TYPE   38  349
                        clus
vv                       DEL PEAK 18(10Q21.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           11
                        clus
vv                       DEL PEAK 18(10Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            349
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK 19(10Q23.31) MUTATION ANALYSIS
D24V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 19(10Q23.31) MUTATED    12   0
  DEL PEAK 19(10Q23.31) WILD-TYPE 470  16
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                             12                             486 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                              0                              16 
$`DEL PEAK 19(10Q23.31) MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A0ZC TCGA-BJ-A190 TCGA-DE-A3KN TCGA-E8-A432 TCGA-EL-A4KI 
       13.78        11.57        20.58        27.32        30.61        23.90 
TCGA-EM-A1YE TCGA-EM-A3O6 TCGA-EM-A3O9 TCGA-ET-A39N TCGA-ET-A3DQ TCGA-FY-A3I5 
       54.08        15.06         9.24       123.32        84.85         7.82 

$`DEL PEAK 19(10Q23.31) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       21.83        23.93         4.24        24.79        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       14.73        41.33        18.87         4.01        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       11.08        18.38        16.57        20.48        18.97        12.82 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       21.63        19.43        23.47        12.30        12.79        12.46 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 
       11.38        10.68        15.02        12.43        12.66        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       50.17        37.64        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12        14.70        14.27         2.76        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        52.27 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        48.07       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.99        30.58        35.41 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42        34.36        37.74        43.96        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       33.93        37.48        36.46        35.11        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       33.53        35.18        39.95        36.92        31.04        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        36.33 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        35.87        40.96        36.99        20.22        30.61 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       40.70        18.97         9.60        35.67        36.43        23.44 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        30.12        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       63.19        52.44        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A433 
       31.50        31.04        31.30        30.84        25.45        31.27 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       31.33        14.96        39.88        33.50        31.00        30.15 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT 
       31.66        26.73       155.54        97.74       158.83        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 
      157.15        37.94        57.01       106.62        79.50        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS 
       69.57       108.36        64.87        49.51       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      136.01        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW 
       49.32        43.36        49.71        83.57       139.00       108.66 
TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       57.63        52.50        29.65       142.52       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        91.17        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        72.69        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        61.02        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       43.59        24.30        27.06        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       48.49        18.05        19.79        19.46        78.61        57.01 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
       14.73        14.50        15.75        10.45        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        40.34        19.73        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        33.07        44.52         8.35        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       16.18        15.02        14.50         7.33        12.53        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       94.59        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       13.81        14.04        21.60        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46        11.01        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
       22.29         5.75         2.47         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
        9.50        36.10        32.45        30.21        12.89         3.02 

  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                           7.82                            0.20 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                         123.32                          178.29 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                         22.240                          31.315 
[1] "7.8 - 123.3 (22.2)" "0.2 - 178.3 (31.3)"
[1] "hr="     "9200000"
D24V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 19(10Q23.31) MUTATED         4        5         2        0         1
  DEL PEAK 19(10Q23.31) WILD-TYPE     278       45       109        2        45
                                 vv
clus                              STAGE IVC
  DEL PEAK 19(10Q23.31) MUTATED           0
  DEL PEAK 19(10Q23.31) WILD-TYPE         6
D24V3, multiclass
           clus
vv          DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  STAGE I                               4                             278
  STAGE II                              5                              45
  STAGE III                             2                             109
  STAGE IV                              0                               2
  STAGE IVA                             1                              45
  STAGE IVC                             0                               6
[1] 6 2
[1] 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(10Q23.31) MUTATED     2   5   5   0
  DEL PEAK 19(10Q23.31) WILD-TYPE 140 160 162  23
D24V4, multiclass
    clus
vv   DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  T1                             2                             140
  T2                             5                             160
  T3                             5                             162
  T4                             0                              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"
D24V5, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10Q23.31) MUTATED     9   1
  DEL PEAK 19(10Q23.31) WILD-TYPE 216 223
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED      9    1
  DEL PEAK 19(10Q23.31) WILD-TYPE  216  223
   clus
vv  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  0                             9                             216
  1                             1                             223
[1] 2 2
[1] FALSE
D24V6, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10Q23.31) MUTATED     3   0
  DEL PEAK 19(10Q23.31) WILD-TYPE 275   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED      3    0
  DEL PEAK 19(10Q23.31) WILD-TYPE  275    9
   clus
vv  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  0                             3                             275
  1                             0                               9
[1] 2 2
[1] FALSE
D24V7, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10Q23.31) MUTATED     7   5
  DEL PEAK 19(10Q23.31) WILD-TYPE 358 129
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED      7    5
  DEL PEAK 19(10Q23.31) WILD-TYPE  358  129
        clus
vv       DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  FEMALE                             7                             358
  MALE                               5                             129
[1] 2 2
[1] FALSE
D24V8, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10Q23.31) MUTATED     3   8
  DEL PEAK 19(10Q23.31) WILD-TYPE 177 295
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED      3    8
  DEL PEAK 19(10Q23.31) WILD-TYPE  177  295
     clus
vv    DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  NO                              3                             177
  YES                             8                             295
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER, SPECIFY
  DEL PEAK 19(10Q23.31) MUTATED                0
  DEL PEAK 19(10Q23.31) WILD-TYPE              7
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 19(10Q23.31) MUTATED                                               7
  DEL PEAK 19(10Q23.31) WILD-TYPE                                           349
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 19(10Q23.31) MUTATED                                                                        5
  DEL PEAK 19(10Q23.31) WILD-TYPE                                                                     95
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 19(10Q23.31) MUTATED                                                                     0
  DEL PEAK 19(10Q23.31) WILD-TYPE                                                                  36
D24V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 19(10Q23.31) MUTATED
  OTHER, SPECIFY                                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      7
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                0
                                                                        clus
vv                                                                       DEL PEAK 19(10Q23.31) WILD-TYPE
  OTHER, SPECIFY                                                                                       7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10Q23.31) MUTATED    10   0
  DEL PEAK 19(10Q23.31) WILD-TYPE 410  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED     10    0
  DEL PEAK 19(10Q23.31) WILD-TYPE  410   17
     clus
vv    DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  NO                             10                             410
  YES                             0                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 19(10Q23.31) MUTATED              2                       0   10
  DEL PEAK 19(10Q23.31) WILD-TYPE          130                      18  320
                                 vv
clus                              VERY ADVANCED (T4B)
  DEL PEAK 19(10Q23.31) MUTATED                     0
  DEL PEAK 19(10Q23.31) WILD-TYPE                   1
D24V11, multiclass
                         clus
vv                        DEL PEAK 19(10Q23.31) MUTATED
  MINIMAL (T3)                                        2
  MODERATE/ADVANCED (T4A)                             0
  NONE                                               10
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        DEL PEAK 19(10Q23.31) WILD-TYPE
  MINIMAL (T3)                                        130
  MODERATE/ADVANCED (T4A)                              18
  NONE                                                320
  VERY ADVANCED (T4B)                                   1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 19(10Q23.31) MUTATED    12   0   0   0
  DEL PEAK 19(10Q23.31) WILD-TYPE 371  51   4  30
D24V12, multiclass
    clus
vv   DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  R0                            12                             371
  R1                             0                              51
  R2                             0                               4
  RX                             0                              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"
D24V13, continuous
D24V14, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10Q23.31) MUTATED     5   6
  DEL PEAK 19(10Q23.31) WILD-TYPE 220 258
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED      5    6
  DEL PEAK 19(10Q23.31) WILD-TYPE  220  258
            clus
vv           DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  MULTIFOCAL                             5                             220
  UNIFOCAL                               6                             258
[1] 2 2
[1] FALSE
D24V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(10Q23.31) MUTATED                                  0     1
  DEL PEAK 19(10Q23.31) WILD-TYPE                                1    51
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(10Q23.31) MUTATED                           0     7
  DEL PEAK 19(10Q23.31) WILD-TYPE                        27   322
D24V16, multiclass
                                  clus
vv                                 DEL PEAK 19(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    0
  WHITE                                                        7
                                  clus
vv                                 DEL PEAK 19(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         51
  BLACK OR AFRICAN AMERICAN                                     27
  WHITE                                                        322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V17, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10Q23.31) MUTATED     0   9
  DEL PEAK 19(10Q23.31) WILD-TYPE  38 351
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED      0    9
  DEL PEAK 19(10Q23.31) WILD-TYPE   38  351
                        clus
vv                       DEL PEAK 19(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                             9
                        clus
vv                       DEL PEAK 19(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  38
  NOT HISPANIC OR LATINO                             351
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK 20(13Q12.3) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(13Q12.3) MUTATED    14   2
  DEL PEAK 20(13Q12.3) WILD-TYPE 468  14
  DEL PEAK 20(13Q12.3) MUTATED DEL PEAK 20(13Q12.3) WILD-TYPE 
                            16                            482 
  DEL PEAK 20(13Q12.3) MUTATED DEL PEAK 20(13Q12.3) WILD-TYPE 
                             2                             14 
$`DEL PEAK 20(13Q12.3) MUTATED`
TCGA-BJ-A3F0 TCGA-BJ-A45C TCGA-DJ-A13P TCGA-DJ-A2Q2 TCGA-EL-A3T0 TCGA-EM-A1YB 
       13.94         7.99       169.32        43.96       142.52        19.46 
TCGA-EM-A22M TCGA-EM-A22Q TCGA-EM-A2OX TCGA-EM-A3O3 TCGA-ET-A39N TCGA-ET-A40S 
       14.53        14.24        19.73        14.50       123.32        40.21 
TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3W9 TCGA-FY-A4B0 
       33.63         7.82        21.63        13.81 

$`DEL PEAK 20(13Q12.3) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3PR TCGA-BJ-A3PT 
       20.48        18.97        12.82        16.01        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
       18.64        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD 
       15.45        21.63        19.43        23.47        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.46        11.38        10.68        15.02        12.43        12.66 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       21.63        50.17        37.64        27.32        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
        2.76        48.79        38.17        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       52.27        43.17        52.37         8.32        48.07       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.99        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       35.41        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 
       28.96         8.78         8.42        34.36        37.74        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       33.93        37.48        36.46        35.11        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       33.53        35.18        39.95        36.92        31.04        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        36.33 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        35.87        40.96        36.99        20.22        30.61 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       40.70        18.97         9.60        35.67        36.43        23.44 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        30.12        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       63.19        52.44        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 
       31.50        31.04        31.30        30.84        25.45        30.61 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       31.27        31.33        14.96        39.88        33.50        31.00 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       30.15        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ 
       60.95       157.15        37.94        57.01       106.62        79.50 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR 
       98.53        69.57       108.36        64.87        49.51       115.10 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       136.01        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      139.99        49.32        43.36        49.71        83.57       139.00 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T1 TCGA-EL-A3T2 
      108.66        57.63        52.50        29.65       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        91.17        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        72.69        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        61.02        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YC TCGA-EM-A1YD 
       20.91        48.49        18.05        19.79        78.61        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N 
       54.08        14.73        14.50        15.75        10.45        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       44.19        41.29        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       40.34        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33        12.53         9.24        27.02        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN 
       24.72        43.99        46.26        44.38        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A 
       68.22       117.40        66.77       112.80        39.95        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82        29.10        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       16.57        18.08        23.31        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       23.87        22.49        19.04        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  DEL PEAK 20(13Q12.3) MUTATED DEL PEAK 20(13Q12.3) WILD-TYPE 
                          7.82                           0.20 
  DEL PEAK 20(13Q12.3) MUTATED DEL PEAK 20(13Q12.3) WILD-TYPE 
                        169.32                         178.29 
  DEL PEAK 20(13Q12.3) MUTATED DEL PEAK 20(13Q12.3) WILD-TYPE 
                        19.595                         31.285 
[1] "7.8 - 169.3 (19.6)" "0.2 - 178.3 (31.3)"
[1] "hr=" "4.6"
D25V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 20(13Q12.3) MUTATED         5        4         6        0         1
  DEL PEAK 20(13Q12.3) WILD-TYPE     277       46       105        2        45
                                vv
clus                             STAGE IVC
  DEL PEAK 20(13Q12.3) MUTATED           0
  DEL PEAK 20(13Q12.3) WILD-TYPE         6
D25V3, multiclass
           clus
vv          DEL PEAK 20(13Q12.3) MUTATED DEL PEAK 20(13Q12.3) WILD-TYPE
  STAGE I                              5                            277
  STAGE II                             4                             46
  STAGE III                            6                            105
  STAGE IV                             0                              2
  STAGE IVA                            1                             45
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 20(13Q12.3) MUTATED     4   5   7   0
  DEL PEAK 20(13Q12.3) WILD-TYPE 138 160 160  23
D25V4, multiclass
    clus
vv   DEL PEAK 20(13Q12.3) MUTATED DEL PEAK 20(13Q12.3) WILD-TYPE
  T1                            4                            138
  T2                            5                            160
  T3                            7                            160
  T4                            0                             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"
D25V5, binary
                                cls
clus                               0   1
  DEL PEAK 20(13Q12.3) MUTATED    10   3
  DEL PEAK 20(13Q12.3) WILD-TYPE 215 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(13Q12.3) MUTATED     10    3
  DEL PEAK 20(13Q12.3) WILD-TYPE  215  221
   clus
vv  DEL PEAK 20(13Q12.3) MUTATED DEL PEAK 20(13Q12.3) WILD-TYPE
  0                           10                            215
  1                            3                            221
[1] 2 2
[1] FALSE
D25V6, binary
                                cls
clus                               0   1
  DEL PEAK 20(13Q12.3) MUTATED     5   0
  DEL PEAK 20(13Q12.3) WILD-TYPE 273   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(13Q12.3) MUTATED      5    0
  DEL PEAK 20(13Q12.3) WILD-TYPE  273    9
   clus
vv  DEL PEAK 20(13Q12.3) MUTATED DEL PEAK 20(13Q12.3) WILD-TYPE
  0                            5                            273
  1                            0                              9
[1] 2 2
[1] FALSE
D25V7, binary
                                cls
clus                               0   1
  DEL PEAK 20(13Q12.3) MUTATED     9   7
  DEL PEAK 20(13Q12.3) WILD-TYPE 356 127
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(13Q12.3) MUTATED      9    7
  DEL PEAK 20(13Q12.3) WILD-TYPE  356  127
        clus
vv       DEL PEAK 20(13Q12.3) MUTATED DEL PEAK 20(13Q12.3) WILD-TYPE
  FEMALE                            9                            356
  MALE                              7                            127
[1] 2 2
[1] FALSE
D25V8, binary
                                cls
clus                               0   1
  DEL PEAK 20(13Q12.3) MUTATED     2  13
  DEL PEAK 20(13Q12.3) WILD-TYPE 178 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(13Q12.3) MUTATED      2   13
  DEL PEAK 20(13Q12.3) WILD-TYPE  178  290
     clus
vv    DEL PEAK 20(13Q12.3) MUTATED DEL PEAK 20(13Q12.3) WILD-TYPE
  NO                             2                            178
  YES                           13                            290
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER, SPECIFY
  DEL PEAK 20(13Q12.3) MUTATED                0
  DEL PEAK 20(13Q12.3) WILD-TYPE              7
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 20(13Q12.3) MUTATED                                              11
  DEL PEAK 20(13Q12.3) WILD-TYPE                                           345
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 20(13Q12.3) MUTATED                                                                        5
  DEL PEAK 20(13Q12.3) WILD-TYPE                                                                     95
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 20(13Q12.3) MUTATED                                                                     0
  DEL PEAK 20(13Q12.3) WILD-TYPE                                                                  36
D25V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 20(13Q12.3) MUTATED
  OTHER, SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    11
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK 20(13Q12.3) WILD-TYPE
  OTHER, SPECIFY                                                                                      7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     345
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, binary
                                cls
clus                               0   1
  DEL PEAK 20(13Q12.3) MUTATED    11   4
  DEL PEAK 20(13Q12.3) WILD-TYPE 409  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(13Q12.3) MUTATED     11    4
  DEL PEAK 20(13Q12.3) WILD-TYPE  409   13
     clus
vv    DEL PEAK 20(13Q12.3) MUTATED DEL PEAK 20(13Q12.3) WILD-TYPE
  NO                            11                            409
  YES                            4                             13
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 20(13Q12.3) MUTATED              3                       0   13
  DEL PEAK 20(13Q12.3) WILD-TYPE          129                      18  317
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 20(13Q12.3) MUTATED                     0
  DEL PEAK 20(13Q12.3) WILD-TYPE                   1
D25V11, multiclass
                         clus
vv                        DEL PEAK 20(13Q12.3) MUTATED
  MINIMAL (T3)                                       3
  MODERATE/ADVANCED (T4A)                            0
  NONE                                              13
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 20(13Q12.3) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               317
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 20(13Q12.3) MUTATED    12   2   0   1
  DEL PEAK 20(13Q12.3) WILD-TYPE 371  49   4  29
D25V12, multiclass
    clus
vv   DEL PEAK 20(13Q12.3) MUTATED DEL PEAK 20(13Q12.3) WILD-TYPE
  R0                           12                            371
  R1                            2                             49
  R2                            0                              4
  RX                            1                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, continuous
D25V14, binary
                                cls
clus                               0   1
  DEL PEAK 20(13Q12.3) MUTATED     8   8
  DEL PEAK 20(13Q12.3) WILD-TYPE 217 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(13Q12.3) MUTATED      8    8
  DEL PEAK 20(13Q12.3) WILD-TYPE  217  256
            clus
vv           DEL PEAK 20(13Q12.3) MUTATED DEL PEAK 20(13Q12.3) WILD-TYPE
  MULTIFOCAL                            8                            217
  UNIFOCAL                              8                            256
[1] 2 2
[1] FALSE
D25V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(13Q12.3) MUTATED                                  0     1
  DEL PEAK 20(13Q12.3) WILD-TYPE                                1    51
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(13Q12.3) MUTATED                           1    10
  DEL PEAK 20(13Q12.3) WILD-TYPE                        26   319
D25V16, multiclass
                                  clus
vv                                 DEL PEAK 20(13Q12.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      10
                                  clus
vv                                 DEL PEAK 20(13Q12.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        51
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       319
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V17, binary
                                cls
clus                               0   1
  DEL PEAK 20(13Q12.3) MUTATED     0  12
  DEL PEAK 20(13Q12.3) WILD-TYPE  38 348
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(13Q12.3) MUTATED      0   12
  DEL PEAK 20(13Q12.3) WILD-TYPE   38  348
                        clus
vv                       DEL PEAK 20(13Q12.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           12
                        clus
vv                       DEL PEAK 20(13Q12.3) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            348
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK 21(13Q14.3) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(13Q14.3) MUTATED    18   2
  DEL PEAK 21(13Q14.3) WILD-TYPE 464  14
  DEL PEAK 21(13Q14.3) MUTATED DEL PEAK 21(13Q14.3) WILD-TYPE 
                            20                            478 
  DEL PEAK 21(13Q14.3) MUTATED DEL PEAK 21(13Q14.3) WILD-TYPE 
                             2                             14 
$`DEL PEAK 21(13Q14.3) MUTATED`
TCGA-CE-A13K TCGA-BJ-A2N9 TCGA-BJ-A3F0 TCGA-BJ-A45C TCGA-DJ-A13P TCGA-DJ-A1QN 
       12.66        20.48        13.94         7.99       169.32        42.58 
TCGA-DJ-A2Q2 TCGA-EM-A1YB TCGA-EM-A22M TCGA-EM-A22Q TCGA-EM-A2OX TCGA-EM-A3O3 
       43.96        19.46        14.53        14.24        19.73        14.50 
TCGA-ET-A39N TCGA-ET-A40S TCGA-FE-A235 TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3W9 
      123.32        40.21       117.40        33.63         7.82        21.63 
TCGA-FY-A4B0 TCGA-IM-A41Z 
       13.81        31.10 

$`DEL PEAK 21(13Q14.3) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-DE-A0XZ TCGA-DJ-A13L TCGA-DJ-A2PR 
       30.21        22.88        23.18        35.84         9.96        27.45 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK TCGA-E3-A3E5 
       23.44        59.57        42.54         3.12        24.76        39.95 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 TCGA-EL-A3GQ 
        7.66        45.53         4.18       139.86        57.11        50.24 
TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO 
       33.50       150.48        17.52       178.29        29.72        50.40 
TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET 
       75.42         1.05         1.68        17.23         2.60        21.83 
TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       23.93         4.24        24.79        13.78        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 
       25.48        15.12        42.08        51.39        41.52        20.58 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
       11.31        30.97        11.08        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D 
       12.82        16.01        36.39        23.31        18.64        10.88 
TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
       21.01         3.45        23.84        28.44        15.45        21.63 
TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       19.43        23.47        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       10.68        15.02        12.43        12.66        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        27.32        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12        14.70        14.27         2.76        48.79 
TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
       38.17        18.58         8.71        56.19        52.27        43.17 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       52.37         8.32        48.07       135.91        30.61        44.98 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       42.51        14.96        17.59         6.02        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       34.36        37.74        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        49.51       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 
       50.20       147.75       101.13       139.99        49.32        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ 
       49.71        83.57       139.00       108.66        57.63        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
       29.65       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       91.17        51.78        62.30        36.03        53.06        72.69 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        61.02        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       18.05        19.79        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       14.50        15.75        10.45        10.65        44.19        41.29 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY 
       12.30        48.46        13.15        22.16        40.34        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        44.52         8.35 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.49        17.39        16.18        15.02        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
       12.53         9.24        27.02        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.85        13.51        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       28.24        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       46.26        44.38        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A236 
       71.44        31.59        79.69        24.69        68.22        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
      112.80        39.95        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       78.77        71.08         4.11        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
      116.09         1.25        20.42        17.82        29.10        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       14.04        21.60        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
       11.01        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 
       16.90        21.83         8.22        25.64        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.47         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 
       35.28        33.24        33.40        40.37         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       32.45        30.21        12.89         3.02 

  DEL PEAK 21(13Q14.3) MUTATED DEL PEAK 21(13Q14.3) WILD-TYPE 
                          7.82                           0.20 
  DEL PEAK 21(13Q14.3) MUTATED DEL PEAK 21(13Q14.3) WILD-TYPE 
                        169.32                         178.29 
  DEL PEAK 21(13Q14.3) MUTATED DEL PEAK 21(13Q14.3) WILD-TYPE 
                        20.105                         31.315 
[1] "7.8 - 169.3 (20.1)" "0.2 - 178.3 (31.3)"
[1] "hr=" "4.1"
D26V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 21(13Q14.3) MUTATED        10        4         5        0         1
  DEL PEAK 21(13Q14.3) WILD-TYPE     272       46       106        2        45
                                vv
clus                             STAGE IVC
  DEL PEAK 21(13Q14.3) MUTATED           0
  DEL PEAK 21(13Q14.3) WILD-TYPE         6
D26V3, multiclass
           clus
vv          DEL PEAK 21(13Q14.3) MUTATED DEL PEAK 21(13Q14.3) WILD-TYPE
  STAGE I                             10                            272
  STAGE II                             4                             46
  STAGE III                            5                            106
  STAGE IV                             0                              2
  STAGE IVA                            1                             45
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 21(13Q14.3) MUTATED     6   7   7   0
  DEL PEAK 21(13Q14.3) WILD-TYPE 136 158 160  23
D26V4, multiclass
    clus
vv   DEL PEAK 21(13Q14.3) MUTATED DEL PEAK 21(13Q14.3) WILD-TYPE
  T1                            6                            136
  T2                            7                            158
  T3                            7                            160
  T4                            0                             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"
D26V5, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.3) MUTATED    13   4
  DEL PEAK 21(13Q14.3) WILD-TYPE 212 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.3) MUTATED     13    4
  DEL PEAK 21(13Q14.3) WILD-TYPE  212  220
   clus
vv  DEL PEAK 21(13Q14.3) MUTATED DEL PEAK 21(13Q14.3) WILD-TYPE
  0                           13                            212
  1                            4                            220
[1] 2 2
[1] FALSE
D26V6, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.3) MUTATED     7   0
  DEL PEAK 21(13Q14.3) WILD-TYPE 271   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.3) MUTATED      7    0
  DEL PEAK 21(13Q14.3) WILD-TYPE  271    9
   clus
vv  DEL PEAK 21(13Q14.3) MUTATED DEL PEAK 21(13Q14.3) WILD-TYPE
  0                            7                            271
  1                            0                              9
[1] 2 2
[1] FALSE
D26V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.3) MUTATED    13   7
  DEL PEAK 21(13Q14.3) WILD-TYPE 352 127
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.3) MUTATED     13    7
  DEL PEAK 21(13Q14.3) WILD-TYPE  352  127
        clus
vv       DEL PEAK 21(13Q14.3) MUTATED DEL PEAK 21(13Q14.3) WILD-TYPE
  FEMALE                           13                            352
  MALE                              7                            127
[1] 2 2
[1] FALSE
D26V8, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.3) MUTATED     5  14
  DEL PEAK 21(13Q14.3) WILD-TYPE 175 289
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.3) MUTATED      5   14
  DEL PEAK 21(13Q14.3) WILD-TYPE  175  289
     clus
vv    DEL PEAK 21(13Q14.3) MUTATED DEL PEAK 21(13Q14.3) WILD-TYPE
  NO                             5                            175
  YES                           14                            289
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER, SPECIFY
  DEL PEAK 21(13Q14.3) MUTATED                0
  DEL PEAK 21(13Q14.3) WILD-TYPE              7
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 21(13Q14.3) MUTATED                                              14
  DEL PEAK 21(13Q14.3) WILD-TYPE                                           342
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 21(13Q14.3) MUTATED                                                                        6
  DEL PEAK 21(13Q14.3) WILD-TYPE                                                                     94
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 21(13Q14.3) MUTATED                                                                     0
  DEL PEAK 21(13Q14.3) WILD-TYPE                                                                  36
D26V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 21(13Q14.3) MUTATED
  OTHER, SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    14
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            6
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK 21(13Q14.3) WILD-TYPE
  OTHER, SPECIFY                                                                                      7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     342
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             94
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.3) MUTATED    14   4
  DEL PEAK 21(13Q14.3) WILD-TYPE 406  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.3) MUTATED     14    4
  DEL PEAK 21(13Q14.3) WILD-TYPE  406   13
     clus
vv    DEL PEAK 21(13Q14.3) MUTATED DEL PEAK 21(13Q14.3) WILD-TYPE
  NO                            14                            406
  YES                            4                             13
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 21(13Q14.3) MUTATED              3                       0   17
  DEL PEAK 21(13Q14.3) WILD-TYPE          129                      18  313
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 21(13Q14.3) MUTATED                     0
  DEL PEAK 21(13Q14.3) WILD-TYPE                   1
D26V11, multiclass
                         clus
vv                        DEL PEAK 21(13Q14.3) MUTATED
  MINIMAL (T3)                                       3
  MODERATE/ADVANCED (T4A)                            0
  NONE                                              17
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 21(13Q14.3) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               313
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 21(13Q14.3) MUTATED    15   3   0   1
  DEL PEAK 21(13Q14.3) WILD-TYPE 368  48   4  29
D26V12, multiclass
    clus
vv   DEL PEAK 21(13Q14.3) MUTATED DEL PEAK 21(13Q14.3) WILD-TYPE
  R0                           15                            368
  R1                            3                             48
  R2                            0                              4
  RX                            1                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, continuous
D26V14, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.3) MUTATED    11   9
  DEL PEAK 21(13Q14.3) WILD-TYPE 214 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.3) MUTATED     11    9
  DEL PEAK 21(13Q14.3) WILD-TYPE  214  255
            clus
vv           DEL PEAK 21(13Q14.3) MUTATED DEL PEAK 21(13Q14.3) WILD-TYPE
  MULTIFOCAL                           11                            214
  UNIFOCAL                              9                            255
[1] 2 2
[1] FALSE
D26V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(13Q14.3) MUTATED                                  0     2
  DEL PEAK 21(13Q14.3) WILD-TYPE                                1    50
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(13Q14.3) MUTATED                           1    12
  DEL PEAK 21(13Q14.3) WILD-TYPE                        26   317
D26V16, multiclass
                                  clus
vv                                 DEL PEAK 21(13Q14.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      12
                                  clus
vv                                 DEL PEAK 21(13Q14.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        50
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V17, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.3) MUTATED     1  15
  DEL PEAK 21(13Q14.3) WILD-TYPE  37 345
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.3) MUTATED      1   15
  DEL PEAK 21(13Q14.3) WILD-TYPE   37  345
                        clus
vv                       DEL PEAK 21(13Q14.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           15
                        clus
vv                       DEL PEAK 21(13Q14.3) WILD-TYPE
  HISPANIC OR LATINO                                 37
  NOT HISPANIC OR LATINO                            345
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK 23(15Q25.3) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(15Q25.3) MUTATED     8   0
  DEL PEAK 23(15Q25.3) WILD-TYPE 474  16
  DEL PEAK 23(15Q25.3) MUTATED DEL PEAK 23(15Q25.3) WILD-TYPE 
                             8                            490 
  DEL PEAK 23(15Q25.3) MUTATED DEL PEAK 23(15Q25.3) WILD-TYPE 
                             0                             16 
$`DEL PEAK 23(15Q25.3) MUTATED`
TCGA-BJ-A3F0 TCGA-DJ-A4UR TCGA-EL-A3GO TCGA-EM-A1YE TCGA-EM-A2OY TCGA-EM-A3O9 
       13.94        34.78        64.87        54.08        32.32         9.24 
TCGA-ET-A39N TCGA-FY-A3I5 
      123.32         7.82 

$`DEL PEAK 23(15Q25.3) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3PR TCGA-BJ-A3PT 
       20.48        18.97        12.82        16.01        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       33.04        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GP 
      106.62        79.50        98.53        69.57       108.36        49.51 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      101.13       139.99        49.32        43.36        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 
      139.00       108.66        57.63        52.50        29.65       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        91.17        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        72.69        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       61.02        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        78.61        57.01        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        44.52         8.35 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
        7.33        12.53        27.02        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.85        13.51        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       28.24        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82        29.10        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08        23.31        21.63        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 
       15.16        23.87        22.49        19.04        13.81        14.04 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       21.60        12.53        17.00        21.67        12.46        11.01 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 
       21.83        31.10         8.22        25.64        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.47         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 
       35.28        33.24        33.40        40.37         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       32.45        30.21        12.89         3.02 

  DEL PEAK 23(15Q25.3) MUTATED DEL PEAK 23(15Q25.3) WILD-TYPE 
                          7.82                           0.20 
  DEL PEAK 23(15Q25.3) MUTATED DEL PEAK 23(15Q25.3) WILD-TYPE 
                        123.32                         178.29 
  DEL PEAK 23(15Q25.3) MUTATED DEL PEAK 23(15Q25.3) WILD-TYPE 
                        33.550                         31.165 
[1] "7.8 - 123.3 (33.5)" "0.2 - 178.3 (31.2)"
[1] "hr="     "9200000"
D27V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 23(15Q25.3) MUTATED         4        3         1        0         0
  DEL PEAK 23(15Q25.3) WILD-TYPE     278       47       110        2        46
                                vv
clus                             STAGE IVC
  DEL PEAK 23(15Q25.3) MUTATED           0
  DEL PEAK 23(15Q25.3) WILD-TYPE         6
D27V3, multiclass
           clus
vv          DEL PEAK 23(15Q25.3) MUTATED DEL PEAK 23(15Q25.3) WILD-TYPE
  STAGE I                              4                            278
  STAGE II                             3                             47
  STAGE III                            1                            110
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] 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(15Q25.3) MUTATED     1   3   4   0
  DEL PEAK 23(15Q25.3) WILD-TYPE 141 162 163  23
D27V4, multiclass
    clus
vv   DEL PEAK 23(15Q25.3) MUTATED DEL PEAK 23(15Q25.3) WILD-TYPE
  T1                            1                            141
  T2                            3                            162
  T3                            4                            163
  T4                            0                             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"
D27V5, binary
                                cls
clus                               0   1
  DEL PEAK 23(15Q25.3) MUTATED     6   1
  DEL PEAK 23(15Q25.3) WILD-TYPE 219 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q25.3) MUTATED      6    1
  DEL PEAK 23(15Q25.3) WILD-TYPE  219  223
   clus
vv  DEL PEAK 23(15Q25.3) MUTATED DEL PEAK 23(15Q25.3) WILD-TYPE
  0                            6                            219
  1                            1                            223
[1] 2 2
[1] FALSE
D27V6, binary
                                cls
clus                               0   1
  DEL PEAK 23(15Q25.3) MUTATED     2   1
  DEL PEAK 23(15Q25.3) WILD-TYPE 276   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q25.3) MUTATED      2    1
  DEL PEAK 23(15Q25.3) WILD-TYPE  276    8
   clus
vv  DEL PEAK 23(15Q25.3) MUTATED DEL PEAK 23(15Q25.3) WILD-TYPE
  0                            2                            276
  1                            1                              8
[1] 2 2
[1] FALSE
D27V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(15Q25.3) MUTATED     7   1
  DEL PEAK 23(15Q25.3) WILD-TYPE 358 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q25.3) MUTATED      7    1
  DEL PEAK 23(15Q25.3) WILD-TYPE  358  133
        clus
vv       DEL PEAK 23(15Q25.3) MUTATED DEL PEAK 23(15Q25.3) WILD-TYPE
  FEMALE                            7                            358
  MALE                              1                            133
[1] 2 2
[1] FALSE
D27V8, binary
                                cls
clus                               0   1
  DEL PEAK 23(15Q25.3) MUTATED     2   5
  DEL PEAK 23(15Q25.3) WILD-TYPE 178 298
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q25.3) MUTATED      2    5
  DEL PEAK 23(15Q25.3) WILD-TYPE  178  298
     clus
vv    DEL PEAK 23(15Q25.3) MUTATED DEL PEAK 23(15Q25.3) WILD-TYPE
  NO                             2                            178
  YES                            5                            298
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER, SPECIFY
  DEL PEAK 23(15Q25.3) MUTATED                0
  DEL PEAK 23(15Q25.3) WILD-TYPE              7
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 23(15Q25.3) MUTATED                                               3
  DEL PEAK 23(15Q25.3) WILD-TYPE                                           353
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 23(15Q25.3) MUTATED                                                                        5
  DEL PEAK 23(15Q25.3) WILD-TYPE                                                                     95
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 23(15Q25.3) MUTATED                                                                     0
  DEL PEAK 23(15Q25.3) WILD-TYPE                                                                  36
D27V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 23(15Q25.3) MUTATED
  OTHER, SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK 23(15Q25.3) WILD-TYPE
  OTHER, SPECIFY                                                                                      7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, binary
                                cls
clus                               0   1
  DEL PEAK 23(15Q25.3) MUTATED     7   0
  DEL PEAK 23(15Q25.3) WILD-TYPE 413  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q25.3) MUTATED      7    0
  DEL PEAK 23(15Q25.3) WILD-TYPE  413   17
     clus
vv    DEL PEAK 23(15Q25.3) MUTATED DEL PEAK 23(15Q25.3) WILD-TYPE
  NO                             7                            413
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 23(15Q25.3) MUTATED              1                       0    7
  DEL PEAK 23(15Q25.3) WILD-TYPE          131                      18  323
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 23(15Q25.3) MUTATED                     0
  DEL PEAK 23(15Q25.3) WILD-TYPE                   1
D27V11, multiclass
                         clus
vv                        DEL PEAK 23(15Q25.3) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               7
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 23(15Q25.3) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               323
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(15Q25.3) MUTATED     8   0   0   0
  DEL PEAK 23(15Q25.3) WILD-TYPE 375  51   4  30
D27V12, multiclass
    clus
vv   DEL PEAK 23(15Q25.3) MUTATED DEL PEAK 23(15Q25.3) WILD-TYPE
  R0                            8                            375
  R1                            0                             51
  R2                            0                              4
  RX                            0                             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"
D27V13, continuous
D27V14, binary
                                cls
clus                               0   1
  DEL PEAK 23(15Q25.3) MUTATED     3   5
  DEL PEAK 23(15Q25.3) WILD-TYPE 222 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q25.3) MUTATED      3    5
  DEL PEAK 23(15Q25.3) WILD-TYPE  222  259
            clus
vv           DEL PEAK 23(15Q25.3) MUTATED DEL PEAK 23(15Q25.3) WILD-TYPE
  MULTIFOCAL                            3                            222
  UNIFOCAL                              5                            259
[1] 2 2
[1] FALSE
D27V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(15Q25.3) MUTATED                                  0     1
  DEL PEAK 23(15Q25.3) WILD-TYPE                                1    51
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(15Q25.3) MUTATED                           0     4
  DEL PEAK 23(15Q25.3) WILD-TYPE                        27   325
D27V16, multiclass
                                  clus
vv                                 DEL PEAK 23(15Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       4
                                  clus
vv                                 DEL PEAK 23(15Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        51
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V17, binary
                                cls
clus                               0   1
  DEL PEAK 23(15Q25.3) MUTATED     1   4
  DEL PEAK 23(15Q25.3) WILD-TYPE  37 356
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q25.3) MUTATED      1    4
  DEL PEAK 23(15Q25.3) WILD-TYPE   37  356
                        clus
vv                       DEL PEAK 23(15Q25.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            4
                        clus
vv                       DEL PEAK 23(15Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                 37
  NOT HISPANIC OR LATINO                            356
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK 24(16Q23.3) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(16Q23.3) MUTATED     5   1
  DEL PEAK 24(16Q23.3) WILD-TYPE 477  15
  DEL PEAK 24(16Q23.3) MUTATED DEL PEAK 24(16Q23.3) WILD-TYPE 
                             6                            492 
  DEL PEAK 24(16Q23.3) MUTATED DEL PEAK 24(16Q23.3) WILD-TYPE 
                             1                             15 
$`DEL PEAK 24(16Q23.3) MUTATED`
TCGA-DJ-A3V7 TCGA-EL-A3GP TCGA-EL-A3H5 TCGA-EL-A3MX TCGA-ET-A2N4 TCGA-ET-A3BT 
       23.21        49.51        83.57        57.63         2.66        87.62 

$`DEL PEAK 24(16Q23.3) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74        43.96        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       39.95        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V8 
       40.96        36.99        20.22        30.61        19.20        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GO TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       64.87       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 
      139.00       108.66        52.50        29.65       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        91.17        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        72.69        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        61.02 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        44.52 
TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
        8.35        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33        12.53         9.24        27.02        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       54.35        83.34        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      108.46        84.89       123.32       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        4.11        22.03         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
       20.42        17.82         7.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       13.81        14.04        21.60        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46        11.01        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
       22.29         5.75         2.47         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
        9.50        36.10        32.45        30.21        12.89         3.02 

  DEL PEAK 24(16Q23.3) MUTATED DEL PEAK 24(16Q23.3) WILD-TYPE 
                          2.66                           0.20 
  DEL PEAK 24(16Q23.3) MUTATED DEL PEAK 24(16Q23.3) WILD-TYPE 
                         87.62                         178.29 
  DEL PEAK 24(16Q23.3) MUTATED DEL PEAK 24(16Q23.3) WILD-TYPE 
                        53.570                         31.165 
[1] "2.7 - 87.6 (53.6)"  "0.2 - 178.3 (31.2)"
[1] "hr=" "3.6"
D28V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 24(16Q23.3) MUTATED         0        0         3        0         2
  DEL PEAK 24(16Q23.3) WILD-TYPE     282       50       108        2        44
                                vv
clus                             STAGE IVC
  DEL PEAK 24(16Q23.3) MUTATED           1
  DEL PEAK 24(16Q23.3) WILD-TYPE         5
D28V3, multiclass
           clus
vv          DEL PEAK 24(16Q23.3) MUTATED DEL PEAK 24(16Q23.3) WILD-TYPE
  STAGE I                              0                            282
  STAGE II                             0                             50
  STAGE III                            3                            108
  STAGE IV                             0                              2
  STAGE IVA                            2                             44
  STAGE IVC                            1                              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 24(16Q23.3) MUTATED     0   1   3   2
  DEL PEAK 24(16Q23.3) WILD-TYPE 142 164 164  21
D28V4, multiclass
    clus
vv   DEL PEAK 24(16Q23.3) MUTATED DEL PEAK 24(16Q23.3) WILD-TYPE
  T1                            0                            142
  T2                            1                            164
  T3                            3                            164
  T4                            2                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V5, binary
                                cls
clus                               0   1
  DEL PEAK 24(16Q23.3) MUTATED     2   4
  DEL PEAK 24(16Q23.3) WILD-TYPE 223 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q23.3) MUTATED      2    4
  DEL PEAK 24(16Q23.3) WILD-TYPE  223  220
   clus
vv  DEL PEAK 24(16Q23.3) MUTATED DEL PEAK 24(16Q23.3) WILD-TYPE
  0                            2                            223
  1                            4                            220
[1] 2 2
[1] FALSE
D28V6, binary
                                cls
clus                               0   1
  DEL PEAK 24(16Q23.3) MUTATED     3   1
  DEL PEAK 24(16Q23.3) WILD-TYPE 275   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q23.3) MUTATED      3    1
  DEL PEAK 24(16Q23.3) WILD-TYPE  275    8
   clus
vv  DEL PEAK 24(16Q23.3) MUTATED DEL PEAK 24(16Q23.3) WILD-TYPE
  0                            3                            275
  1                            1                              8
[1] 2 2
[1] FALSE
D28V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(16Q23.3) MUTATED     5   1
  DEL PEAK 24(16Q23.3) WILD-TYPE 360 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q23.3) MUTATED      5    1
  DEL PEAK 24(16Q23.3) WILD-TYPE  360  133
        clus
vv       DEL PEAK 24(16Q23.3) MUTATED DEL PEAK 24(16Q23.3) WILD-TYPE
  FEMALE                            5                            360
  MALE                              1                            133
[1] 2 2
[1] FALSE
D28V8, binary
                                cls
clus                               0   1
  DEL PEAK 24(16Q23.3) MUTATED     1   5
  DEL PEAK 24(16Q23.3) WILD-TYPE 179 298
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q23.3) MUTATED      1    5
  DEL PEAK 24(16Q23.3) WILD-TYPE  179  298
     clus
vv    DEL PEAK 24(16Q23.3) MUTATED DEL PEAK 24(16Q23.3) WILD-TYPE
  NO                             1                            179
  YES                            5                            298
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER, SPECIFY
  DEL PEAK 24(16Q23.3) MUTATED                0
  DEL PEAK 24(16Q23.3) WILD-TYPE              7
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 24(16Q23.3) MUTATED                                               3
  DEL PEAK 24(16Q23.3) WILD-TYPE                                           353
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 24(16Q23.3) MUTATED                                                                        1
  DEL PEAK 24(16Q23.3) WILD-TYPE                                                                     99
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 24(16Q23.3) MUTATED                                                                     2
  DEL PEAK 24(16Q23.3) WILD-TYPE                                                                  34
D28V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 24(16Q23.3) MUTATED
  OTHER, SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               2
                                                                        clus
vv                                                                       DEL PEAK 24(16Q23.3) WILD-TYPE
  OTHER, SPECIFY                                                                                      7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, binary
                                cls
clus                               0   1
  DEL PEAK 24(16Q23.3) MUTATED     5   1
  DEL PEAK 24(16Q23.3) WILD-TYPE 415  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q23.3) MUTATED      5    1
  DEL PEAK 24(16Q23.3) WILD-TYPE  415   16
     clus
vv    DEL PEAK 24(16Q23.3) MUTATED DEL PEAK 24(16Q23.3) WILD-TYPE
  NO                             5                            415
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 24(16Q23.3) MUTATED              3                       1    2
  DEL PEAK 24(16Q23.3) WILD-TYPE          129                      17  328
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 24(16Q23.3) MUTATED                     0
  DEL PEAK 24(16Q23.3) WILD-TYPE                   1
D28V11, multiclass
                         clus
vv                        DEL PEAK 24(16Q23.3) MUTATED
  MINIMAL (T3)                                       3
  MODERATE/ADVANCED (T4A)                            1
  NONE                                               2
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 24(16Q23.3) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             17
  NONE                                               328
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 24(16Q23.3) MUTATED     3   1   0   2
  DEL PEAK 24(16Q23.3) WILD-TYPE 380  50   4  28
D28V12, multiclass
    clus
vv   DEL PEAK 24(16Q23.3) MUTATED DEL PEAK 24(16Q23.3) WILD-TYPE
  R0                            3                            380
  R1                            1                             50
  R2                            0                              4
  RX                            2                             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, continuous
D28V14, binary
                                cls
clus                               0   1
  DEL PEAK 24(16Q23.3) MUTATED     3   3
  DEL PEAK 24(16Q23.3) WILD-TYPE 222 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q23.3) MUTATED      3    3
  DEL PEAK 24(16Q23.3) WILD-TYPE  222  261
            clus
vv           DEL PEAK 24(16Q23.3) MUTATED DEL PEAK 24(16Q23.3) WILD-TYPE
  MULTIFOCAL                            3                            222
  UNIFOCAL                              3                            261
[1] 2 2
[1] FALSE
D28V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(16Q23.3) MUTATED                                  0     0
  DEL PEAK 24(16Q23.3) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(16Q23.3) MUTATED                           1     5
  DEL PEAK 24(16Q23.3) WILD-TYPE                        26   324
D28V16, multiclass
                                  clus
vv                                 DEL PEAK 24(16Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                       5
                                  clus
vv                                 DEL PEAK 24(16Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V17, binary
                                cls
clus                               0   1
  DEL PEAK 24(16Q23.3) MUTATED     0   6
  DEL PEAK 24(16Q23.3) WILD-TYPE  38 354
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q23.3) MUTATED      0    6
  DEL PEAK 24(16Q23.3) WILD-TYPE   38  354
                        clus
vv                       DEL PEAK 24(16Q23.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       DEL PEAK 24(16Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            354
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK 25(17P13.1) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(17P13.1) MUTATED     8   0
  DEL PEAK 25(17P13.1) WILD-TYPE 474  16
  DEL PEAK 25(17P13.1) MUTATED DEL PEAK 25(17P13.1) WILD-TYPE 
                             8                            490 
  DEL PEAK 25(17P13.1) MUTATED DEL PEAK 25(17P13.1) WILD-TYPE 
                             0                             16 
$`DEL PEAK 25(17P13.1) MUTATED`
TCGA-EL-A3D5 TCGA-E8-A432 TCGA-EL-A3ZM TCGA-EM-A1YE TCGA-EM-A3O9 TCGA-EM-A3OB 
       57.11        30.61        36.03        54.08         9.24        38.66 
TCGA-FE-A22Z TCGA-FE-A238 
       73.74        39.95 

$`DEL PEAK 25(17P13.1) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3GQ 
       39.95         7.66        45.53         4.18       139.86        50.24 
TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO 
       33.50       150.48        17.52       178.29        29.72        50.40 
TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET 
       75.42         1.05         1.68        17.23         2.60        21.83 
TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       23.93         4.24        24.79        13.78        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 
       25.48        15.12        42.08        51.39        41.52        20.58 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.31        30.97        11.08        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97        12.82        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
       28.44        15.45        21.63        19.43        23.47        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       12.66        21.63        50.17        37.64        27.32        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       48.07       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       30.84        25.45        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       51.78        62.30        53.06        72.69        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       61.02        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        78.61        57.01        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        44.52 
TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
        8.35        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3ST TCGA-EM-A3SU 
       15.06         7.33        12.53        27.02        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.85        13.51        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89       123.32       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       31.40        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
      117.40        66.77       112.80        33.63        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE 
       85.15        85.68        78.77        71.08         4.11        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        7.82        29.10        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08        23.31        21.63        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 
       15.16        23.87        22.49        19.04        13.81        14.04 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       21.60        12.53        17.00        21.67        12.46        11.01 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 
       21.83        31.10         8.22        25.64        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.47         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 
       35.28        33.24        33.40        40.37         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       32.45        30.21        12.89         3.02 

  DEL PEAK 25(17P13.1) MUTATED DEL PEAK 25(17P13.1) WILD-TYPE 
                          9.24                           0.20 
  DEL PEAK 25(17P13.1) MUTATED DEL PEAK 25(17P13.1) WILD-TYPE 
                         73.74                         178.29 
  DEL PEAK 25(17P13.1) MUTATED DEL PEAK 25(17P13.1) WILD-TYPE 
                        39.305                         31.070 
[1] "9.2 - 73.7 (39.3)"  "0.2 - 178.3 (31.1)"
[1] "hr="     "9200000"
D29V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 25(17P13.1) MUTATED         4        2         0        0         2
  DEL PEAK 25(17P13.1) WILD-TYPE     278       48       111        2        44
                                vv
clus                             STAGE IVC
  DEL PEAK 25(17P13.1) MUTATED           0
  DEL PEAK 25(17P13.1) WILD-TYPE         6
D29V3, multiclass
           clus
vv          DEL PEAK 25(17P13.1) MUTATED DEL PEAK 25(17P13.1) WILD-TYPE
  STAGE I                              4                            278
  STAGE II                             2                             48
  STAGE III                            0                            111
  STAGE IV                             0                              2
  STAGE IVA                            2                             44
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 25(17P13.1) MUTATED     0   3   3   2
  DEL PEAK 25(17P13.1) WILD-TYPE 142 162 164  21
D29V4, multiclass
    clus
vv   DEL PEAK 25(17P13.1) MUTATED DEL PEAK 25(17P13.1) WILD-TYPE
  T1                            0                            142
  T2                            3                            162
  T3                            3                            164
  T4                            2                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V5, binary
                                cls
clus                               0   1
  DEL PEAK 25(17P13.1) MUTATED     5   3
  DEL PEAK 25(17P13.1) WILD-TYPE 220 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(17P13.1) MUTATED      5    3
  DEL PEAK 25(17P13.1) WILD-TYPE  220  221
   clus
vv  DEL PEAK 25(17P13.1) MUTATED DEL PEAK 25(17P13.1) WILD-TYPE
  0                            5                            220
  1                            3                            221
[1] 2 2
[1] FALSE
D29V6, binary
                                cls
clus                               0   1
  DEL PEAK 25(17P13.1) MUTATED     3   0
  DEL PEAK 25(17P13.1) WILD-TYPE 275   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(17P13.1) MUTATED      3    0
  DEL PEAK 25(17P13.1) WILD-TYPE  275    9
   clus
vv  DEL PEAK 25(17P13.1) MUTATED DEL PEAK 25(17P13.1) WILD-TYPE
  0                            3                            275
  1                            0                              9
[1] 2 2
[1] FALSE
D29V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(17P13.1) MUTATED     6   2
  DEL PEAK 25(17P13.1) WILD-TYPE 359 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(17P13.1) MUTATED      6    2
  DEL PEAK 25(17P13.1) WILD-TYPE  359  132
        clus
vv       DEL PEAK 25(17P13.1) MUTATED DEL PEAK 25(17P13.1) WILD-TYPE
  FEMALE                            6                            359
  MALE                              2                            132
[1] 2 2
[1] FALSE
D29V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(17P13.1) MUTATED     4   4
  DEL PEAK 25(17P13.1) WILD-TYPE 176 299
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(17P13.1) MUTATED      4    4
  DEL PEAK 25(17P13.1) WILD-TYPE  176  299
     clus
vv    DEL PEAK 25(17P13.1) MUTATED DEL PEAK 25(17P13.1) WILD-TYPE
  NO                             4                            176
  YES                            4                            299
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER, SPECIFY
  DEL PEAK 25(17P13.1) MUTATED                0
  DEL PEAK 25(17P13.1) WILD-TYPE              7
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 25(17P13.1) MUTATED                                               4
  DEL PEAK 25(17P13.1) WILD-TYPE                                           352
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 25(17P13.1) MUTATED                                                                        4
  DEL PEAK 25(17P13.1) WILD-TYPE                                                                     96
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 25(17P13.1) MUTATED                                                                     0
  DEL PEAK 25(17P13.1) WILD-TYPE                                                                  36
D29V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 25(17P13.1) MUTATED
  OTHER, SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK 25(17P13.1) WILD-TYPE
  OTHER, SPECIFY                                                                                      7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, binary
                                cls
clus                               0   1
  DEL PEAK 25(17P13.1) MUTATED     7   1
  DEL PEAK 25(17P13.1) WILD-TYPE 413  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(17P13.1) MUTATED      7    1
  DEL PEAK 25(17P13.1) WILD-TYPE  413   16
     clus
vv    DEL PEAK 25(17P13.1) MUTATED DEL PEAK 25(17P13.1) WILD-TYPE
  NO                             7                            413
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 25(17P13.1) MUTATED              2                       2    4
  DEL PEAK 25(17P13.1) WILD-TYPE          130                      16  326
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 25(17P13.1) MUTATED                     0
  DEL PEAK 25(17P13.1) WILD-TYPE                   1
D29V11, multiclass
                         clus
vv                        DEL PEAK 25(17P13.1) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            2
  NONE                                               4
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 25(17P13.1) WILD-TYPE
  MINIMAL (T3)                                       130
  MODERATE/ADVANCED (T4A)                             16
  NONE                                               326
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(17P13.1) MUTATED     6   2   0   0
  DEL PEAK 25(17P13.1) WILD-TYPE 377  49   4  30
D29V12, multiclass
    clus
vv   DEL PEAK 25(17P13.1) MUTATED DEL PEAK 25(17P13.1) WILD-TYPE
  R0                            6                            377
  R1                            2                             49
  R2                            0                              4
  RX                            0                             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"
D29V13, continuous
D29V14, binary
                                cls
clus                               0   1
  DEL PEAK 25(17P13.1) MUTATED     3   5
  DEL PEAK 25(17P13.1) WILD-TYPE 222 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(17P13.1) MUTATED      3    5
  DEL PEAK 25(17P13.1) WILD-TYPE  222  259
            clus
vv           DEL PEAK 25(17P13.1) MUTATED DEL PEAK 25(17P13.1) WILD-TYPE
  MULTIFOCAL                            3                            222
  UNIFOCAL                              5                            259
[1] 2 2
[1] FALSE
D29V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(17P13.1) MUTATED                                  0     1
  DEL PEAK 25(17P13.1) WILD-TYPE                                1    51
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(17P13.1) MUTATED                           0     3
  DEL PEAK 25(17P13.1) WILD-TYPE                        27   326
D29V16, multiclass
                                  clus
vv                                 DEL PEAK 25(17P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       3
                                  clus
vv                                 DEL PEAK 25(17P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        51
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V17, binary
                                cls
clus                               0   1
  DEL PEAK 25(17P13.1) MUTATED     0   4
  DEL PEAK 25(17P13.1) WILD-TYPE  38 356
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(17P13.1) MUTATED      0    4
  DEL PEAK 25(17P13.1) WILD-TYPE   38  356
                        clus
vv                       DEL PEAK 25(17P13.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            4
                        clus
vv                       DEL PEAK 25(17P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            356
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK 26(18Q21.33) MUTATION ANALYSIS
D30V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 26(18Q21.33) MUTATED     5   0
  DEL PEAK 26(18Q21.33) WILD-TYPE 477  16
  DEL PEAK 26(18Q21.33) MUTATED DEL PEAK 26(18Q21.33) WILD-TYPE 
                              5                             493 
  DEL PEAK 26(18Q21.33) MUTATED DEL PEAK 26(18Q21.33) WILD-TYPE 
                              0                              16 
$`DEL PEAK 26(18Q21.33) MUTATED`
TCGA-DJ-A2Q0 TCGA-EL-A3GO TCGA-EM-A1YE TCGA-EM-A3SY TCGA-ET-A3BP 
       34.36        64.87        54.08        13.51        79.10 

$`DEL PEAK 26(18Q21.33) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 
       21.83        23.93         4.24        24.79        13.78        49.78 
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       16.34        14.73        41.33        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       16.73        25.48        15.12        42.08        51.39        41.52 
TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.58         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        11.31        30.97        11.08        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97        12.82        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        28.44        15.45        21.63        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.99        30.58        35.41        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 
       47.21        66.38        80.52        63.19        52.44        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04        31.30 
TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       30.84        25.45        30.61        31.27        31.33        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       39.88        33.50        31.00        30.15        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      155.54        97.74       158.83        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 
       57.01       106.62        79.50        98.53        69.57       108.36 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        78.61        57.01        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BQ TCGA-ET-A3BS 
       94.13        55.10        98.20        28.24        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25        20.42        17.82         7.82        29.10        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
       21.63        17.06        17.36        15.16        23.87        22.49 
TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04        13.81        14.04        21.60        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46        11.01        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       25.64        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F 
       24.69        22.29         5.75         2.47         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV 
       40.37         9.50        36.10        32.45        30.21        12.89 
TCGA-E8-A418 
        3.02 

  DEL PEAK 26(18Q21.33) MUTATED DEL PEAK 26(18Q21.33) WILD-TYPE 
                          13.51                            0.20 
  DEL PEAK 26(18Q21.33) MUTATED DEL PEAK 26(18Q21.33) WILD-TYPE 
                          79.10                          178.29 
  DEL PEAK 26(18Q21.33) MUTATED DEL PEAK 26(18Q21.33) WILD-TYPE 
                          54.08                           31.10 
[1] "13.5 - 79.1 (54.1)" "0.2 - 178.3 (31.1)"
[1] "hr="     "9200000"
D30V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 26(18Q21.33) MUTATED         3        2         0        0         0
  DEL PEAK 26(18Q21.33) WILD-TYPE     279       48       111        2        46
                                 vv
clus                              STAGE IVC
  DEL PEAK 26(18Q21.33) MUTATED           0
  DEL PEAK 26(18Q21.33) WILD-TYPE         6
D30V3, multiclass
           clus
vv          DEL PEAK 26(18Q21.33) MUTATED DEL PEAK 26(18Q21.33) WILD-TYPE
  STAGE I                               3                             279
  STAGE II                              2                              48
  STAGE III                             0                             111
  STAGE IV                              0                               2
  STAGE IVA                             0                              46
  STAGE IVC                             0                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 26(18Q21.33) MUTATED     1   4   0   0
  DEL PEAK 26(18Q21.33) WILD-TYPE 141 161 167  23
D30V4, multiclass
    clus
vv   DEL PEAK 26(18Q21.33) MUTATED DEL PEAK 26(18Q21.33) WILD-TYPE
  T1                             1                             141
  T2                             4                             161
  T3                             0                             167
  T4                             0                              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"
D30V5, binary
                                 cls
clus                                0   1
  DEL PEAK 26(18Q21.33) MUTATED     3   1
  DEL PEAK 26(18Q21.33) WILD-TYPE 222 223
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(18Q21.33) MUTATED      3    1
  DEL PEAK 26(18Q21.33) WILD-TYPE  222  223
   clus
vv  DEL PEAK 26(18Q21.33) MUTATED DEL PEAK 26(18Q21.33) WILD-TYPE
  0                             3                             222
  1                             1                             223
[1] 2 2
[1] FALSE
D30V6, binary
                                 cls
clus                                0   1
  DEL PEAK 26(18Q21.33) MUTATED     2   0
  DEL PEAK 26(18Q21.33) WILD-TYPE 276   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(18Q21.33) MUTATED      2    0
  DEL PEAK 26(18Q21.33) WILD-TYPE  276    9
   clus
vv  DEL PEAK 26(18Q21.33) MUTATED DEL PEAK 26(18Q21.33) WILD-TYPE
  0                             2                             276
  1                             0                               9
[1] 2 2
[1] FALSE
D30V7, binary
                                 cls
clus                                0   1
  DEL PEAK 26(18Q21.33) MUTATED     4   1
  DEL PEAK 26(18Q21.33) WILD-TYPE 361 133
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(18Q21.33) MUTATED      4    1
  DEL PEAK 26(18Q21.33) WILD-TYPE  361  133
        clus
vv       DEL PEAK 26(18Q21.33) MUTATED DEL PEAK 26(18Q21.33) WILD-TYPE
  FEMALE                             4                             361
  MALE                               1                             133
[1] 2 2
[1] FALSE
D30V8, binary
                                 cls
clus                                0   1
  DEL PEAK 26(18Q21.33) MUTATED     3   2
  DEL PEAK 26(18Q21.33) WILD-TYPE 177 301
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(18Q21.33) MUTATED      3    2
  DEL PEAK 26(18Q21.33) WILD-TYPE  177  301
     clus
vv    DEL PEAK 26(18Q21.33) MUTATED DEL PEAK 26(18Q21.33) WILD-TYPE
  NO                              3                             177
  YES                             2                             301
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER, SPECIFY
  DEL PEAK 26(18Q21.33) MUTATED                0
  DEL PEAK 26(18Q21.33) WILD-TYPE              7
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 26(18Q21.33) MUTATED                                               3
  DEL PEAK 26(18Q21.33) WILD-TYPE                                           353
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 26(18Q21.33) MUTATED                                                                        2
  DEL PEAK 26(18Q21.33) WILD-TYPE                                                                     98
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 26(18Q21.33) MUTATED                                                                     0
  DEL PEAK 26(18Q21.33) WILD-TYPE                                                                  36
D30V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 26(18Q21.33) MUTATED
  OTHER, SPECIFY                                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                0
                                                                        clus
vv                                                                       DEL PEAK 26(18Q21.33) WILD-TYPE
  OTHER, SPECIFY                                                                                       7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, binary
                                 cls
clus                                0   1
  DEL PEAK 26(18Q21.33) MUTATED     5   0
  DEL PEAK 26(18Q21.33) WILD-TYPE 415  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(18Q21.33) MUTATED      5    0
  DEL PEAK 26(18Q21.33) WILD-TYPE  415   17
     clus
vv    DEL PEAK 26(18Q21.33) MUTATED DEL PEAK 26(18Q21.33) WILD-TYPE
  NO                              5                             415
  YES                             0                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 26(18Q21.33) MUTATED              0                       0    5
  DEL PEAK 26(18Q21.33) WILD-TYPE          132                      18  325
                                 vv
clus                              VERY ADVANCED (T4B)
  DEL PEAK 26(18Q21.33) MUTATED                     0
  DEL PEAK 26(18Q21.33) WILD-TYPE                   1
D30V11, multiclass
                         clus
vv                        DEL PEAK 26(18Q21.33) MUTATED
  MINIMAL (T3)                                        0
  MODERATE/ADVANCED (T4A)                             0
  NONE                                                5
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        DEL PEAK 26(18Q21.33) WILD-TYPE
  MINIMAL (T3)                                        132
  MODERATE/ADVANCED (T4A)                              18
  NONE                                                325
  VERY ADVANCED (T4B)                                   1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 26(18Q21.33) MUTATED     5   0   0   0
  DEL PEAK 26(18Q21.33) WILD-TYPE 378  51   4  30
D30V12, multiclass
    clus
vv   DEL PEAK 26(18Q21.33) MUTATED DEL PEAK 26(18Q21.33) WILD-TYPE
  R0                             5                             378
  R1                             0                              51
  R2                             0                               4
  RX                             0                              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"
D30V13, continuous
D30V14, binary
                                 cls
clus                                0   1
  DEL PEAK 26(18Q21.33) MUTATED     1   4
  DEL PEAK 26(18Q21.33) WILD-TYPE 224 260
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(18Q21.33) MUTATED      1    4
  DEL PEAK 26(18Q21.33) WILD-TYPE  224  260
            clus
vv           DEL PEAK 26(18Q21.33) MUTATED DEL PEAK 26(18Q21.33) WILD-TYPE
  MULTIFOCAL                             1                             224
  UNIFOCAL                               4                             260
[1] 2 2
[1] FALSE
D30V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(18Q21.33) MUTATED                                  0     0
  DEL PEAK 26(18Q21.33) WILD-TYPE                                1    52
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(18Q21.33) MUTATED                           0     3
  DEL PEAK 26(18Q21.33) WILD-TYPE                        27   326
D30V16, multiclass
                                  clus
vv                                 DEL PEAK 26(18Q21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    0
  WHITE                                                        3
                                  clus
vv                                 DEL PEAK 26(18Q21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         52
  BLACK OR AFRICAN AMERICAN                                     27
  WHITE                                                        326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V17, binary
                                 cls
clus                                0   1
  DEL PEAK 26(18Q21.33) MUTATED     2   1
  DEL PEAK 26(18Q21.33) WILD-TYPE  36 359
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(18Q21.33) MUTATED      2    1
  DEL PEAK 26(18Q21.33) WILD-TYPE   36  359
                        clus
vv                       DEL PEAK 26(18Q21.33) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                             1
                        clus
vv                       DEL PEAK 26(18Q21.33) WILD-TYPE
  HISPANIC OR LATINO                                  36
  NOT HISPANIC OR LATINO                             359
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK 27(19P13.2) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(19P13.2) MUTATED     6   1
  DEL PEAK 27(19P13.2) WILD-TYPE 476  15
  DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE 
                             7                            491 
  DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE 
                             1                             15 
$`DEL PEAK 27(19P13.2) MUTATED`
TCGA-EL-A3D5 TCGA-EL-A3H2 TCGA-BJ-A0YZ TCGA-BJ-A192 TCGA-ET-A39N TCGA-FY-A3WA 
       57.11        33.50        24.79        44.35       123.32        17.06 
TCGA-FY-A4B0 
       13.81 

$`DEL PEAK 27(19P13.2) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3GQ 
       39.95         7.66        45.53         4.18       139.86        50.24 
TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO TCGA-ET-A3BV 
      150.48        17.52       178.29        29.72        50.40        75.42 
TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET TCGA-MK-A84Z 
        1.05         1.68        17.23         2.60        21.83        23.93 
TCGA-4C-A93U TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
        4.24        13.78        49.78        16.34        14.73        41.33 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73        25.48        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A28R 
       42.08        51.39        41.52        20.58         4.83        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04        35.54        32.45        11.31        30.97        11.08 
TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ 
       18.38        16.57        20.48        18.97        12.82        16.01 
TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D 
       13.94        36.39        23.31        18.64         7.99        10.88 
TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
       21.01         3.45        23.84        28.44        15.45        21.63 
TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       19.43        23.47        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       10.68        15.02        12.43        12.66        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        27.32        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12        14.70        14.27         2.76        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        52.27 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        48.07       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.99        30.58        35.41 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42        34.36        37.74        43.96        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       33.93        37.48        36.46        35.11        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       33.53        35.18        39.95        36.92        31.04        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        36.33 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        35.87        40.96        36.99        20.22        30.61 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       40.70        18.97         9.60        35.67        36.43        23.44 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        30.12        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       63.19        52.44        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 
       31.50        31.04        31.30        30.84        25.45        30.61 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       31.27        31.33        14.96        39.88        33.50        31.00 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       30.15        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ 
       60.95       157.15        37.94        57.01       106.62        79.50 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR 
       98.53        69.57       108.36        64.87        49.51       115.10 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       136.01        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      139.99        49.32        43.36        49.71        83.57       139.00 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 
      108.66        57.63        52.50        29.65       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        91.17        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        72.69        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        61.02 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        44.52 
TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
        8.35        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33        12.53         9.24        27.02        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25        20.42        17.82         7.82        29.10        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08        23.31 
TCGA-FY-A3W9 TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       21.63        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       14.04        21.60        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
       11.01        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 
       16.90        21.83        31.10         8.22        25.64        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        5.75         2.47         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU 
       84.72        35.28        33.24        33.40        40.37         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       36.10        32.45        30.21        12.89         3.02 

  DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE 
                         13.81                           0.20 
  DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE 
                        123.32                         178.29 
  DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE 
                         33.50                          31.23 
[1] "13.8 - 123.3 (33.5)" "0.2 - 178.3 (31.2)" 
[1] "hr=" "4.2"
D31V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 27(19P13.2) MUTATED         4        2         1        0         0
  DEL PEAK 27(19P13.2) WILD-TYPE     278       48       110        2        46
                                vv
clus                             STAGE IVC
  DEL PEAK 27(19P13.2) MUTATED           0
  DEL PEAK 27(19P13.2) WILD-TYPE         6
D31V3, multiclass
           clus
vv          DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE
  STAGE I                              4                            278
  STAGE II                             2                             48
  STAGE III                            1                            110
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 27(19P13.2) MUTATED     2   2   3   0
  DEL PEAK 27(19P13.2) WILD-TYPE 140 163 164  23
D31V4, multiclass
    clus
vv   DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE
  T1                            2                            140
  T2                            2                            163
  T3                            3                            164
  T4                            0                             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"
D31V5, binary
                                cls
clus                               0   1
  DEL PEAK 27(19P13.2) MUTATED     2   1
  DEL PEAK 27(19P13.2) WILD-TYPE 223 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(19P13.2) MUTATED      2    1
  DEL PEAK 27(19P13.2) WILD-TYPE  223  223
   clus
vv  DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE
  0                            2                            223
  1                            1                            223
[1] 2 2
[1] FALSE
D31V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(19P13.2) MUTATED     3   0
  DEL PEAK 27(19P13.2) WILD-TYPE 275   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(19P13.2) MUTATED      3    0
  DEL PEAK 27(19P13.2) WILD-TYPE  275    9
   clus
vv  DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE
  0                            3                            275
  1                            0                              9
[1] 2 2
[1] FALSE
D31V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(19P13.2) MUTATED     4   3
  DEL PEAK 27(19P13.2) WILD-TYPE 361 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(19P13.2) MUTATED      4    3
  DEL PEAK 27(19P13.2) WILD-TYPE  361  131
        clus
vv       DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE
  FEMALE                            4                            361
  MALE                              3                            131
[1] 2 2
[1] FALSE
D31V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(19P13.2) MUTATED     3   4
  DEL PEAK 27(19P13.2) WILD-TYPE 177 299
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(19P13.2) MUTATED      3    4
  DEL PEAK 27(19P13.2) WILD-TYPE  177  299
     clus
vv    DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE
  NO                             3                            177
  YES                            4                            299
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER, SPECIFY
  DEL PEAK 27(19P13.2) MUTATED                0
  DEL PEAK 27(19P13.2) WILD-TYPE              7
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 27(19P13.2) MUTATED                                               6
  DEL PEAK 27(19P13.2) WILD-TYPE                                           350
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 27(19P13.2) MUTATED                                                                        1
  DEL PEAK 27(19P13.2) WILD-TYPE                                                                     99
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 27(19P13.2) MUTATED                                                                     0
  DEL PEAK 27(19P13.2) WILD-TYPE                                                                  36
D31V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 27(19P13.2) MUTATED
  OTHER, SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK 27(19P13.2) WILD-TYPE
  OTHER, SPECIFY                                                                                      7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, binary
                                cls
clus                               0   1
  DEL PEAK 27(19P13.2) MUTATED     5   2
  DEL PEAK 27(19P13.2) WILD-TYPE 415  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(19P13.2) MUTATED      5    2
  DEL PEAK 27(19P13.2) WILD-TYPE  415   15
     clus
vv    DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE
  NO                             5                            415
  YES                            2                             15
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 27(19P13.2) MUTATED              2                       0    5
  DEL PEAK 27(19P13.2) WILD-TYPE          130                      18  325
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 27(19P13.2) MUTATED                     0
  DEL PEAK 27(19P13.2) WILD-TYPE                   1
D31V11, multiclass
                         clus
vv                        DEL PEAK 27(19P13.2) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               5
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 27(19P13.2) WILD-TYPE
  MINIMAL (T3)                                       130
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               325
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(19P13.2) MUTATED     4   2   0   1
  DEL PEAK 27(19P13.2) WILD-TYPE 379  49   4  29
D31V12, multiclass
    clus
vv   DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE
  R0                            4                            379
  R1                            2                             49
  R2                            0                              4
  RX                            1                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, continuous
[1] "Remove cluster labels:"       "DEL PEAK 27(19P13.2) MUTATED"
clus
  DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE 
                             1                            385 
                    TCGA-BJ-A290                     TCGA-BJ-A291 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A45K                     TCGA-CE-A13K 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DE-A0XZ                     TCGA-DJ-A2PR 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3UU                     TCGA-DJ-A3UW 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3V4                     TCGA-DJ-A3VI 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3VK                     TCGA-E3-A3E5 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3CR                     TCGA-EL-A3CS 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3CY                     TCGA-EL-A3D0 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3GQ                     TCGA-EL-A3H8 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3AQ                     TCGA-ET-A3BO 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A3BV                     TCGA-J8-A3NZ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-J8-A4HW                     TCGA-4C-A93U 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A0Z0                     TCGA-BJ-A0Z3 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A0Z5                     TCGA-BJ-A0Z9 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A0ZA                     TCGA-BJ-A0ZB 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A0ZH                     TCGA-BJ-A0ZJ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A18Y                     TCGA-BJ-A18Z 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A190                     TCGA-BJ-A191 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A28R                     TCGA-BJ-A28T 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A28W                     TCGA-BJ-A28X 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A28Z                     TCGA-BJ-A2N8 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A2N9                     TCGA-BJ-A2NA 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A3EZ                     TCGA-BJ-A3PR 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A3PU                     TCGA-BJ-A45C 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A45D                     TCGA-BJ-A45E 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A45G                     TCGA-BJ-A45I 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A45J                     TCGA-BJ-A4O8 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A4O9                     TCGA-CE-A3MD 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-CE-A483                     TCGA-CE-A484 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-CE-A485                     TCGA-DE-A0Y2 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DE-A0Y3                     TCGA-DE-A3KN 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DE-A4M8                     TCGA-DE-A4MA 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DE-A4MB                     TCGA-DE-A4MC 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DE-A4MD                     TCGA-DE-A69K 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DE-A7U5                     TCGA-DJ-A13M 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A13O                     TCGA-DJ-A13R 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A13T                     TCGA-DJ-A13V 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A13W                     TCGA-DJ-A13X 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A1QG                     TCGA-DJ-A1QH 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A1QM                     TCGA-DJ-A2PO 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2PP                     TCGA-DJ-A2PQ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2PS                     TCGA-DJ-A2PT 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2PU                     TCGA-DJ-A2PV 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2PW                     TCGA-DJ-A2PX 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2PY                     TCGA-DJ-A2PZ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2Q0                     TCGA-DJ-A2Q1 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2Q2                     TCGA-DJ-A2Q3 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2Q4                     TCGA-DJ-A2Q5 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2Q6                     TCGA-DJ-A2Q7 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2Q8                     TCGA-DJ-A2Q9 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2QA                     TCGA-DJ-A2QB 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3UK                     TCGA-DJ-A3UM 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3UN                     TCGA-DJ-A3UO 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3UP                     TCGA-DJ-A3UQ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3UR                     TCGA-DJ-A3UX 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3UZ                     TCGA-DJ-A3V0 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3V2                     TCGA-DJ-A3V3 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3V5                     TCGA-DJ-A3V7 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3V8                     TCGA-DJ-A3V9 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3VA                     TCGA-DJ-A3VB 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3VD                     TCGA-DJ-A3VF 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3VG                     TCGA-DJ-A3VJ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3VL                     TCGA-DJ-A4UL 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A4UP                     TCGA-DJ-A4UQ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A4UR                     TCGA-DJ-A4UW 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A4V2                     TCGA-DJ-A4V5 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-DO-A1K0                     TCGA-DO-A2HM 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-E3-A3DY                     TCGA-E3-A3DZ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-E3-A3E0                     TCGA-E3-A3E1 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-E3-A3E2                     TCGA-E3-A3E3 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-E8-A242                     TCGA-E8-A2EA 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-E8-A414                     TCGA-E8-A415 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-E8-A417                     TCGA-E8-A419 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-E8-A433                     TCGA-E8-A436 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-E8-A438                     TCGA-E8-A44K 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3CM                     TCGA-EL-A3CN 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3CO                     TCGA-EL-A3CT 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3CU                     TCGA-EL-A3CV 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3CW                     TCGA-EL-A3CX 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3CZ                     TCGA-EL-A3D1 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3D4                     TCGA-EL-A3D6 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3GO                     TCGA-EL-A3GP 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3GS                     TCGA-EL-A3GU 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3GV                     TCGA-EL-A3GX 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3H3                     TCGA-EL-A3H4 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3H5                     TCGA-EL-A3H7 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3MW                     TCGA-EL-A3MX 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3MZ                     TCGA-EL-A3N2 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3T0                     TCGA-EL-A3T1 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3T2                     TCGA-EL-A3TB 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3ZH                     TCGA-EL-A3ZK 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3ZL                     TCGA-EL-A3ZM 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3ZN                     TCGA-EL-A3ZO 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3ZP                     TCGA-EL-A3ZS 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4JV                     TCGA-EL-A4JW 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4JX                     TCGA-EL-A4JZ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4K0                     TCGA-EL-A4K1 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4K2                     TCGA-EL-A4K4 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4K6                     TCGA-EL-A4K7 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4KD                     TCGA-EL-A4KG 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4KI                     TCGA-EM-A1CS 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A1CT                     TCGA-EM-A1CU 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A1CV                     TCGA-EM-A1CW 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A1YC                     TCGA-EM-A1YD 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A1YE                     TCGA-EM-A22I 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A22J                     TCGA-EM-A22K 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A22L                     TCGA-EM-A22M 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A22N                     TCGA-EM-A22O 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A22P                     TCGA-EM-A22Q 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2CK                     TCGA-EM-A2CN 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2CP                     TCGA-EM-A2CQ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2CT                     TCGA-EM-A2CU 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2OV                     TCGA-EM-A2OX 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2OY                     TCGA-EM-A2OZ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2P0                     TCGA-EM-A2P1 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2P2                     TCGA-EM-A3AJ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3AK                     TCGA-EM-A3AL 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3AN                     TCGA-EM-A3AO 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3AR                     TCGA-EM-A3FJ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3FK                     TCGA-EM-A3FM 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3FN                     TCGA-EM-A3FO 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3FP                     TCGA-EM-A3FQ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3FR                     TCGA-EM-A3O3 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3O8                     TCGA-EM-A3O9 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3OA                     TCGA-EM-A3OB 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3ST                     TCGA-EM-A3SU 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3SX                     TCGA-EM-A3SZ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A4FF                     TCGA-EM-A4FM 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A4FN                     TCGA-EM-A4FO 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A4FQ                     TCGA-EM-A4FR 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-EM-A4FV                     TCGA-EM-A4G1 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A25G                     TCGA-ET-A25I 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A25J                     TCGA-ET-A25K 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A25L                     TCGA-ET-A25M 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A25N                     TCGA-ET-A25O 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A25P                     TCGA-ET-A2MX 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A2MZ                     TCGA-ET-A2N0 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A2N1                     TCGA-ET-A2N4 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A39K                     TCGA-ET-A39L 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A39O                     TCGA-ET-A39P 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A39R                     TCGA-ET-A39S 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A39T                     TCGA-ET-A3BP 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A3BQ                     TCGA-ET-A3BS 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A3BT                     TCGA-ET-A3BU 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A3BX                     TCGA-ET-A3DQ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A3DR                     TCGA-ET-A3DS 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A3DT                     TCGA-ET-A3DU 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A3DV                     TCGA-ET-A3DW 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A40P                     TCGA-ET-A40Q 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A40R                     TCGA-ET-A40S 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-ET-A40T                     TCGA-ET-A4KN 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FE-A22Z                     TCGA-FE-A230 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FE-A231                     TCGA-FE-A232 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FE-A233                     TCGA-FE-A234 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FE-A235                     TCGA-FE-A236 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FE-A237                     TCGA-FE-A238 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FE-A239                     TCGA-FE-A23A 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FE-A3PB                     TCGA-FE-A3PC 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FE-A3PD                     TCGA-FK-A3S3 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FK-A3SB                     TCGA-FK-A3SE 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FK-A3SG                     TCGA-FK-A3SH 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FK-A4UB                     TCGA-FY-A2QD 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FY-A3I4                     TCGA-FY-A3I5 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FY-A3NM                     TCGA-FY-A3NN 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FY-A3ON                     TCGA-FY-A3R6 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FY-A3R7                     TCGA-FY-A3R9 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FY-A3TY                     TCGA-FY-A3W9 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FY-A3YR                     TCGA-FY-A40K 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FY-A40L                     TCGA-FY-A40M 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FY-A40N                     TCGA-FY-A4B3 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-FY-A4B4                     TCGA-GE-A2C6 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-H2-A26U                     TCGA-H2-A2K9 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-H2-A3RH                     TCGA-H2-A3RI 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-H2-A421                     TCGA-H2-A422 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-IM-A3EB                     TCGA-IM-A3ED 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-IM-A3U2                     TCGA-IM-A3U3 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-IM-A41Y                     TCGA-IM-A41Z 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-IM-A420                     TCGA-IM-A4EB 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-J8-A3O0                     TCGA-J8-A3O1 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-J8-A3O2                     TCGA-J8-A3YD 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-J8-A3YE                     TCGA-J8-A3YF 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-J8-A3YG                     TCGA-J8-A3YH 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-J8-A42S                     TCGA-J8-A4HY 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-KS-A41F                     TCGA-KS-A41I 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-KS-A41J                     TCGA-KS-A41L 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-KS-A4I1                     TCGA-KS-A4I3 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-KS-A4I5                     TCGA-KS-A4I7 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-KS-A4I9                     TCGA-KS-A4IB 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-KS-A4IC                     TCGA-KS-A4ID 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-L6-A4EP                     TCGA-L6-A4EQ 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-L6-A4EU                     TCGA-MK-A4N6 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-MK-A4N7                     TCGA-MK-A4N9 
"DEL PEAK 27(19P13.2) WILD-TYPE" "DEL PEAK 27(19P13.2) WILD-TYPE" 
                    TCGA-QD-A8IV 
"DEL PEAK 27(19P13.2) WILD-TYPE" 
D31V14, binary
                                cls
clus                               0   1
  DEL PEAK 27(19P13.2) MUTATED     2   5
  DEL PEAK 27(19P13.2) WILD-TYPE 223 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(19P13.2) MUTATED      2    5
  DEL PEAK 27(19P13.2) WILD-TYPE  223  259
            clus
vv           DEL PEAK 27(19P13.2) MUTATED DEL PEAK 27(19P13.2) WILD-TYPE
  MULTIFOCAL                            2                            223
  UNIFOCAL                              5                            259
[1] 2 2
[1] FALSE
D31V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(19P13.2) MUTATED                                  0     0
  DEL PEAK 27(19P13.2) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(19P13.2) MUTATED                           0     7
  DEL PEAK 27(19P13.2) WILD-TYPE                        27   322
D31V16, multiclass
                                  clus
vv                                 DEL PEAK 27(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       7
                                  clus
vv                                 DEL PEAK 27(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V17, binary
                                cls
clus                               0   1
  DEL PEAK 27(19P13.2) MUTATED     0   6
  DEL PEAK 27(19P13.2) WILD-TYPE  38 354
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(19P13.2) MUTATED      0    6
  DEL PEAK 27(19P13.2) WILD-TYPE   38  354
                        clus
vv                       DEL PEAK 27(19P13.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       DEL PEAK 27(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            354
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK 28(19P13.12) MUTATION ANALYSIS
D32V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(19P13.12) MUTATED     7   1
  DEL PEAK 28(19P13.12) WILD-TYPE 475  15
  DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE 
                              8                             490 
  DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE 
                              1                              15 
$`DEL PEAK 28(19P13.12) MUTATED`
TCGA-EL-A3D5 TCGA-EL-A3H2 TCGA-BJ-A0YZ TCGA-DE-A69J TCGA-ET-A39N TCGA-FY-A2QD 
       57.11        33.50        24.79        14.70       123.32         1.25 
TCGA-FY-A3WA TCGA-FY-A4B0 
       17.06        13.81 

$`DEL PEAK 28(19P13.12) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3GQ 
       39.95         7.66        45.53         4.18       139.86        50.24 
TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO TCGA-ET-A3BV 
      150.48        17.52       178.29        29.72        50.40        75.42 
TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET TCGA-MK-A84Z 
        1.05         1.68        17.23         2.60        21.83        23.93 
TCGA-4C-A93U TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
        4.24        13.78        49.78        16.34        14.73        41.33 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73        25.48        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       42.08        51.39        41.52        20.58         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       11.08        18.38        16.57        20.48        18.97        12.82 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       21.63        19.43        23.47        12.30        12.79        12.46 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 
       11.38        10.68        15.02        12.43        12.66        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        27.32        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       11.57        30.02        25.12        14.27         2.76        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        52.27 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        48.07       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.99        30.58        35.41 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42        34.36        37.74        43.96        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       33.93        37.48        36.46        35.11        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       33.53        35.18        39.95        36.92        31.04        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        36.33 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        35.87        40.96        36.99        20.22        30.61 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       40.70        18.97         9.60        35.67        36.43        23.44 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        30.12        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       63.19        52.44        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A432 
       31.50        31.04        31.30        30.84        25.45        30.61 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       31.27        31.33        14.96        39.88        33.50        31.00 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       30.15        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ 
       60.95       157.15        37.94        57.01       106.62        79.50 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR 
       98.53        69.57       108.36        64.87        49.51       115.10 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       136.01        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      139.99        49.32        43.36        49.71        83.57       139.00 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 
      108.66        57.63        52.50        29.65       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        91.17        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        72.69        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        61.02 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        44.52 
TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
        8.35        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33        12.53         9.24        27.02        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        98.20        28.24        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       87.62        77.82        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       71.08         4.11        22.03         0.92        48.10       116.09 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
       20.42        17.82         7.82        29.10        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08        23.31        21.63 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16        23.87        22.49        19.04        14.04 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       21.60        12.53        17.00        21.67        12.46        11.01 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 
       21.83        31.10         8.22        25.64        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.47         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 
       35.28        33.24        33.40        40.37         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       32.45        30.21        12.89         3.02 

  DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE 
                           1.25                            0.20 
  DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE 
                         123.32                          178.29 
  DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE 
                         20.925                          31.270 
[1] "1.2 - 123.3 (20.9)" "0.2 - 178.3 (31.3)"
[1] "hr=" "4.7"
D32V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 28(19P13.12) MUTATED         5        2         0        0         0
  DEL PEAK 28(19P13.12) WILD-TYPE     277       48       111        2        46
                                 vv
clus                              STAGE IVC
  DEL PEAK 28(19P13.12) MUTATED           0
  DEL PEAK 28(19P13.12) WILD-TYPE         6
D32V3, multiclass
           clus
vv          DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE
  STAGE I                               5                             277
  STAGE II                              2                              48
  STAGE III                             0                             111
  STAGE IV                              0                               2
  STAGE IVA                             0                              46
  STAGE IVC                             0                               6
[1] 6 2
[1] 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 28(19P13.12) MUTATED     3   3   2   0
  DEL PEAK 28(19P13.12) WILD-TYPE 139 162 165  23
D32V4, multiclass
    clus
vv   DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE
  T1                             3                             139
  T2                             3                             162
  T3                             2                             165
  T4                             0                              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"
D32V5, binary
                                 cls
clus                                0   1
  DEL PEAK 28(19P13.12) MUTATED     3   1
  DEL PEAK 28(19P13.12) WILD-TYPE 222 223
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(19P13.12) MUTATED      3    1
  DEL PEAK 28(19P13.12) WILD-TYPE  222  223
   clus
vv  DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE
  0                             3                             222
  1                             1                             223
[1] 2 2
[1] FALSE
D32V6, binary
                                 cls
clus                                0   1
  DEL PEAK 28(19P13.12) MUTATED     3   0
  DEL PEAK 28(19P13.12) WILD-TYPE 275   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(19P13.12) MUTATED      3    0
  DEL PEAK 28(19P13.12) WILD-TYPE  275    9
   clus
vv  DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE
  0                             3                             275
  1                             0                               9
[1] 2 2
[1] FALSE
D32V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(19P13.12) MUTATED     5   3
  DEL PEAK 28(19P13.12) WILD-TYPE 360 131
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(19P13.12) MUTATED      5    3
  DEL PEAK 28(19P13.12) WILD-TYPE  360  131
        clus
vv       DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE
  FEMALE                             5                             360
  MALE                               3                             131
[1] 2 2
[1] FALSE
D32V8, binary
                                 cls
clus                                0   1
  DEL PEAK 28(19P13.12) MUTATED     2   5
  DEL PEAK 28(19P13.12) WILD-TYPE 178 298
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(19P13.12) MUTATED      2    5
  DEL PEAK 28(19P13.12) WILD-TYPE  178  298
     clus
vv    DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE
  NO                              2                             178
  YES                             5                             298
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER, SPECIFY
  DEL PEAK 28(19P13.12) MUTATED                0
  DEL PEAK 28(19P13.12) WILD-TYPE              7
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 28(19P13.12) MUTATED                                               7
  DEL PEAK 28(19P13.12) WILD-TYPE                                           349
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 28(19P13.12) MUTATED                                                                        1
  DEL PEAK 28(19P13.12) WILD-TYPE                                                                     99
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 28(19P13.12) MUTATED                                                                     0
  DEL PEAK 28(19P13.12) WILD-TYPE                                                                  36
D32V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 28(19P13.12) MUTATED
  OTHER, SPECIFY                                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      7
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                0
                                                                        clus
vv                                                                       DEL PEAK 28(19P13.12) WILD-TYPE
  OTHER, SPECIFY                                                                                       7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, binary
                                 cls
clus                                0   1
  DEL PEAK 28(19P13.12) MUTATED     5   2
  DEL PEAK 28(19P13.12) WILD-TYPE 415  15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(19P13.12) MUTATED      5    2
  DEL PEAK 28(19P13.12) WILD-TYPE  415   15
     clus
vv    DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE
  NO                              5                             415
  YES                             2                              15
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 28(19P13.12) MUTATED              1                       0    7
  DEL PEAK 28(19P13.12) WILD-TYPE          131                      18  323
                                 vv
clus                              VERY ADVANCED (T4B)
  DEL PEAK 28(19P13.12) MUTATED                     0
  DEL PEAK 28(19P13.12) WILD-TYPE                   1
D32V11, multiclass
                         clus
vv                        DEL PEAK 28(19P13.12) MUTATED
  MINIMAL (T3)                                        1
  MODERATE/ADVANCED (T4A)                             0
  NONE                                                7
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        DEL PEAK 28(19P13.12) WILD-TYPE
  MINIMAL (T3)                                        131
  MODERATE/ADVANCED (T4A)                              18
  NONE                                                323
  VERY ADVANCED (T4B)                                   1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(19P13.12) MUTATED     5   2   0   0
  DEL PEAK 28(19P13.12) WILD-TYPE 378  49   4  30
D32V12, multiclass
    clus
vv   DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE
  R0                             5                             378
  R1                             2                              49
  R2                             0                               4
  RX                             0                              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"
D32V13, continuous
[1] "Remove cluster labels:"        "DEL PEAK 28(19P13.12) MUTATED"
clus
  DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE 
                              2                             384 
                     TCGA-BJ-A290                      TCGA-BJ-A291 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A45K                      TCGA-CE-A13K 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DE-A0XZ                      TCGA-DJ-A2PR 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3UU                      TCGA-DJ-A3UW 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3V4                      TCGA-DJ-A3VI 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3VK                      TCGA-E3-A3E5 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3CR                      TCGA-EL-A3CS 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3CY                      TCGA-EL-A3D0 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3GQ                      TCGA-EL-A3H8 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3AQ                      TCGA-ET-A3BO 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A3BV                      TCGA-J8-A3NZ 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-J8-A4HW                      TCGA-4C-A93U 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A0Z0                      TCGA-BJ-A0Z3 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A0Z5                      TCGA-BJ-A0Z9 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A0ZA                      TCGA-BJ-A0ZB 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A0ZH                      TCGA-BJ-A0ZJ 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A18Y                      TCGA-BJ-A18Z 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A190                      TCGA-BJ-A191 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A28R                      TCGA-BJ-A28T 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A28W                      TCGA-BJ-A28X 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A28Z                      TCGA-BJ-A2N8 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A2N9                      TCGA-BJ-A2NA 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A3EZ                      TCGA-BJ-A3PR 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A3PU                      TCGA-BJ-A45C 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A45D                      TCGA-BJ-A45E 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A45G                      TCGA-BJ-A45I 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A45J                      TCGA-BJ-A4O8 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A4O9                      TCGA-CE-A3MD 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-CE-A483                      TCGA-CE-A484 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-CE-A485                      TCGA-DE-A0Y2 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DE-A0Y3                      TCGA-DE-A3KN 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DE-A4M8                      TCGA-DE-A4MA 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DE-A4MB                      TCGA-DE-A4MC 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DE-A4MD                      TCGA-DE-A69K 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DE-A7U5                      TCGA-DJ-A13M 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A13O                      TCGA-DJ-A13R 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A13T                      TCGA-DJ-A13V 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A13W                      TCGA-DJ-A13X 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A1QG                      TCGA-DJ-A1QH 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A1QM                      TCGA-DJ-A2PO 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2PP                      TCGA-DJ-A2PQ 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2PS                      TCGA-DJ-A2PT 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2PU                      TCGA-DJ-A2PV 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2PW                      TCGA-DJ-A2PX 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2PY                      TCGA-DJ-A2PZ 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2Q0                      TCGA-DJ-A2Q1 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2Q2                      TCGA-DJ-A2Q3 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2Q4                      TCGA-DJ-A2Q5 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2Q6                      TCGA-DJ-A2Q7 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2Q8                      TCGA-DJ-A2Q9 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2QA                      TCGA-DJ-A2QB 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3UK                      TCGA-DJ-A3UM 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3UN                      TCGA-DJ-A3UO 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3UP                      TCGA-DJ-A3UQ 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3UR                      TCGA-DJ-A3UX 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3UZ                      TCGA-DJ-A3V0 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3V2                      TCGA-DJ-A3V3 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3V5                      TCGA-DJ-A3V7 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3V8                      TCGA-DJ-A3V9 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3VA                      TCGA-DJ-A3VB 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3VD                      TCGA-DJ-A3VF 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3VG                      TCGA-DJ-A3VJ 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3VL                      TCGA-DJ-A4UL 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A4UP                      TCGA-DJ-A4UQ 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A4UR                      TCGA-DJ-A4UW 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A4V2                      TCGA-DJ-A4V5 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-DO-A1K0                      TCGA-DO-A2HM 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-E3-A3DY                      TCGA-E3-A3DZ 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-E3-A3E0                      TCGA-E3-A3E1 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-E3-A3E2                      TCGA-E3-A3E3 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-E8-A242                      TCGA-E8-A2EA 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-E8-A414                      TCGA-E8-A415 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-E8-A417                      TCGA-E8-A419 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-E8-A433                      TCGA-E8-A436 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-E8-A438                      TCGA-E8-A44K 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3CM                      TCGA-EL-A3CN 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3CO                      TCGA-EL-A3CT 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3CU                      TCGA-EL-A3CV 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3CW                      TCGA-EL-A3CX 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3CZ                      TCGA-EL-A3D1 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3D4                      TCGA-EL-A3D6 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3GO                      TCGA-EL-A3GP 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3GS                      TCGA-EL-A3GU 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3GV                      TCGA-EL-A3GX 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3H3                      TCGA-EL-A3H4 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3H5                      TCGA-EL-A3H7 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3MW                      TCGA-EL-A3MX 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3MZ                      TCGA-EL-A3N2 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3T0                      TCGA-EL-A3T1 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3T2                      TCGA-EL-A3TB 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3ZH                      TCGA-EL-A3ZK 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3ZL                      TCGA-EL-A3ZM 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3ZN                      TCGA-EL-A3ZO 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3ZP                      TCGA-EL-A3ZS 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4JV                      TCGA-EL-A4JW 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4JX                      TCGA-EL-A4JZ 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4K0                      TCGA-EL-A4K1 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4K2                      TCGA-EL-A4K4 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4K6                      TCGA-EL-A4K7 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4KD                      TCGA-EL-A4KG 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4KI                      TCGA-EM-A1CS 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A1CT                      TCGA-EM-A1CU 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A1CV                      TCGA-EM-A1CW 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A1YC                      TCGA-EM-A1YD 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A1YE                      TCGA-EM-A22I 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A22J                      TCGA-EM-A22K 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A22L                      TCGA-EM-A22M 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A22N                      TCGA-EM-A22O 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A22P                      TCGA-EM-A22Q 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2CK                      TCGA-EM-A2CN 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2CP                      TCGA-EM-A2CQ 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2CT                      TCGA-EM-A2CU 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2OV                      TCGA-EM-A2OX 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2OY                      TCGA-EM-A2OZ 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2P0                      TCGA-EM-A2P1 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2P2                      TCGA-EM-A3AJ 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3AK                      TCGA-EM-A3AL 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3AN                      TCGA-EM-A3AO 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3AR                      TCGA-EM-A3FJ 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3FK                      TCGA-EM-A3FM 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3FN                      TCGA-EM-A3FO 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3FP                      TCGA-EM-A3FQ 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3FR                      TCGA-EM-A3O3 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3O8                      TCGA-EM-A3O9 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3OA                      TCGA-EM-A3OB 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3ST                      TCGA-EM-A3SU 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3SX                      TCGA-EM-A3SZ 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A4FF                      TCGA-EM-A4FM 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A4FN                      TCGA-EM-A4FO 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A4FQ                      TCGA-EM-A4FR 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-EM-A4FV                      TCGA-EM-A4G1 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A25G                      TCGA-ET-A25I 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A25J                      TCGA-ET-A25K 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A25L                      TCGA-ET-A25M 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A25N                      TCGA-ET-A25O 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A25P                      TCGA-ET-A2MX 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A2MZ                      TCGA-ET-A2N0 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A2N1                      TCGA-ET-A2N4 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A39K                      TCGA-ET-A39L 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A39O                      TCGA-ET-A39P 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A39R                      TCGA-ET-A39S 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A39T                      TCGA-ET-A3BP 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A3BQ                      TCGA-ET-A3BS 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A3BT                      TCGA-ET-A3BU 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A3BX                      TCGA-ET-A3DQ 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A3DR                      TCGA-ET-A3DS 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A3DT                      TCGA-ET-A3DU 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A3DV                      TCGA-ET-A3DW 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A40P                      TCGA-ET-A40Q 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A40R                      TCGA-ET-A40S 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-ET-A40T                      TCGA-ET-A4KN 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FE-A22Z                      TCGA-FE-A230 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FE-A231                      TCGA-FE-A232 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FE-A233                      TCGA-FE-A234 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FE-A235                      TCGA-FE-A236 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FE-A237                      TCGA-FE-A238 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FE-A239                      TCGA-FE-A23A 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FE-A3PB                      TCGA-FE-A3PC 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FE-A3PD                      TCGA-FK-A3S3 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FK-A3SB                      TCGA-FK-A3SE 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FK-A3SG                      TCGA-FK-A3SH 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FK-A4UB                      TCGA-FY-A3I4 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FY-A3I5                      TCGA-FY-A3NM 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FY-A3NN                      TCGA-FY-A3ON 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FY-A3R6                      TCGA-FY-A3R7 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FY-A3R9                      TCGA-FY-A3TY 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FY-A3W9                      TCGA-FY-A3YR 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FY-A40K                      TCGA-FY-A40L 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FY-A40M                      TCGA-FY-A40N 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-FY-A4B3                      TCGA-FY-A4B4 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-GE-A2C6                      TCGA-H2-A26U 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-H2-A2K9                      TCGA-H2-A3RH 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-H2-A3RI                      TCGA-H2-A421 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-H2-A422                      TCGA-IM-A3EB 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-IM-A3ED                      TCGA-IM-A3U2 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-IM-A3U3                      TCGA-IM-A41Y 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-IM-A41Z                      TCGA-IM-A420 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-IM-A4EB                      TCGA-J8-A3O0 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-J8-A3O1                      TCGA-J8-A3O2 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-J8-A3YD                      TCGA-J8-A3YE 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-J8-A3YF                      TCGA-J8-A3YG 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-J8-A3YH                      TCGA-J8-A42S 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-J8-A4HY                      TCGA-KS-A41F 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-KS-A41I                      TCGA-KS-A41J 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-KS-A41L                      TCGA-KS-A4I1 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-KS-A4I3                      TCGA-KS-A4I5 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-KS-A4I7                      TCGA-KS-A4I9 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-KS-A4IB                      TCGA-KS-A4IC 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-KS-A4ID                      TCGA-L6-A4EP 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-L6-A4EQ                      TCGA-L6-A4EU 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-MK-A4N6                      TCGA-MK-A4N7 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
                     TCGA-MK-A4N9                      TCGA-QD-A8IV 
"DEL PEAK 28(19P13.12) WILD-TYPE" "DEL PEAK 28(19P13.12) WILD-TYPE" 
D32V14, binary
                                 cls
clus                                0   1
  DEL PEAK 28(19P13.12) MUTATED     4   4
  DEL PEAK 28(19P13.12) WILD-TYPE 221 260
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(19P13.12) MUTATED      4    4
  DEL PEAK 28(19P13.12) WILD-TYPE  221  260
            clus
vv           DEL PEAK 28(19P13.12) MUTATED DEL PEAK 28(19P13.12) WILD-TYPE
  MULTIFOCAL                             4                             221
  UNIFOCAL                               4                             260
[1] 2 2
[1] FALSE
D32V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(19P13.12) MUTATED                                  0     0
  DEL PEAK 28(19P13.12) WILD-TYPE                                1    52
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(19P13.12) MUTATED                           2     6
  DEL PEAK 28(19P13.12) WILD-TYPE                        25   323
D32V16, multiclass
                                  clus
vv                                 DEL PEAK 28(19P13.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    2
  WHITE                                                        6
                                  clus
vv                                 DEL PEAK 28(19P13.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         52
  BLACK OR AFRICAN AMERICAN                                     25
  WHITE                                                        323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V17, binary
                                 cls
clus                                0   1
  DEL PEAK 28(19P13.12) MUTATED     0   8
  DEL PEAK 28(19P13.12) WILD-TYPE  38 352
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(19P13.12) MUTATED      0    8
  DEL PEAK 28(19P13.12) WILD-TYPE   38  352
                        clus
vv                       DEL PEAK 28(19P13.12) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                             8
                        clus
vv                       DEL PEAK 28(19P13.12) WILD-TYPE
  HISPANIC OR LATINO                                  38
  NOT HISPANIC OR LATINO                             352
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK 30(21Q21.1) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(21Q21.1) MUTATED     9   0
  DEL PEAK 30(21Q21.1) WILD-TYPE 473  16
  DEL PEAK 30(21Q21.1) MUTATED DEL PEAK 30(21Q21.1) WILD-TYPE 
                             9                            489 
  DEL PEAK 30(21Q21.1) MUTATED DEL PEAK 30(21Q21.1) WILD-TYPE 
                             0                             16 
$`DEL PEAK 30(21Q21.1) MUTATED`
TCGA-J8-A4HW TCGA-BJ-A190 TCGA-CE-A485 TCGA-DJ-A2Q0 TCGA-E8-A432 TCGA-EM-A22P 
        2.60        20.58        12.66        34.36        30.61        41.29 
TCGA-EM-A2OY TCGA-ET-A25L TCGA-FY-A3I5 
       32.32        56.58         7.82 

$`DEL PEAK 30(21Q21.1) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-L6-A4ET 
       50.40        75.42         1.05         1.68        17.23        21.83 
TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       23.93         4.24        24.79        13.78        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 
       25.48        15.12        42.08        51.39        41.52         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.97        11.08        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       12.82        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD 
       15.45        21.63        19.43        23.47        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-DE-A0Y2 
       12.46        11.38        10.68        15.02        12.43        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        27.32        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       52.27        43.17        52.37         8.32        48.07       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.99        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       35.41        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
       28.96         8.78         8.42        37.74        43.96        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       33.93        37.48        36.46        35.11        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       33.53        35.18        39.95        36.92        31.04        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        36.33 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        35.87        40.96        36.99        20.22        30.61 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       40.70        18.97         9.60        35.67        36.43        23.44 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        30.12        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       63.19        52.44        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 TCGA-E8-A433 
       31.50        31.04        31.30        30.84        25.45        31.27 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       31.33        14.96        39.88        33.50        31.00        30.15 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT 
       31.66        26.73       155.54        97.74       158.83        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 
      157.15        37.94        57.01       106.62        79.50        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS 
       69.57       108.36        64.87        49.51       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      136.01        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW 
       49.32        43.36        49.71        83.57       139.00       108.66 
TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       57.63        52.50        29.65       142.52       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        91.17        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        72.69        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        61.02        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       57.01        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       14.53        10.65        44.19        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        40.34        19.73        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        33.07        44.52         8.35        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        27.02        38.66        38.86        29.95        29.85 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M 
       13.68        81.93        81.70        77.56        70.42        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       33.24       106.09       107.41       108.46        84.89       123.32 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW 
       79.10        76.64         5.79        87.62        77.82        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77       112.80        39.95        33.63        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE 
       85.15        85.68        78.77        71.08         4.11        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       29.10        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08        23.31        21.63        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 
       23.87        22.49        19.04        13.81        14.04        21.60 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46        11.01        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
       31.10         8.22        25.64        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.24        33.40        40.37         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       30.21        12.89         3.02 

  DEL PEAK 30(21Q21.1) MUTATED DEL PEAK 30(21Q21.1) WILD-TYPE 
                           2.6                            0.2 
  DEL PEAK 30(21Q21.1) MUTATED DEL PEAK 30(21Q21.1) WILD-TYPE 
                         56.58                         178.29 
  DEL PEAK 30(21Q21.1) MUTATED DEL PEAK 30(21Q21.1) WILD-TYPE 
                         30.61                          31.27 
[1] "2.6 - 56.6 (30.6)"  "0.2 - 178.3 (31.3)"
[1] "hr="     "9100000"
D33V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 30(21Q21.1) MUTATED         1        4         2        0         2
  DEL PEAK 30(21Q21.1) WILD-TYPE     281       46       109        2        44
                                vv
clus                             STAGE IVC
  DEL PEAK 30(21Q21.1) MUTATED           0
  DEL PEAK 30(21Q21.1) WILD-TYPE         6
D33V3, multiclass
           clus
vv          DEL PEAK 30(21Q21.1) MUTATED DEL PEAK 30(21Q21.1) WILD-TYPE
  STAGE I                              1                            281
  STAGE II                             4                             46
  STAGE III                            2                            109
  STAGE IV                             0                              2
  STAGE IVA                            2                             44
  STAGE IVC                            0                              6
[1] 6 2
[1] 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 30(21Q21.1) MUTATED     1   6   2   0
  DEL PEAK 30(21Q21.1) WILD-TYPE 141 159 165  23
D33V4, multiclass
    clus
vv   DEL PEAK 30(21Q21.1) MUTATED DEL PEAK 30(21Q21.1) WILD-TYPE
  T1                            1                            141
  T2                            6                            159
  T3                            2                            165
  T4                            0                             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"
D33V5, binary
                                cls
clus                               0   1
  DEL PEAK 30(21Q21.1) MUTATED     5   4
  DEL PEAK 30(21Q21.1) WILD-TYPE 220 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(21Q21.1) MUTATED      5    4
  DEL PEAK 30(21Q21.1) WILD-TYPE  220  220
   clus
vv  DEL PEAK 30(21Q21.1) MUTATED DEL PEAK 30(21Q21.1) WILD-TYPE
  0                            5                            220
  1                            4                            220
[1] 2 2
[1] FALSE
D33V6, binary
                                cls
clus                               0   1
  DEL PEAK 30(21Q21.1) MUTATED     4   0
  DEL PEAK 30(21Q21.1) WILD-TYPE 274   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(21Q21.1) MUTATED      4    0
  DEL PEAK 30(21Q21.1) WILD-TYPE  274    9
   clus
vv  DEL PEAK 30(21Q21.1) MUTATED DEL PEAK 30(21Q21.1) WILD-TYPE
  0                            4                            274
  1                            0                              9
[1] 2 2
[1] FALSE
D33V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(21Q21.1) MUTATED     6   3
  DEL PEAK 30(21Q21.1) WILD-TYPE 359 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(21Q21.1) MUTATED      6    3
  DEL PEAK 30(21Q21.1) WILD-TYPE  359  131
        clus
vv       DEL PEAK 30(21Q21.1) MUTATED DEL PEAK 30(21Q21.1) WILD-TYPE
  FEMALE                            6                            359
  MALE                              3                            131
[1] 2 2
[1] FALSE
D33V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(21Q21.1) MUTATED     3   5
  DEL PEAK 30(21Q21.1) WILD-TYPE 177 298
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(21Q21.1) MUTATED      3    5
  DEL PEAK 30(21Q21.1) WILD-TYPE  177  298
     clus
vv    DEL PEAK 30(21Q21.1) MUTATED DEL PEAK 30(21Q21.1) WILD-TYPE
  NO                             3                            177
  YES                            5                            298
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER, SPECIFY
  DEL PEAK 30(21Q21.1) MUTATED                0
  DEL PEAK 30(21Q21.1) WILD-TYPE              7
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 30(21Q21.1) MUTATED                                               6
  DEL PEAK 30(21Q21.1) WILD-TYPE                                           350
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 30(21Q21.1) MUTATED                                                                        2
  DEL PEAK 30(21Q21.1) WILD-TYPE                                                                     98
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 30(21Q21.1) MUTATED                                                                     1
  DEL PEAK 30(21Q21.1) WILD-TYPE                                                                  35
D33V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 30(21Q21.1) MUTATED
  OTHER, SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               1
                                                                        clus
vv                                                                       DEL PEAK 30(21Q21.1) WILD-TYPE
  OTHER, SPECIFY                                                                                      7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, binary
                                cls
clus                               0   1
  DEL PEAK 30(21Q21.1) MUTATED     8   0
  DEL PEAK 30(21Q21.1) WILD-TYPE 412  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(21Q21.1) MUTATED      8    0
  DEL PEAK 30(21Q21.1) WILD-TYPE  412   17
     clus
vv    DEL PEAK 30(21Q21.1) MUTATED DEL PEAK 30(21Q21.1) WILD-TYPE
  NO                             8                            412
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 30(21Q21.1) MUTATED              1                       0    8
  DEL PEAK 30(21Q21.1) WILD-TYPE          131                      18  322
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 30(21Q21.1) MUTATED                     0
  DEL PEAK 30(21Q21.1) WILD-TYPE                   1
D33V11, multiclass
                         clus
vv                        DEL PEAK 30(21Q21.1) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               8
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 30(21Q21.1) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               322
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(21Q21.1) MUTATED     7   2   0   0
  DEL PEAK 30(21Q21.1) WILD-TYPE 376  49   4  30
D33V12, multiclass
    clus
vv   DEL PEAK 30(21Q21.1) MUTATED DEL PEAK 30(21Q21.1) WILD-TYPE
  R0                            7                            376
  R1                            2                             49
  R2                            0                              4
  RX                            0                             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"
D33V13, continuous
D33V14, binary
                                cls
clus                               0   1
  DEL PEAK 30(21Q21.1) MUTATED     6   3
  DEL PEAK 30(21Q21.1) WILD-TYPE 219 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(21Q21.1) MUTATED      6    3
  DEL PEAK 30(21Q21.1) WILD-TYPE  219  261
            clus
vv           DEL PEAK 30(21Q21.1) MUTATED DEL PEAK 30(21Q21.1) WILD-TYPE
  MULTIFOCAL                            6                            219
  UNIFOCAL                              3                            261
[1] 2 2
[1] FALSE
D33V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(21Q21.1) MUTATED                                  0     2
  DEL PEAK 30(21Q21.1) WILD-TYPE                                1    50
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(21Q21.1) MUTATED                           0     5
  DEL PEAK 30(21Q21.1) WILD-TYPE                        27   324
D33V16, multiclass
                                  clus
vv                                 DEL PEAK 30(21Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       5
                                  clus
vv                                 DEL PEAK 30(21Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        50
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V17, binary
                                cls
clus                               0   1
  DEL PEAK 30(21Q21.1) MUTATED     0   6
  DEL PEAK 30(21Q21.1) WILD-TYPE  38 354
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(21Q21.1) MUTATED      0    6
  DEL PEAK 30(21Q21.1) WILD-TYPE   38  354
                        clus
vv                       DEL PEAK 30(21Q21.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       DEL PEAK 30(21Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            354
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 31(22Q13.1) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(22Q13.1) MUTATED    88   1
  DEL PEAK 31(22Q13.1) WILD-TYPE 394  15
  DEL PEAK 31(22Q13.1) MUTATED DEL PEAK 31(22Q13.1) WILD-TYPE 
                            89                            409 
  DEL PEAK 31(22Q13.1) MUTATED DEL PEAK 31(22Q13.1) WILD-TYPE 
                             1                             15 
$`DEL PEAK 31(22Q13.1) MUTATED`
TCGA-DE-A0XZ TCGA-DJ-A3VK TCGA-E3-A3E5 TCGA-EL-A3D0 TCGA-MK-A84Z TCGA-4C-A93U 
       35.84        24.76        39.95       139.86        23.93         4.24 
TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A2P4 
       49.78        14.73        15.12        51.39        20.58        12.82 
TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A4M8 TCGA-DJ-A13M 
       23.31        10.88         3.45        12.43        18.54        48.79 
TCGA-DJ-A13T TCGA-DJ-A1QG TCGA-DJ-A1QN TCGA-DJ-A2PS TCGA-DJ-A2Q0 TCGA-DJ-A2Q7 
       56.19        44.98        42.58        26.20        34.36        35.11 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       33.53        35.18        36.92        32.42        31.46        16.41 
TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E8-A432 TCGA-E8-A434 TCGA-EL-A3CL 
       27.62        34.78        47.21        30.61        31.33        31.66 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3GP TCGA-EL-A3GW TCGA-EL-A3T2 TCGA-EL-A3ZL 
       98.53        69.57        49.51        50.20        32.48        62.30 
TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4JZ TCGA-EL-A4K6 TCGA-EL-A4K9 TCGA-EL-A4KI 
       60.16        57.47        61.02        44.15        47.84        23.90 
TCGA-EM-A1CS TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ 
       26.86        15.75        10.45        14.53        41.29        47.57 
TCGA-EM-A2OY TCGA-EM-A3AP TCGA-EM-A3FO TCGA-EM-A3O9 TCGA-EM-A3SX TCGA-EM-A3SZ 
       32.32         8.35        17.49         9.24        29.85        12.79 
TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FU TCGA-ET-A25L TCGA-ET-A25O TCGA-ET-A2N4 
       26.37        21.53        60.49        56.58        65.29         2.66 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A3BP TCGA-ET-A3DS TCGA-ET-A40P 
      108.46        84.89       123.32        79.10        66.84        43.99 
TCGA-ET-A40T TCGA-FE-A237 TCGA-FE-A3PB TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A3WA 
       37.48       112.80        85.15        16.27        21.63        17.06 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-IM-A3U3 TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD 
       21.60        12.53        16.90        31.10        43.17        31.82 
TCGA-J8-A3YH TCGA-KS-A41I TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-QD-A8IV 
        5.75        15.98        32.45        84.72        12.89 

$`DEL PEAK 31(22Q13.1) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DJ-A13L TCGA-DJ-A2PR 
       30.21        22.88        23.18        12.66         9.96        27.45 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-EL-A3CR TCGA-EL-A3CS 
       23.44        59.57        42.54         3.12         7.66        45.53 
TCGA-EL-A3CY TCGA-EL-A3D5 TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY 
        4.18        57.11        50.24        33.50       150.48        17.52 
TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V 
      178.29        29.72        50.40        75.42         1.05         1.68 
TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z3 
       17.23         2.60        21.83        24.79        13.78        16.34 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZJ TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       42.08        41.52         4.83        44.35        42.15        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 
       35.54        32.45        11.31        30.97        11.08        18.38 
TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       16.57        20.48        18.97        16.01        13.94        36.39 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45E TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       18.64         7.99        21.01        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       21.63        19.43        23.47        12.30        12.79        12.46 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       11.38        10.68        15.02        12.66        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       37.64        27.32        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13O TCGA-DJ-A13P 
       25.12        14.70        14.27         2.76        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
       18.58         8.71        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
       48.07       135.91        30.61        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
        6.02        47.41        17.56        10.09         7.99        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       35.41        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42        37.74        43.96        40.24        33.93 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QC TCGA-DJ-A3UM 
       37.48        36.46        39.09        35.90        39.95        31.04 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UP 
        9.60        35.67        36.43        23.44        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       33.04        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3E0 
       35.38        54.90        21.53         2.33        92.55        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       80.52        63.19        52.44        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 
       29.98        31.50        31.04        31.30        30.84        25.45 
TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       31.27        14.96        39.88        33.50        31.00        30.15 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D6 TCGA-EL-A3GO 
       37.94        57.01       106.62        79.50       108.36        64.87 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY 
      115.10        65.39       136.01        50.37       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      139.99        49.32        43.36        49.71        83.57       139.00 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 
      108.66        57.63        52.50        29.65       142.52       129.57 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZM TCGA-EL-A3ZN 
       82.82        89.56        91.17        51.78        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW 
       72.69        65.49        61.22         7.07        59.44        34.72 
TCGA-EL-A4JX TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 
       45.96        31.04        34.39        30.51        53.36        41.13 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       43.59        24.30        27.06        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        78.61        57.01        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CK 
       14.73        14.50        10.65        44.19        14.24        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        40.34        19.73        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       14.14        33.07        44.52        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       47.38        21.01        12.07        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       14.50        15.06         7.33        12.53        27.02        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SY TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       38.86        29.95        13.51        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        5.33        26.37        22.45        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25P 
       81.70        77.56        70.42        60.20        63.39        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39O 
       83.34        80.88        33.24       106.09       107.41       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BQ 
       95.34        94.13        55.10        98.20        28.24        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       94.59        84.85        80.58        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A4KN TCGA-ET-A4KQ 
       24.72        46.26        44.38        40.21        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
      117.40        66.77        39.95        33.63        81.83       106.36 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10       116.09         1.25        20.42        17.82         7.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       29.10        19.56        13.91        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       23.31        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       13.81        14.04        17.00        21.67        12.46        11.01 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A41Y 
       20.05        18.61        48.92        47.41        18.51        21.83 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF 
        8.22        25.64        27.19        11.24        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A41L 
       22.29         2.47         0.20       143.57        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID 
       26.70        43.69        18.64        87.39        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-E8-A418 
        3.02 

  DEL PEAK 31(22Q13.1) MUTATED DEL PEAK 31(22Q13.1) WILD-TYPE 
                          2.66                           0.20 
  DEL PEAK 31(22Q13.1) MUTATED DEL PEAK 31(22Q13.1) WILD-TYPE 
                        139.86                         178.29 
  DEL PEAK 31(22Q13.1) MUTATED DEL PEAK 31(22Q13.1) WILD-TYPE 
                         32.42                          30.97 
[1] "2.7 - 139.9 (32.4)" "0.2 - 178.3 (31.0)"
[1] "hr=" "3.2"
D34V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 31(22Q13.1) MUTATED        49       10        18        1        10
  DEL PEAK 31(22Q13.1) WILD-TYPE     233       40        93        1        36
                                vv
clus                             STAGE IVC
  DEL PEAK 31(22Q13.1) MUTATED           1
  DEL PEAK 31(22Q13.1) WILD-TYPE         5
D34V3, multiclass
           clus
vv          DEL PEAK 31(22Q13.1) MUTATED DEL PEAK 31(22Q13.1) WILD-TYPE
  STAGE I                             49                            233
  STAGE II                            10                             40
  STAGE III                           18                             93
  STAGE IV                             1                              1
  STAGE IVA                           10                             36
  STAGE IVC                            1                              5
[1] 6 2
[1] 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 31(22Q13.1) MUTATED    24  33  28   4
  DEL PEAK 31(22Q13.1) WILD-TYPE 118 132 139  19
D34V4, multiclass
    clus
vv   DEL PEAK 31(22Q13.1) MUTATED DEL PEAK 31(22Q13.1) WILD-TYPE
  T1                           24                            118
  T2                           33                            132
  T3                           28                            139
  T4                            4                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V5, binary
                                cls
clus                               0   1
  DEL PEAK 31(22Q13.1) MUTATED    45  36
  DEL PEAK 31(22Q13.1) WILD-TYPE 180 188
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q13.1) MUTATED     45   36
  DEL PEAK 31(22Q13.1) WILD-TYPE  180  188
   clus
vv  DEL PEAK 31(22Q13.1) MUTATED DEL PEAK 31(22Q13.1) WILD-TYPE
  0                           45                            180
  1                           36                            188
[1] 2 2
[1] FALSE
D34V6, binary
                                cls
clus                               0   1
  DEL PEAK 31(22Q13.1) MUTATED    45   2
  DEL PEAK 31(22Q13.1) WILD-TYPE 233   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q13.1) MUTATED     45    2
  DEL PEAK 31(22Q13.1) WILD-TYPE  233    7
   clus
vv  DEL PEAK 31(22Q13.1) MUTATED DEL PEAK 31(22Q13.1) WILD-TYPE
  0                           45                            233
  1                            2                              7
[1] 2 2
[1] FALSE
D34V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(22Q13.1) MUTATED    62  27
  DEL PEAK 31(22Q13.1) WILD-TYPE 303 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q13.1) MUTATED     62   27
  DEL PEAK 31(22Q13.1) WILD-TYPE  303  107
        clus
vv       DEL PEAK 31(22Q13.1) MUTATED DEL PEAK 31(22Q13.1) WILD-TYPE
  FEMALE                           62                            303
  MALE                             27                            107
[1] 2 2
[1] FALSE
D34V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(22Q13.1) MUTATED    25  63
  DEL PEAK 31(22Q13.1) WILD-TYPE 155 240
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q13.1) MUTATED     25   63
  DEL PEAK 31(22Q13.1) WILD-TYPE  155  240
     clus
vv    DEL PEAK 31(22Q13.1) MUTATED DEL PEAK 31(22Q13.1) WILD-TYPE
  NO                            25                            155
  YES                           63                            240
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER, SPECIFY
  DEL PEAK 31(22Q13.1) MUTATED                1
  DEL PEAK 31(22Q13.1) WILD-TYPE              6
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 31(22Q13.1) MUTATED                                              61
  DEL PEAK 31(22Q13.1) WILD-TYPE                                           295
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 31(22Q13.1) MUTATED                                                                       24
  DEL PEAK 31(22Q13.1) WILD-TYPE                                                                     76
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 31(22Q13.1) MUTATED                                                                     3
  DEL PEAK 31(22Q13.1) WILD-TYPE                                                                  33
D34V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 31(22Q13.1) MUTATED
  OTHER, SPECIFY                                                                                    1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    61
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           24
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               3
                                                                        clus
vv                                                                       DEL PEAK 31(22Q13.1) WILD-TYPE
  OTHER, SPECIFY                                                                                      6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     295
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             76
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, binary
                                cls
clus                               0   1
  DEL PEAK 31(22Q13.1) MUTATED    79   1
  DEL PEAK 31(22Q13.1) WILD-TYPE 341  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q13.1) MUTATED     79    1
  DEL PEAK 31(22Q13.1) WILD-TYPE  341   16
     clus
vv    DEL PEAK 31(22Q13.1) MUTATED DEL PEAK 31(22Q13.1) WILD-TYPE
  NO                            79                            341
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 31(22Q13.1) MUTATED             19                       2   63
  DEL PEAK 31(22Q13.1) WILD-TYPE          113                      16  267
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 31(22Q13.1) MUTATED                     0
  DEL PEAK 31(22Q13.1) WILD-TYPE                   1
D34V11, multiclass
                         clus
vv                        DEL PEAK 31(22Q13.1) MUTATED
  MINIMAL (T3)                                      19
  MODERATE/ADVANCED (T4A)                            2
  NONE                                              63
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 31(22Q13.1) WILD-TYPE
  MINIMAL (T3)                                       113
  MODERATE/ADVANCED (T4A)                             16
  NONE                                               267
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(22Q13.1) MUTATED    68   6   1   8
  DEL PEAK 31(22Q13.1) WILD-TYPE 315  45   3  22
D34V12, multiclass
    clus
vv   DEL PEAK 31(22Q13.1) MUTATED DEL PEAK 31(22Q13.1) WILD-TYPE
  R0                           68                            315
  R1                            6                             45
  R2                            1                              3
  RX                            8                             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, continuous
D34V14, binary
                                cls
clus                               0   1
  DEL PEAK 31(22Q13.1) MUTATED    45  42
  DEL PEAK 31(22Q13.1) WILD-TYPE 180 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q13.1) MUTATED     45   42
  DEL PEAK 31(22Q13.1) WILD-TYPE  180  222
            clus
vv           DEL PEAK 31(22Q13.1) MUTATED DEL PEAK 31(22Q13.1) WILD-TYPE
  MULTIFOCAL                           45                            180
  UNIFOCAL                             42                            222
[1] 2 2
[1] FALSE
D34V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(22Q13.1) MUTATED                                  0    11
  DEL PEAK 31(22Q13.1) WILD-TYPE                                1    41
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(22Q13.1) MUTATED                           7    54
  DEL PEAK 31(22Q13.1) WILD-TYPE                        20   275
D34V16, multiclass
                                  clus
vv                                 DEL PEAK 31(22Q13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      11
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      54
                                  clus
vv                                 DEL PEAK 31(22Q13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        41
  BLACK OR AFRICAN AMERICAN                                    20
  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"
D34V17, binary
                                cls
clus                               0   1
  DEL PEAK 31(22Q13.1) MUTATED     6  63
  DEL PEAK 31(22Q13.1) WILD-TYPE  32 297
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q13.1) MUTATED      6   63
  DEL PEAK 31(22Q13.1) WILD-TYPE   32  297
                        clus
vv                       DEL PEAK 31(22Q13.1) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           63
                        clus
vv                       DEL PEAK 31(22Q13.1) WILD-TYPE
  HISPANIC OR LATINO                                 32
  NOT HISPANIC OR LATINO                            297
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 32(22Q13.32) MUTATION ANALYSIS
D35V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 32(22Q13.32) MUTATED    89   1
  DEL PEAK 32(22Q13.32) WILD-TYPE 393  15
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             90                             408 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                              1                              15 
$`DEL PEAK 32(22Q13.32) MUTATED`
TCGA-DE-A0XZ TCGA-DJ-A3VK TCGA-E3-A3E5 TCGA-EL-A3D0 TCGA-MK-A84Z TCGA-4C-A93U 
       35.84        24.76        39.95       139.86        23.93         4.24 
TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A2P4 
       49.78        14.73        15.12        51.39        20.58        12.82 
TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A4M8 TCGA-DJ-A13M 
       23.31        10.88         3.45        12.43        18.54        48.79 
TCGA-DJ-A13T TCGA-DJ-A1QG TCGA-DJ-A1QN TCGA-DJ-A2PS TCGA-DJ-A2Q0 TCGA-DJ-A2Q7 
       56.19        44.98        42.58        26.20        34.36        35.11 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       33.53        35.18        36.92        32.42        31.46        16.41 
TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E8-A432 TCGA-E8-A434 TCGA-EL-A3CL 
       27.62        34.78        47.21        30.61        31.33        31.66 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3GP TCGA-EL-A3GW TCGA-EL-A3T2 TCGA-EL-A3ZL 
       98.53        69.57        49.51        50.20        32.48        62.30 
TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4JZ TCGA-EL-A4K6 TCGA-EL-A4K9 TCGA-EL-A4KI 
       60.16        57.47        61.02        44.15        47.84        23.90 
TCGA-EM-A1CS TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ 
       26.86        15.75        10.45        14.53        41.29        47.57 
TCGA-EM-A2OY TCGA-EM-A3AP TCGA-EM-A3FO TCGA-EM-A3O9 TCGA-EM-A3SX TCGA-EM-A3SZ 
       32.32         8.35        17.49         9.24        29.85        12.79 
TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FU TCGA-ET-A25L TCGA-ET-A25O TCGA-ET-A2N4 
       26.37        21.53        60.49        56.58        65.29         2.66 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A3BP TCGA-ET-A3DS TCGA-ET-A40P 
      108.46        84.89       123.32        79.10        66.84        43.99 
TCGA-ET-A40T TCGA-FE-A237 TCGA-FE-A3PB TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A3WA 
       37.48       112.80        85.15        16.27        21.63        17.06 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A3RH TCGA-IM-A3U3 TCGA-IM-A41Z TCGA-J8-A3O0 
       21.60        12.53        12.46        16.90        31.10        43.17 
TCGA-J8-A3YD TCGA-J8-A3YH TCGA-KS-A41I TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-QD-A8IV 
       31.82         5.75        15.98        32.45        84.72        12.89 

$`DEL PEAK 32(22Q13.32) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DJ-A13L TCGA-DJ-A2PR 
       30.21        22.88        23.18        12.66         9.96        27.45 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-EL-A3CR TCGA-EL-A3CS 
       23.44        59.57        42.54         3.12         7.66        45.53 
TCGA-EL-A3CY TCGA-EL-A3D5 TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY 
        4.18        57.11        50.24        33.50       150.48        17.52 
TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V 
      178.29        29.72        50.40        75.42         1.05         1.68 
TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z3 
       17.23         2.60        21.83        24.79        13.78        16.34 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZJ TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       42.08        41.52         4.83        44.35        42.15        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 
       35.54        32.45        11.31        30.97        11.08        18.38 
TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       16.57        20.48        18.97        16.01        13.94        36.39 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45E TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       18.64         7.99        21.01        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       21.63        19.43        23.47        12.30        12.79        12.46 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       11.38        10.68        15.02        12.66        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       37.64        27.32        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13O TCGA-DJ-A13P 
       25.12        14.70        14.27         2.76        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
       18.58         8.71        52.27        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
       48.07       135.91        30.61        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
        6.02        47.41        17.56        10.09         7.99        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       35.41        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42        37.74        43.96        40.24        33.93 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QC TCGA-DJ-A3UM 
       37.48        36.46        39.09        35.90        39.95        31.04 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY 
       19.56        36.33        32.81        36.33        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       40.96        36.99        20.22        30.61        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        40.70        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UP 
        9.60        35.67        36.43        23.44        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       33.04        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3E0 
       35.38        54.90        21.53         2.33        92.55        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       80.52        63.19        52.44        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 
       29.98        31.50        31.04        31.30        30.84        25.45 
TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       31.27        14.96        39.88        33.50        31.00        30.15 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU 
       26.73       155.54        97.74       158.83        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D6 TCGA-EL-A3GO 
       37.94        57.01       106.62        79.50       108.36        64.87 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY 
      115.10        65.39       136.01        50.37       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      139.99        49.32        43.36        49.71        83.57       139.00 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 
      108.66        57.63        52.50        29.65       142.52       129.57 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZM TCGA-EL-A3ZN 
       82.82        89.56        91.17        51.78        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW 
       72.69        65.49        61.22         7.07        59.44        34.72 
TCGA-EL-A4JX TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 
       45.96        31.04        34.39        30.51        53.36        41.13 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       43.59        24.30        27.06        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        78.61        57.01        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CK 
       14.73        14.50        10.65        44.19        14.24        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        40.34        19.73        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       14.14        33.07        44.52        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       47.38        21.01        12.07        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       14.50        15.06         7.33        12.53        27.02        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SY TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       38.86        29.95        13.51        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        5.33        26.37        22.45        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25P 
       81.70        77.56        70.42        60.20        63.39        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39O 
       83.34        80.88        33.24       106.09       107.41       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BQ 
       95.34        94.13        55.10        98.20        28.24        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.79        87.62        77.82        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       94.59        84.85        80.58        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A4KN TCGA-ET-A4KQ 
       24.72        46.26        44.38        40.21        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
      117.40        66.77        39.95        33.63        81.83       106.36 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        71.08         4.11        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10       116.09         1.25        20.42        17.82         7.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       29.10        19.56        13.91        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       23.31        17.36        15.16        23.87        22.49        19.04 
TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RI TCGA-H2-A421 
       13.81        14.04        17.00        21.67        11.01        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A41Y TCGA-IM-A420 
       18.61        48.92        47.41        18.51        21.83         8.22 
TCGA-IM-A4EB TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       25.64        27.19        11.24        27.85        24.69        22.29 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        2.47         0.20       143.57        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       43.69        18.64        87.39        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-E8-A418 
       40.37         9.50        36.10        32.45        30.21         3.02 

  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                           2.66                            0.20 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                         139.86                          178.29 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                         32.370                          30.985 
[1] "2.7 - 139.9 (32.4)" "0.2 - 178.3 (31.0)"
[1] "hr=" "3.2"
D35V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 32(22Q13.32) MUTATED        50       10        18        1        10
  DEL PEAK 32(22Q13.32) WILD-TYPE     232       40        93        1        36
                                 vv
clus                              STAGE IVC
  DEL PEAK 32(22Q13.32) MUTATED           1
  DEL PEAK 32(22Q13.32) WILD-TYPE         5
D35V3, multiclass
           clus
vv          DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  STAGE I                              50                             232
  STAGE II                             10                              40
  STAGE III                            18                              93
  STAGE IV                              1                               1
  STAGE IVA                            10                              36
  STAGE IVC                             1                               5
[1] 6 2
[1] 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 32(22Q13.32) MUTATED    25  33  28   4
  DEL PEAK 32(22Q13.32) WILD-TYPE 117 132 139  19
D35V4, multiclass
    clus
vv   DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  T1                            25                             117
  T2                            33                             132
  T3                            28                             139
  T4                             4                              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V5, binary
                                 cls
clus                                0   1
  DEL PEAK 32(22Q13.32) MUTATED    46  36
  DEL PEAK 32(22Q13.32) WILD-TYPE 179 188
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     46   36
  DEL PEAK 32(22Q13.32) WILD-TYPE  179  188
   clus
vv  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  0                            46                             179
  1                            36                             188
[1] 2 2
[1] FALSE
D35V6, binary
                                 cls
clus                                0   1
  DEL PEAK 32(22Q13.32) MUTATED    46   2
  DEL PEAK 32(22Q13.32) WILD-TYPE 232   7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     46    2
  DEL PEAK 32(22Q13.32) WILD-TYPE  232    7
   clus
vv  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  0                            46                             232
  1                             2                               7
[1] 2 2
[1] FALSE
D35V7, binary
                                 cls
clus                                0   1
  DEL PEAK 32(22Q13.32) MUTATED    63  27
  DEL PEAK 32(22Q13.32) WILD-TYPE 302 107
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     63   27
  DEL PEAK 32(22Q13.32) WILD-TYPE  302  107
        clus
vv       DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  FEMALE                            63                             302
  MALE                              27                             107
[1] 2 2
[1] FALSE
D35V8, binary
                                 cls
clus                                0   1
  DEL PEAK 32(22Q13.32) MUTATED    25  64
  DEL PEAK 32(22Q13.32) WILD-TYPE 155 239
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     25   64
  DEL PEAK 32(22Q13.32) WILD-TYPE  155  239
     clus
vv    DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  NO                             25                             155
  YES                            64                             239
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER, SPECIFY
  DEL PEAK 32(22Q13.32) MUTATED                1
  DEL PEAK 32(22Q13.32) WILD-TYPE              6
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 32(22Q13.32) MUTATED                                              61
  DEL PEAK 32(22Q13.32) WILD-TYPE                                           295
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 32(22Q13.32) MUTATED                                                                       25
  DEL PEAK 32(22Q13.32) WILD-TYPE                                                                     75
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 32(22Q13.32) MUTATED                                                                     3
  DEL PEAK 32(22Q13.32) WILD-TYPE                                                                  33
D35V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 32(22Q13.32) MUTATED
  OTHER, SPECIFY                                                                                     1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     61
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            25
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                3
                                                                        clus
vv                                                                       DEL PEAK 32(22Q13.32) WILD-TYPE
  OTHER, SPECIFY                                                                                       6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      295
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              75
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, binary
                                 cls
clus                                0   1
  DEL PEAK 32(22Q13.32) MUTATED    80   1
  DEL PEAK 32(22Q13.32) WILD-TYPE 340  16
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     80    1
  DEL PEAK 32(22Q13.32) WILD-TYPE  340   16
     clus
vv    DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  NO                             80                             340
  YES                             1                              16
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 32(22Q13.32) MUTATED             19                       2   64
  DEL PEAK 32(22Q13.32) WILD-TYPE          113                      16  266
                                 vv
clus                              VERY ADVANCED (T4B)
  DEL PEAK 32(22Q13.32) MUTATED                     0
  DEL PEAK 32(22Q13.32) WILD-TYPE                   1
D35V11, multiclass
                         clus
vv                        DEL PEAK 32(22Q13.32) MUTATED
  MINIMAL (T3)                                       19
  MODERATE/ADVANCED (T4A)                             2
  NONE                                               64
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        DEL PEAK 32(22Q13.32) WILD-TYPE
  MINIMAL (T3)                                        113
  MODERATE/ADVANCED (T4A)                              16
  NONE                                                266
  VERY ADVANCED (T4B)                                   1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 32(22Q13.32) MUTATED    68   6   1   8
  DEL PEAK 32(22Q13.32) WILD-TYPE 315  45   3  22
D35V12, multiclass
    clus
vv   DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  R0                            68                             315
  R1                             6                              45
  R2                             1                               3
  RX                             8                              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, continuous
D35V14, binary
                                 cls
clus                                0   1
  DEL PEAK 32(22Q13.32) MUTATED    46  42
  DEL PEAK 32(22Q13.32) WILD-TYPE 179 222
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     46   42
  DEL PEAK 32(22Q13.32) WILD-TYPE  179  222
            clus
vv           DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  MULTIFOCAL                            46                             179
  UNIFOCAL                              42                             222
[1] 2 2
[1] FALSE
D35V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(22Q13.32) MUTATED                                  0    11
  DEL PEAK 32(22Q13.32) WILD-TYPE                                1    41
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(22Q13.32) MUTATED                           7    55
  DEL PEAK 32(22Q13.32) WILD-TYPE                        20   274
D35V16, multiclass
                                  clus
vv                                 DEL PEAK 32(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                       55
                                  clus
vv                                 DEL PEAK 32(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         41
  BLACK OR AFRICAN AMERICAN                                     20
  WHITE                                                        274
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V17, binary
                                 cls
clus                                0   1
  DEL PEAK 32(22Q13.32) MUTATED     6  64
  DEL PEAK 32(22Q13.32) WILD-TYPE  32 296
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED      6   64
  DEL PEAK 32(22Q13.32) WILD-TYPE   32  296
                        clus
vv                       DEL PEAK 32(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            64
                        clus
vv                       DEL PEAK 32(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                  32
  NOT HISPANIC OR LATINO                             296
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 33(XQ28) MUTATION ANALYSIS
D36V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 33(XQ28) MUTATED     4   0
  DEL PEAK 33(XQ28) WILD-TYPE 478  16
  DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE 
                          4                         494 
  DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE 
                          0                          16 
$`DEL PEAK 33(XQ28) MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A190 TCGA-EM-A1YE TCGA-ET-A40S 
       13.78        20.58        54.08        40.21 

$`DEL PEAK 33(XQ28) WILD-TYPE`
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A13L 
       30.21        22.88        23.18        12.66        35.84         9.96 
TCGA-DJ-A2PR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK 
       27.45        23.44        59.57        42.54         3.12        24.76 
TCGA-E3-A3E5 TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 
       39.95         7.66        45.53         4.18       139.86        57.11 
TCGA-EL-A3GQ TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ 
       50.24        33.50       150.48        17.52       178.29        29.72 
TCGA-ET-A3BO TCGA-ET-A3BV TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW 
       50.40        75.42         1.05         1.68        17.23         2.60 
TCGA-L6-A4ET TCGA-MK-A84Z TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 
       21.83        23.93         4.24        24.79        49.78        16.34 
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       14.73        41.33        18.87         4.01        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 
       25.48        15.12        42.08        51.39        41.52         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.97        11.08        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       12.82        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD 
       15.45        21.63        19.43        23.47        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.46        11.38        10.68        15.02        12.43        12.66 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       21.63        50.17        37.64        27.32        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        52.27        43.17        52.37         8.32        48.07 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       30.58        35.41        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       43.96        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        39.95        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       32.81        36.33        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       20.22        30.61        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        40.70        18.97         9.60        35.67 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       36.43        23.44        27.62        30.87        30.12        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04        31.30        30.84 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61        31.27        31.33        14.96        39.88 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50        31.00        30.15        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
       97.74       158.83        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62        79.50        98.53        69.57       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 
       83.57       139.00       108.66        57.63        52.50        29.65 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        91.17 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        72.69        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        61.02        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        78.61        57.01        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       44.52         8.35        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33        12.53         9.24        27.02 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP 
       95.34        94.13        55.10        98.20        28.24        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
       76.64         5.79        87.62        77.82        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       78.77        71.08         4.11        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
      116.09         1.25        20.42        17.82         7.82        29.10 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       23.31        21.63        17.06        17.36        15.16        23.87 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 
       22.49        19.04        13.81        14.04        21.60        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46        11.01        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.22        25.64        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37         9.50        36.10        32.45        30.21 
TCGA-QD-A8IV TCGA-E8-A418 
       12.89         3.02 

  DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE 
                      13.78                        0.20 
  DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE 
                      54.08                      178.29 
  DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE 
                     30.395                      31.250 
[1] "13.8 - 54.1 (30.4)" "0.2 - 178.3 (31.2)"
[1] "hr="     "3300000"
D36V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 33(XQ28) MUTATED         0        4         0        0         0
  DEL PEAK 33(XQ28) WILD-TYPE     282       46       111        2        46
                             vv
clus                          STAGE IVC
  DEL PEAK 33(XQ28) MUTATED           0
  DEL PEAK 33(XQ28) WILD-TYPE         6
D36V3, multiclass
           clus
vv          DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE
  STAGE I                           0                         282
  STAGE II                          4                          46
  STAGE III                         0                         111
  STAGE IV                          0                           2
  STAGE IVA                         0                          46
  STAGE IVC                         0                           6
[1] 6 2
[1] 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 33(XQ28) MUTATED     0   4   0   0
  DEL PEAK 33(XQ28) WILD-TYPE 142 161 167  23
D36V4, multiclass
    clus
vv   DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE
  T1                         0                         142
  T2                         4                         161
  T3                         0                         167
  T4                         0                          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"
D36V5, binary
                             cls
clus                            0   1
  DEL PEAK 33(XQ28) MUTATED     4   0
  DEL PEAK 33(XQ28) WILD-TYPE 221 224
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 33(XQ28) MUTATED      4    0
  DEL PEAK 33(XQ28) WILD-TYPE  221  224
   clus
vv  DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE
  0                         4                         221
  1                         0                         224
[1] 2 2
[1] FALSE
D36V6, binary
                             cls
clus                            0   1
  DEL PEAK 33(XQ28) MUTATED     0   0
  DEL PEAK 33(XQ28) WILD-TYPE 278   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 33(XQ28) MUTATED      0    0
  DEL PEAK 33(XQ28) WILD-TYPE  278    9
D36V7, binary
                             cls
clus                            0   1
  DEL PEAK 33(XQ28) MUTATED     1   3
  DEL PEAK 33(XQ28) WILD-TYPE 364 131
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 33(XQ28) MUTATED      1    3
  DEL PEAK 33(XQ28) WILD-TYPE  364  131
        clus
vv       DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE
  FEMALE                         1                         364
  MALE                           3                         131
[1] 2 2
[1] FALSE
D36V8, binary
                             cls
clus                            0   1
  DEL PEAK 33(XQ28) MUTATED     0   4
  DEL PEAK 33(XQ28) WILD-TYPE 180 299
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 33(XQ28) MUTATED      0    4
  DEL PEAK 33(XQ28) WILD-TYPE  180  299
     clus
vv    DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE
  NO                          0                         180
  YES                         4                         299
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER, SPECIFY
  DEL PEAK 33(XQ28) MUTATED                0
  DEL PEAK 33(XQ28) WILD-TYPE              7
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 33(XQ28) MUTATED                                               3
  DEL PEAK 33(XQ28) WILD-TYPE                                           353
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 33(XQ28) MUTATED                                                                        1
  DEL PEAK 33(XQ28) WILD-TYPE                                                                     99
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 33(XQ28) MUTATED                                                                     0
  DEL PEAK 33(XQ28) WILD-TYPE                                                                  36
D36V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 33(XQ28) MUTATED
  OTHER, SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            0
                                                                        clus
vv                                                                       DEL PEAK 33(XQ28) WILD-TYPE
  OTHER, SPECIFY                                                                                   7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, binary
                             cls
clus                            0   1
  DEL PEAK 33(XQ28) MUTATED     2   1
  DEL PEAK 33(XQ28) WILD-TYPE 418  16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 33(XQ28) MUTATED      2    1
  DEL PEAK 33(XQ28) WILD-TYPE  418   16
     clus
vv    DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE
  NO                          2                         418
  YES                         1                          16
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 33(XQ28) MUTATED              0                       0    4
  DEL PEAK 33(XQ28) WILD-TYPE          132                      18  326
                             vv
clus                          VERY ADVANCED (T4B)
  DEL PEAK 33(XQ28) MUTATED                     0
  DEL PEAK 33(XQ28) WILD-TYPE                   1
D36V11, multiclass
                         clus
vv                        DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE
  MINIMAL (T3)                                    0                         132
  MODERATE/ADVANCED (T4A)                         0                          18
  NONE                                            4                         326
  VERY ADVANCED (T4B)                             0                           1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 33(XQ28) MUTATED     3   0   0   1
  DEL PEAK 33(XQ28) WILD-TYPE 380  51   4  29
D36V12, multiclass
    clus
vv   DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE
  R0                         3                         380
  R1                         0                          51
  R2                         0                           4
  RX                         1                          29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, continuous
D36V14, binary
                             cls
clus                            0   1
  DEL PEAK 33(XQ28) MUTATED     2   2
  DEL PEAK 33(XQ28) WILD-TYPE 223 262
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 33(XQ28) MUTATED      2    2
  DEL PEAK 33(XQ28) WILD-TYPE  223  262
            clus
vv           DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE
  MULTIFOCAL                         2                         223
  UNIFOCAL                           2                         262
[1] 2 2
[1] FALSE
D36V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(XQ28) MUTATED                                  0     0
  DEL PEAK 33(XQ28) WILD-TYPE                                1    52
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(XQ28) MUTATED                           0     2
  DEL PEAK 33(XQ28) WILD-TYPE                        27   327
D36V16, multiclass
[1] "Remove cluster labels:"    "DEL PEAK 33(XQ28) MUTATED"
clus
  DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE 
                          2                         407 
                 TCGA-BJ-A290                  TCGA-BJ-A291 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A45K                  TCGA-CE-A13K 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DE-A0XZ                  TCGA-DJ-A13L 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A2PR                  TCGA-DJ-A3UU 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A3UW                  TCGA-DJ-A3V4 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A3VI                  TCGA-DJ-A3VK 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-E3-A3E5                  TCGA-EL-A3CR 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3CS                  TCGA-EL-A3CY 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3D0                  TCGA-EL-A3D5 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3GQ                  TCGA-EL-A3H2 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3H8                  TCGA-EL-A3MY 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3N3                  TCGA-ET-A3BO 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A3BV                  TCGA-FK-A3SD 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FY-A76V                  TCGA-J8-A3NZ 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-J8-A4HW                  TCGA-L6-A4ET 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-MK-A84Z                  TCGA-4C-A93U 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A0YZ                  TCGA-BJ-A0Z2 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A0Z3                  TCGA-BJ-A0Z5 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A0Z9                  TCGA-BJ-A0ZA 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A0ZB                  TCGA-BJ-A0ZC 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A0ZE                  TCGA-BJ-A0ZG 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A0ZH                  TCGA-BJ-A0ZJ 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A18Y                  TCGA-BJ-A18Z 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A191                  TCGA-BJ-A192 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A28R                  TCGA-BJ-A28S 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A28T                  TCGA-BJ-A28V 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A28W                  TCGA-BJ-A28X 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A28Z                  TCGA-BJ-A2N7 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A2N8                  TCGA-BJ-A2N9 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A2NA                  TCGA-BJ-A2P4 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A3EZ                  TCGA-BJ-A3F0 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A3PR                  TCGA-BJ-A3PT 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A3PU                  TCGA-BJ-A45C 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A45D                  TCGA-BJ-A45E 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A45F                  TCGA-BJ-A45G 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A45H                  TCGA-BJ-A45I 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A45J                  TCGA-BJ-A4O8 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-BJ-A4O9                  TCGA-CE-A27D 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-CE-A3MD                  TCGA-CE-A3ME 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-CE-A481                  TCGA-CE-A482 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-CE-A483                  TCGA-CE-A484 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-CE-A485                  TCGA-DE-A0Y2 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DE-A0Y3                  TCGA-DE-A2OL 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DE-A3KN                  TCGA-DE-A4M8 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DE-A4M9                  TCGA-DE-A4MA 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DE-A4MB                  TCGA-DE-A4MC 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DE-A4MD                  TCGA-DE-A69J 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DE-A69K                  TCGA-DE-A7U5 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A13M                  TCGA-DJ-A13O 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A13P                  TCGA-DJ-A13R 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A13S                  TCGA-DJ-A13T 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A13U                  TCGA-DJ-A13W 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A1QD                  TCGA-DJ-A1QE 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A1QF                  TCGA-DJ-A1QG 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A1QH                  TCGA-DJ-A1QI 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A1QM                  TCGA-DJ-A1QO 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A1QQ                  TCGA-DJ-A2PN 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A2PO                  TCGA-DJ-A2PQ 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A2PS                  TCGA-DJ-A2PT 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A2PU                  TCGA-DJ-A2PV 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A2PW                  TCGA-DJ-A2PX 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A2PY                  TCGA-DJ-A2PZ 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A2Q0                  TCGA-DJ-A2Q1 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A2Q2                  TCGA-DJ-A2Q3 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A2Q4                  TCGA-DJ-A2Q5 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A2Q6                  TCGA-DJ-A2Q7 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A2Q9                  TCGA-DJ-A2QA 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A2QB                  TCGA-DJ-A3UK 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A3UM                  TCGA-DJ-A3UN 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A3UO                  TCGA-DJ-A3UQ 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A3UR                  TCGA-DJ-A3US 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A3UT                  TCGA-DJ-A3UX 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A3UY                  TCGA-DJ-A3UZ 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A3V2                  TCGA-DJ-A3V3 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A3V5                  TCGA-DJ-A3V7 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A3V8                  TCGA-DJ-A3V9 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A3VD                  TCGA-DJ-A3VE 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A3VF                  TCGA-DJ-A3VG 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A3VJ                  TCGA-DJ-A3VL 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A3VM                  TCGA-DJ-A4UL 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A4UP                  TCGA-DJ-A4UQ 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A4UR                  TCGA-DJ-A4UT 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A4UW                  TCGA-DJ-A4V0 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DJ-A4V4                  TCGA-DJ-A4V5 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DO-A1JZ                  TCGA-DO-A1K0 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-DO-A2HM                  TCGA-E3-A3DY 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-E3-A3DZ                  TCGA-E3-A3E0 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-E3-A3E1                  TCGA-E3-A3E2 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-E3-A3E3                  TCGA-E8-A242 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-E8-A2EA                  TCGA-E8-A3X7 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-E8-A413                  TCGA-E8-A414 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-E8-A415                  TCGA-E8-A416 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-E8-A417                  TCGA-E8-A419 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-E8-A432                  TCGA-E8-A433 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-E8-A434                  TCGA-E8-A436 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-E8-A437                  TCGA-E8-A438 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-E8-A44K                  TCGA-E8-A44M 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3CL                  TCGA-EL-A3CM 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3CN                  TCGA-EL-A3CO 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3CP                  TCGA-EL-A3CT 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3CU                  TCGA-EL-A3CV 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3CW                  TCGA-EL-A3CX 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3CZ                  TCGA-EL-A3D1 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3D4                  TCGA-EL-A3D6 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3GO                  TCGA-EL-A3GP 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3GR                  TCGA-EL-A3GS 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3GU                  TCGA-EL-A3GV 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3GW                  TCGA-EL-A3GX 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3GY                  TCGA-EL-A3GZ 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3H1                  TCGA-EL-A3H3 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3H4                  TCGA-EL-A3H5 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3H7                  TCGA-EL-A3MW 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3MX                  TCGA-EL-A3MZ 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3N2                  TCGA-EL-A3T0 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3T1                  TCGA-EL-A3T2 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3T3                  TCGA-EL-A3T6 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3T7                  TCGA-EL-A3T8 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3T9                  TCGA-EL-A3TA 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3TB                  TCGA-EL-A3ZG 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3ZH                  TCGA-EL-A3ZK 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3ZL                  TCGA-EL-A3ZN 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3ZO                  TCGA-EL-A3ZP 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3ZQ                  TCGA-EL-A3ZR 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A3ZS                  TCGA-EL-A3ZT 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A4JV                  TCGA-EL-A4JW 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A4JX                  TCGA-EL-A4JZ 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A4K0                  TCGA-EL-A4K1 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A4K2                  TCGA-EL-A4K4 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A4K6                  TCGA-EL-A4K7 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A4K9                  TCGA-EL-A4KD 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A4KG                  TCGA-EL-A4KH 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EL-A4KI                  TCGA-EM-A22M 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EM-A22O                  TCGA-EM-A2OV 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-EM-A3AI                  TCGA-ET-A25G 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A25I                  TCGA-ET-A25J 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A25K                  TCGA-ET-A25L 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A25M                  TCGA-ET-A25N 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A25O                  TCGA-ET-A25P 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A25R                  TCGA-ET-A2MX 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A2MY                  TCGA-ET-A2MZ 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A2N0                  TCGA-ET-A2N1 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A2N3                  TCGA-ET-A2N4 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A2N5                  TCGA-ET-A39I 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A39J                  TCGA-ET-A39K 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A39M                  TCGA-ET-A39N 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A39O                  TCGA-ET-A39P 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A39R                  TCGA-ET-A39S 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A39T                  TCGA-ET-A3BN 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A3BP                  TCGA-ET-A3BQ 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A3BS                  TCGA-ET-A3BT 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A3BU                  TCGA-ET-A3BW 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A3BX                  TCGA-ET-A3DO 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A3DP                  TCGA-ET-A3DQ 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A3DR                  TCGA-ET-A3DS 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A3DT                  TCGA-ET-A3DU 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A3DV                  TCGA-ET-A3DW 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A40P                  TCGA-ET-A40Q 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A40R                  TCGA-ET-A40T 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-ET-A4KN                  TCGA-ET-A4KQ 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FE-A22Z                  TCGA-FE-A230 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FE-A231                  TCGA-FE-A232 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FE-A233                  TCGA-FE-A234 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FE-A235                  TCGA-FE-A236 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FE-A237                  TCGA-FE-A238 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FE-A239                  TCGA-FE-A23A 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FE-A3PA                  TCGA-FE-A3PB 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FE-A3PC                  TCGA-FE-A3PD 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FK-A3S3                  TCGA-FK-A3SB 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FK-A3SE                  TCGA-FK-A3SG 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FK-A3SH                  TCGA-FK-A4UB 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FY-A2QD                  TCGA-FY-A3BL 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FY-A3I4                  TCGA-FY-A3I5 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FY-A3NM                  TCGA-FY-A3ON 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FY-A3R6                  TCGA-FY-A3R7 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FY-A3R8                  TCGA-FY-A3R9 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FY-A3RA                  TCGA-FY-A3TY 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FY-A3W9                  TCGA-FY-A3WA 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FY-A3YR                  TCGA-FY-A40K 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FY-A40L                  TCGA-FY-A40M 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FY-A40N                  TCGA-FY-A4B0 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-FY-A4B3                  TCGA-FY-A4B4 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-GE-A2C6                  TCGA-H2-A26U 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-H2-A2K9                  TCGA-H2-A3RH 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-H2-A3RI                  TCGA-H2-A421 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-H2-A422                  TCGA-IM-A3EB 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-IM-A3ED                  TCGA-IM-A3U2 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-IM-A3U3                  TCGA-IM-A41Y 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-IM-A41Z                  TCGA-IM-A420 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-IM-A4EB                  TCGA-J8-A3O0 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-J8-A3O1                  TCGA-J8-A3O2 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-J8-A3YD                  TCGA-J8-A3YE 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-J8-A3YF                  TCGA-J8-A3YG 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-J8-A3YH                  TCGA-J8-A42S 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-J8-A4HY                  TCGA-KS-A41F 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-KS-A41I                  TCGA-KS-A41J 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-KS-A41L                  TCGA-KS-A4I1 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-KS-A4I3                  TCGA-KS-A4I5 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-KS-A4I7                  TCGA-KS-A4I9 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-KS-A4IB                  TCGA-KS-A4IC 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-KS-A4ID                  TCGA-L6-A4EP 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-L6-A4EQ                  TCGA-L6-A4EU 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-MK-A4N6                  TCGA-MK-A4N7 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-MK-A4N9                  TCGA-QD-A8IV 
"DEL PEAK 33(XQ28) WILD-TYPE" "DEL PEAK 33(XQ28) WILD-TYPE" 
                 TCGA-E8-A418 
"DEL PEAK 33(XQ28) WILD-TYPE" 
D36V17, binary
                             cls
clus                            0   1
  DEL PEAK 33(XQ28) MUTATED     0   3
  DEL PEAK 33(XQ28) WILD-TYPE  38 357
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 33(XQ28) MUTATED      0    3
  DEL PEAK 33(XQ28) WILD-TYPE   38  357
                        clus
vv                       DEL PEAK 33(XQ28) MUTATED DEL PEAK 33(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         3                         357
[1] 2 2
[1] FALSE
