[1] "ofn"       "-oTLGG-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/LGG-TP/15082624/LGG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/15087635/transformed.cor.cli.txt"

nPatients in clinical file=475, in cluster file=513, common to both=472
[1]  52 472
[1] "AMP PEAK  1(1Q22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         39                         433 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         39                         433 
[1] "AMP PEAK  2(1Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           39                           433 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           39                           433 
[1] "AMP PEAK  3(2P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           22                           450 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           22                           450 
[1] "AMP PEAK  4(3Q26.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                            19                            453 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                            19                            453 
[1] "AMP PEAK  5(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         27                         445 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         27                         445 
[1] "AMP PEAK  6(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                          117                           355 
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                          117                           355 
[1] "AMP PEAK  7(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                          164                           308 
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                          164                           308 
[1] "AMP PEAK  8(7Q32.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                          170                           302 
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                          170                           302 
[1] "AMP PEAK  9(8Q24.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                            93                            379 
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                            93                            379 
[1] "AMP PEAK 10(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                           43                           429 
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                           43                           429 
[1] "AMP PEAK 11(10P15.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                            66                            406 
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                            66                            406 
[1] "AMP PEAK 12(11Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                            82                            390 
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                            82                            390 
[1] "AMP PEAK 13(12P13.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                             64                             408 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                             64                             408 
[1] "AMP PEAK 14(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            34                            438 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            34                            438 
[1] "AMP PEAK 15(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          21                          451 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          21                          451 
[1] "AMP PEAK 16(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            15                            457 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            15                            457 
[1] "AMP PEAK 17(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                            39                            433 
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                            39                            433 
[1] "AMP PEAK 18(19P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                           120                            352 
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                           120                            352 
[1] "AMP PEAK 19(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                           113                            359 
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                           113                            359 
[1] "AMP PEAK 20(XP11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                            41                            431 
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                            41                            431 
[1] "AMP PEAK 21(XP11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE 
                            57                            415 
  AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE 
                            57                            415 
[1] "DEL PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                           191                            281 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                           191                            281 
[1] "DEL PEAK  2(1P32.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                          181                           291 
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                          181                           291 
[1] "DEL PEAK  3(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         27                         445 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         27                         445 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           69                           403 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           69                           403 
[1] "DEL PEAK  5(3P21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            44                            428 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            44                            428 
[1] "DEL PEAK  6(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE 
                            35                            437 
  DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE 
                            35                            437 
[1] "DEL PEAK  7(3Q29) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                         40                         432 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                         40                         432 
[1] "DEL PEAK  8(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                          125                           347 
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                          125                           347 
[1] "DEL PEAK  9(5P15.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE 
                            46                            426 
  DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE 
                            46                            426 
[1] "DEL PEAK 10(5Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE 
                         60                         412 
  DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE 
                         60                         412 
[1] "DEL PEAK 11(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                           44                           428 
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                           44                           428 
[1] "DEL PEAK 12(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE 
                            69                            403 
  DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE 
                            69                            403 
[1] "DEL PEAK 13(6Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(6Q24.3) MUTATED DEL PEAK 13(6Q24.3) WILD-TYPE 
                           72                           400 
  DEL PEAK 13(6Q24.3) MUTATED DEL PEAK 13(6Q24.3) WILD-TYPE 
                           72                           400 
[1] "DEL PEAK 14(7P22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           19                           453 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           19                           453 
[1] "DEL PEAK 15(8Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE 
                           26                           446 
  DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE 
                           26                           446 
[1] "DEL PEAK 16(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                        134                         338 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                        134                         338 
[1] "DEL PEAK 17(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                          161                           311 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                          161                           311 
[1] "DEL PEAK 18(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE 
                           135                            337 
  DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE 
                           135                            337 
[1] "DEL PEAK 19(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE 
                            94                            378 
  DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE 
                            94                            378 
[1] "DEL PEAK 20(11P15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE 
                            66                            406 
  DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE 
                            66                            406 
[1] "DEL PEAK 21(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE 
                            35                            437 
  DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE 
                            35                            437 
[1] "DEL PEAK 22(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE 
                          66                          406 
  DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE 
                          66                          406 
[1] "DEL PEAK 23(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                           129                            343 
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                           129                            343 
[1] "DEL PEAK 24(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE 
                           131                            341 
  DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE 
                           131                            341 
[1] "DEL PEAK 25(13Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                          99                          373 
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                          99                          373 
[1] "DEL PEAK 26(14Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(14Q24.3) MUTATED DEL PEAK 26(14Q24.3) WILD-TYPE 
                           108                            364 
  DEL PEAK 26(14Q24.3) MUTATED DEL PEAK 26(14Q24.3) WILD-TYPE 
                           108                            364 
[1] "DEL PEAK 27(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(18Q23) MUTATED DEL PEAK 27(18Q23) WILD-TYPE 
                          74                          398 
  DEL PEAK 27(18Q23) MUTATED DEL PEAK 27(18Q23) WILD-TYPE 
                          74                          398 
[1] "DEL PEAK 28(19Q13.41) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(19Q13.41) MUTATED DEL PEAK 28(19Q13.41) WILD-TYPE 
                            247                             225 
  DEL PEAK 28(19Q13.41) MUTATED DEL PEAK 28(19Q13.41) WILD-TYPE 
                            247                             225 
[1] "DEL PEAK 29(19Q13.42) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(19Q13.42) MUTATED DEL PEAK 29(19Q13.42) WILD-TYPE 
                            255                             217 
  DEL PEAK 29(19Q13.42) MUTATED DEL PEAK 29(19Q13.42) WILD-TYPE 
                            255                             217 
[1] "DEL PEAK 30(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(22Q13.31) MUTATED DEL PEAK 30(22Q13.31) WILD-TYPE 
                             68                             404 
  DEL PEAK 30(22Q13.31) MUTATED DEL PEAK 30(22Q13.31) WILD-TYPE 
                             68                             404 
[1] "DEL PEAK 31(XQ21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(XQ21.1) MUTATED DEL PEAK 31(XQ21.1) WILD-TYPE 
                           66                           406 
  DEL PEAK 31(XQ21.1) MUTATED DEL PEAK 31(XQ21.1) WILD-TYPE 
                           66                           406 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "DCC_UPLOAD_DATE"                       
 [7] "GENDER"                                
 [8] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
 [9] "DAYS_TO_LAST_KNOWN_ALIVE"              
[10] "RADIATION_THERAPY"                     
[11] "KARNOFSKY_PERFORMANCE_SCORE"           
[12] "HISTOLOGICAL_TYPE"                     
[13] "RADIATIONS_RADIATION_REGIMENINDICATION"
[14] "RACE"                                  
[15] "ETHNICITY"                             
[16] "BATCH_NUMBER"                          

Input Data has 16 rows and 472 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=92,	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=354,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 9:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 10:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH_NUMBER':	nDistinctValues=21,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 472 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"                        
[2] "GENDER"                                
[3] "KARNOFSKY_PERFORMANCE_SCORE"           
[4] "HISTOLOGICAL_TYPE"                     
[5] "RADIATIONS_RADIATION_REGIMENINDICATION"
[6] "RACE"                                  
[7] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q22) MUTATION ANALYSIS
D1V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  1(1Q22) MUTATED    25  14
  AMP PEAK  1(1Q22) WILD-TYPE 351  80
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         39                         431 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         14                          80 
$`AMP PEAK  1(1Q22) MUTATED`
TCGA-CS-4941 TCGA-CS-6665 TCGA-DB-A64L TCGA-DH-A669 TCGA-DU-6392 TCGA-DU-6396 
        7.69        12.43        24.20        30.21       211.17        75.16 
TCGA-DU-6400 TCGA-DU-6403 TCGA-DU-7010 TCGA-DU-7015 TCGA-DU-7290 TCGA-DU-7304 
        1.22        11.64        14.99        90.77        10.36        23.31 
TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A6S7 TCGA-DU-A7TB 
       14.60        19.13        15.12         4.96         7.23        42.31 
TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5319 TCGA-FG-5962 TCGA-FG-8185 TCGA-HT-7475 
       50.14        41.13        95.57        47.77        14.24        17.42 
TCGA-HT-7477 TCGA-HT-7677 TCGA-HT-7688 TCGA-HT-8108 TCGA-HT-A4DS TCGA-HT-A5R7 
       24.26        16.24        31.69         2.50         0.23        20.22 
TCGA-HW-A5KM TCGA-QH-A6CV TCGA-S9-A6WM TCGA-S9-A7R1 TCGA-TM-A84B TCGA-TM-A84I 
       20.71        14.53        19.86       169.84        24.92        28.08 
TCGA-TM-A84J TCGA-VM-A8CA TCGA-WH-A86K 
       24.16        13.51        13.32 

$`AMP PEAK  1(1Q22) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       31.63        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       17.88        30.74        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       14.40         8.02        42.05        27.81        17.19        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       54.25        13.12        13.38         3.45        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
      182.33        18.94        17.49        15.16        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6404 
       49.02        46.06        65.75        87.45         7.04       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
       11.47        62.96       156.23       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 
        8.84       117.40        30.67        26.30         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 
       18.94        44.02        62.01        25.91        60.30        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
        2.76         5.10        23.74        20.68        21.40        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TU TCGA-DU-A5TW 
       15.48        14.17        14.24        12.59         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K 
       12.20         8.65         2.70        77.98         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5305 
       23.51         7.50        44.42         0.56        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
       57.93       134.27        78.21       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 
       36.82        32.35        14.33         0.23         0.20        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       12.95        13.68        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72        27.52         0.10         6.67        11.54        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7478 
        0.13         0.03        16.54         3.75         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
       14.27         0.16         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
        0.10        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 
       33.01        12.23         6.25         0.10         0.46         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       26.04         0.13         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       20.35        12.76        20.81        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       72.59        80.12        32.45        84.99        31.10        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 
       15.06        13.12        28.37        13.02        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F 
       48.33        49.32        34.78        48.39        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       40.64        30.44        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       30.08         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A859 
       16.01        23.21         8.05        51.06        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                       0.23                        0.03 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                     211.17                      182.33 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                      19.86                       18.61 
[1] "0.2 - 211.2 (19.9)" "0.0 - 182.3 (18.6)"
[1] "hr=" "1.6"
D1V2, continuous
D1V3, binary
                             cls
clus                            0   1
  AMP PEAK  1(1Q22) MUTATED    17  22
  AMP PEAK  1(1Q22) WILD-TYPE 189 244
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED     17   22
  AMP PEAK  1(1Q22) WILD-TYPE  189  244
        clus
vv       AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  FEMALE                        17                         189
  MALE                          22                         244
[1] 2 2
[1] FALSE
D1V4, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  1(1Q22) MUTATED            17                6                16
  AMP PEAK  1(1Q22) WILD-TYPE         159              112               162
D1V5, multiclass
                   clus
vv                  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  ASTROCYTOMA                              17                         159
  OLIGOASTROCYTOMA                          6                         112
  OLIGODENDROGLIOMA                        16                         162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                             cls
clus                            0   1
  AMP PEAK  1(1Q22) MUTATED    10  29
  AMP PEAK  1(1Q22) WILD-TYPE  82 351
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED     10   29
  AMP PEAK  1(1Q22) WILD-TYPE   82  351
     clus
vv    AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  NO                         10                          82
  YES                        29                         351
[1] 2 2
[1] FALSE
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(1Q22) MUTATED                                  0     2
  AMP PEAK  1(1Q22) WILD-TYPE                                1     6
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q22) MUTATED                           1    35
  AMP PEAK  1(1Q22) WILD-TYPE                        14   402
D1V7, multiclass
                                  clus
vv                                 AMP PEAK  1(1Q22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                                1
  WHITE                                                   35
                                  clus
vv                                 AMP PEAK  1(1Q22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    402
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                             cls
clus                            0   1
  AMP PEAK  1(1Q22) MUTATED     0  37
  AMP PEAK  1(1Q22) WILD-TYPE  18 382
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED      0   37
  AMP PEAK  1(1Q22) WILD-TYPE   18  382
                        clus
vv                       AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  HISPANIC OR LATINO                             0                          18
  NOT HISPANIC OR LATINO                        37                         382
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q32.1) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1Q32.1) MUTATED    22  17
  AMP PEAK  2(1Q32.1) WILD-TYPE 354  77
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           39                           431 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           17                            77 
$`AMP PEAK  2(1Q32.1) MUTATED`
TCGA-CS-4941 TCGA-CS-5395 TCGA-CS-6665 TCGA-DB-5277 TCGA-DB-A64L TCGA-DH-A669 
        7.69        21.01        12.43        50.86        24.20        30.21 
TCGA-DU-6392 TCGA-DU-6400 TCGA-DU-6403 TCGA-DU-7010 TCGA-DU-7015 TCGA-DU-7290 
      211.17         1.22        11.64        14.99        90.77        10.36 
TCGA-DU-7292 TCGA-DU-7304 TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A7TB 
        7.96        23.31        14.60        19.13         4.96        42.31 
TCGA-DU-A7TD TCGA-FG-5962 TCGA-FG-6688 TCGA-FG-A4MW TCGA-HT-7475 TCGA-HT-7603 
        7.50        47.77        18.77        18.38        17.42        23.18 
TCGA-HT-7688 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-A4DS TCGA-HT-A5R7 TCGA-QH-A6CV 
       31.69        16.24        12.23         0.23        20.22        14.53 
TCGA-QH-A6CX TCGA-S9-A6WM TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A84B 
       12.23        19.86       169.84        10.39        49.45        24.92 
TCGA-TM-A84I TCGA-VM-A8CA TCGA-WH-A86K 
       28.08        13.51        13.32 

$`AMP PEAK  2(1Q32.1) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
        0.10         9.96         6.38        17.69        23.84        17.95 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
        8.48         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
       81.96        75.25        47.93        72.92        50.17        44.52 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        46.42        18.84        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64O 
       39.78        37.45        33.57        72.95        31.63        25.48 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       30.12         5.98        31.40        27.45        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O 
       14.40        18.51        12.10        11.24        17.88        30.74 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       16.18        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 
       46.06        65.75        87.45         7.04       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       138.28       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
      117.40        30.67        26.30        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       62.01        25.91        60.30        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       23.74        20.68        21.40        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       14.24        12.59        15.12         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TC TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
       23.51        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 
        0.20        25.48        34.36        36.82        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        18.44        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX 
       14.96        22.52        32.61        38.27        10.72        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 
       40.11         0.13         0.03        16.54         3.75         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7605 
      172.77         4.01         5.03        29.85       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74         0.10        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       11.28        31.43         1.64         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       37.87        33.01         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       15.72        26.04         0.13         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       21.40        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.04        19.33        14.83        13.61         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R3 
       17.03        15.06        13.12        28.37        13.02        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 
       30.05        98.63        31.59        18.71        11.97        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       49.32        34.78        48.39        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       30.44        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       30.08         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A859 
       16.01        23.21         8.05        51.06        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                         0.23                          0.03 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                       211.17                        182.33 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                        18.38                         18.71 
[1] "0.2 - 211.2 (18.4)" "0.0 - 182.3 (18.7)"
[1] "hr=" "2.4"
D2V2, continuous
D2V3, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    16  23
  AMP PEAK  2(1Q32.1) WILD-TYPE 190 243
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     16   23
  AMP PEAK  2(1Q32.1) WILD-TYPE  190  243
        clus
vv       AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  FEMALE                          16                           190
  MALE                            23                           243
[1] 2 2
[1] FALSE
D2V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  2(1Q32.1) MUTATED            19                7                13
  AMP PEAK  2(1Q32.1) WILD-TYPE         157              111               165
D2V5, multiclass
                   clus
vv                  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  ASTROCYTOMA                                19                           157
  OLIGOASTROCYTOMA                            7                           111
  OLIGODENDROGLIOMA                          13                           165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    10  29
  AMP PEAK  2(1Q32.1) WILD-TYPE  82 351
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     10   29
  AMP PEAK  2(1Q32.1) WILD-TYPE   82  351
     clus
vv    AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  NO                           10                            82
  YES                          29                           351
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(1Q32.1) MUTATED                                  0     2
  AMP PEAK  2(1Q32.1) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q32.1) MUTATED                           2    34
  AMP PEAK  2(1Q32.1) WILD-TYPE                        13   403
D2V7, multiclass
                                  clus
vv                                 AMP PEAK  2(1Q32.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     34
                                  clus
vv                                 AMP PEAK  2(1Q32.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                      403
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED     0  37
  AMP PEAK  2(1Q32.1) WILD-TYPE  18 382
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED      0   37
  AMP PEAK  2(1Q32.1) WILD-TYPE   18  382
                        clus
vv                       AMP PEAK  2(1Q32.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          37
                        clus
vv                       AMP PEAK  2(1Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                18
  NOT HISPANIC OR LATINO                           382
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(2P24.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(2P24.3) MUTATED    14   8
  AMP PEAK  3(2P24.3) WILD-TYPE 362  86
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                           22                           448 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                            8                            86 
$`AMP PEAK  3(2P24.3) MUTATED`
TCGA-DB-5274 TCGA-DB-5277 TCGA-DH-A669 TCGA-DH-A7UR TCGA-DU-6407 TCGA-DU-8165 
       75.25        50.86        30.21        54.25        94.52        19.13 
TCGA-E1-5304 TCGA-E1-A7YV TCGA-FG-A711 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 
       41.13        32.45        48.69        15.72         0.23         0.13 
TCGA-HT-A61B TCGA-HW-A5KM TCGA-P5-A5F2 TCGA-S9-A6U0 TCGA-S9-A6WM TCGA-S9-A7J0 
       17.52        20.71         7.63        22.95        19.86        20.02 
TCGA-TM-A84Q TCGA-VM-A8CA TCGA-VM-A8CD TCGA-VW-A8FI 
       25.38        13.51         7.89         8.05 

$`AMP PEAK  3(2P24.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 
        7.40         6.61       122.73        81.96        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31        14.40         8.02        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       17.19        13.12        13.38         3.45        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
      114.08         7.96         7.73        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      138.28        14.99       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       21.40        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       15.12         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
        7.13        21.30        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       23.51         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       75.02        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        18.44        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       26.04        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       12.76        20.81        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        5.88         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       28.70        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       32.45        84.99        31.10        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
       30.08         0.10        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       23.21        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                         0.13                          0.03 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                        94.52                        211.17 
  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE 
                       20.365                        18.560 
[1] "0.1 - 94.5 (20.4)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.9"
D3V2, continuous
D3V3, binary
                               cls
clus                              0   1
  AMP PEAK  3(2P24.3) MUTATED    11  11
  AMP PEAK  3(2P24.3) WILD-TYPE 195 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED     11   11
  AMP PEAK  3(2P24.3) WILD-TYPE  195  255
        clus
vv       AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  FEMALE                          11                           195
  MALE                            11                           255
[1] 2 2
[1] FALSE
D3V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  3(2P24.3) MUTATED            12                2                 8
  AMP PEAK  3(2P24.3) WILD-TYPE         164              116               170
D3V5, multiclass
                   clus
vv                  AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  ASTROCYTOMA                                12                           164
  OLIGOASTROCYTOMA                            2                           116
  OLIGODENDROGLIOMA                           8                           170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                               cls
clus                              0   1
  AMP PEAK  3(2P24.3) MUTATED     3  19
  AMP PEAK  3(2P24.3) WILD-TYPE  89 361
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED      3   19
  AMP PEAK  3(2P24.3) WILD-TYPE   89  361
     clus
vv    AMP PEAK  3(2P24.3) MUTATED AMP PEAK  3(2P24.3) WILD-TYPE
  NO                            3                            89
  YES                          19                           361
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(2P24.3) MUTATED                                  0     0
  AMP PEAK  3(2P24.3) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(2P24.3) MUTATED                           0    21
  AMP PEAK  3(2P24.3) WILD-TYPE                        15   416
D3V7, multiclass
                                  clus
vv                                 AMP PEAK  3(2P24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     21
                                  clus
vv                                 AMP PEAK  3(2P24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   15
  WHITE                                                      416
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK  3(2P24.3) MUTATED     2  17
  AMP PEAK  3(2P24.3) WILD-TYPE  16 402
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2P24.3) MUTATED      2   17
  AMP PEAK  3(2P24.3) WILD-TYPE   16  402
                        clus
vv                       AMP PEAK  3(2P24.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          17
                        clus
vv                       AMP PEAK  3(2P24.3) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           402
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(3Q26.33) MUTATION ANALYSIS
D4V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  4(3Q26.33) MUTATED    10   8
  AMP PEAK  4(3Q26.33) WILD-TYPE 366  86
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                            18                            452 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                             8                             86 
$`AMP PEAK  4(3Q26.33) MUTATED`
TCGA-CS-4942 TCGA-CS-5395 TCGA-DU-6400 TCGA-DU-7013 TCGA-DU-8158 TCGA-DU-A5TW 
       43.89        21.01         1.22         8.84         5.10         5.65 
TCGA-E1-5304 TCGA-FG-5962 TCGA-FG-7636 TCGA-FG-A6J3 TCGA-HT-7606 TCGA-HT-7676 
       41.13        47.77        17.88        22.26        17.29         0.16 
TCGA-HT-A4DS TCGA-HT-A5RA TCGA-QH-A870 TCGA-S9-A6WM TCGA-TM-A84B TCGA-VW-A8FI 
        0.23        27.35        12.99        19.86        24.92         8.05 

$`AMP PEAK  4(3Q26.33) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
        0.10         9.96         6.38        17.69        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       12.43         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       65.75        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       23.31        41.98         2.76        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 
       12.59        15.12         4.96         3.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
        7.13        21.30        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       23.51         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
        0.20        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 
       24.99        23.97        18.44        15.35        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       16.44        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
      122.47         4.57         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
       57.60         0.23        14.27        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59        34.19        28.27        15.72        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
       20.22         0.07         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C 
        1.81        16.14        16.83        21.40        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       19.89         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       11.08        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       80.12        32.45        84.99        31.10        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F 
       48.33        49.32        34.78        48.39        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       35.93        23.47        37.05        16.01        23.21        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                          0.16                           0.03 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                         47.77                         211.17 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                        17.585                         18.710 
[1] "0.2 - 47.8 (17.6)"  "0.0 - 211.2 (18.7)"
[1] "hr=" "4.4"
D4V2, continuous
D4V3, binary
                                cls
clus                               0   1
  AMP PEAK  4(3Q26.33) MUTATED    10   9
  AMP PEAK  4(3Q26.33) WILD-TYPE 196 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED     10    9
  AMP PEAK  4(3Q26.33) WILD-TYPE  196  257
        clus
vv       AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  FEMALE                           10                            196
  MALE                              9                            257
[1] 2 2
[1] FALSE
D4V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  4(3Q26.33) MUTATED            14                1                 4
  AMP PEAK  4(3Q26.33) WILD-TYPE         162              117               174
D4V5, multiclass
                   clus
vv                  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  ASTROCYTOMA                                 14                            162
  OLIGOASTROCYTOMA                             1                            117
  OLIGODENDROGLIOMA                            4                            174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                                cls
clus                               0   1
  AMP PEAK  4(3Q26.33) MUTATED     6  13
  AMP PEAK  4(3Q26.33) WILD-TYPE  86 367
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED      6   13
  AMP PEAK  4(3Q26.33) WILD-TYPE   86  367
     clus
vv    AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  NO                             6                             86
  YES                           13                            367
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(3Q26.33) MUTATED                                  0     0
  AMP PEAK  4(3Q26.33) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(3Q26.33) MUTATED                           3    16
  AMP PEAK  4(3Q26.33) WILD-TYPE                        12   421
D4V7, multiclass
                                  clus
vv                                 AMP PEAK  4(3Q26.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      16
                                  clus
vv                                 AMP PEAK  4(3Q26.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       421
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                                cls
clus                               0   1
  AMP PEAK  4(3Q26.33) MUTATED     0  17
  AMP PEAK  4(3Q26.33) WILD-TYPE  18 402
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED      0   17
  AMP PEAK  4(3Q26.33) WILD-TYPE   18  402
                        clus
vv                       AMP PEAK  4(3Q26.33) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           17
                        clus
vv                       AMP PEAK  4(3Q26.33) WILD-TYPE
  HISPANIC OR LATINO                                 18
  NOT HISPANIC OR LATINO                            402
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(4Q12) MUTATION ANALYSIS
D5V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  5(4Q12) MUTATED    19   8
  AMP PEAK  5(4Q12) WILD-TYPE 357  86
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         27                         443 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                          8                          86 
$`AMP PEAK  5(4Q12) MUTATED`
TCGA-CS-4943 TCGA-CS-6665 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-A75O TCGA-DH-A7UU 
       18.15        12.43         8.48        50.86        30.74         3.45 
TCGA-DU-7010 TCGA-DU-7302 TCGA-DU-7309 TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A7TD 
       14.99        60.30         2.76        15.12         4.96         7.50 
TCGA-E1-5304 TCGA-E1-5307 TCGA-FG-A6J3 TCGA-FG-A87Q TCGA-HT-7477 TCGA-HT-7856 
       41.13        57.93        22.26         5.72        24.26        39.09 
TCGA-HT-7882 TCGA-HT-A5R7 TCGA-S9-A6U0 TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7J0 
        3.72        20.22        22.95        14.07         7.92        20.02 
TCGA-S9-A89Z TCGA-TM-A84I TCGA-VW-A8FI 
       11.97        28.08         8.05 

$`AMP PEAK  5(4Q12) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       17.95         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
       81.96        75.25        47.93        72.92        50.17        44.52 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        46.42        18.84        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       39.78        37.45        33.57        72.95        31.63        24.20 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       29.23        14.40        18.51        12.10        11.24        17.88 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       16.18        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       30.21        42.05        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.12        13.38        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 
       62.01        25.91        23.31        41.98         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       14.17        14.24        12.59         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       42.31        23.51        44.42         0.56        50.14        67.46 
TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       79.99       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        18.44        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       15.02        16.44        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       20.45        13.58        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
       40.11         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
        6.54         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       39.48        19.23         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C 
        1.81        16.14        16.83        21.40        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       19.89         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       31.33        28.70        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       18.61        15.16        36.13        22.32        23.51         7.13 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59        18.71        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       16.01        23.21        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                       2.76                        0.03 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                      60.30                      211.17 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                      15.12                       18.71 
[1] "2.8 - 60.3 (15.1)"  "0.0 - 211.2 (18.7)"
[1] "hr=" "2.4"
D5V2, continuous
D5V3, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED    11  16
  AMP PEAK  5(4Q12) WILD-TYPE 195 250
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     11   16
  AMP PEAK  5(4Q12) WILD-TYPE  195  250
        clus
vv       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  FEMALE                        11                         195
  MALE                          16                         250
[1] 2 2
[1] FALSE
D5V4, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  5(4Q12) MUTATED            18                2                 7
  AMP PEAK  5(4Q12) WILD-TYPE         158              116               171
D5V5, multiclass
                   clus
vv                  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  ASTROCYTOMA                              18                         158
  OLIGOASTROCYTOMA                          2                         116
  OLIGODENDROGLIOMA                         7                         171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     4  23
  AMP PEAK  5(4Q12) WILD-TYPE  88 357
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      4   23
  AMP PEAK  5(4Q12) WILD-TYPE   88  357
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  NO                          4                          88
  YES                        23                         357
[1] 2 2
[1] FALSE
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(4Q12) MUTATED                                  0     0
  AMP PEAK  5(4Q12) WILD-TYPE                                1     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(4Q12) MUTATED                           1    26
  AMP PEAK  5(4Q12) WILD-TYPE                        14   411
D5V7, multiclass
                                  clus
vv                                 AMP PEAK  5(4Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                1
  WHITE                                                   26
                                  clus
vv                                 AMP PEAK  5(4Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    411
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     1  25
  AMP PEAK  5(4Q12) WILD-TYPE  17 394
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      1   25
  AMP PEAK  5(4Q12) WILD-TYPE   17  394
                        clus
vv                       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             1                          17
  NOT HISPANIC OR LATINO                        25                         394
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(7P11.2) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(7P11.2) MUTATED    75  42
  AMP PEAK  6(7P11.2) WILD-TYPE 301  52
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                          117                           353 
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                           42                            52 
$`AMP PEAK  6(7P11.2) MUTATED`
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
        7.69        43.89        40.18        21.01         9.96         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5277 
       17.69        23.84        12.43         6.61       122.73        50.86 
TCGA-DB-A4X9 TCGA-DB-A4XE TCGA-DB-A64O TCGA-DH-5142 TCGA-DH-A669 TCGA-DH-A66G 
       46.42        37.45        25.48        30.31        30.21        17.19 
TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6395 
       13.38        18.61         6.74         8.45       211.17        49.02 
TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
        1.22         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       94.52         7.96        11.47       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7292 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
      117.40        90.77         7.96         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU 
       20.68        19.13        16.96        12.59         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7TA TCGA-DU-A7TD 
        5.65        12.20        11.41        26.76        77.88         7.50 
TCGA-DU-A7TJ TCGA-E1-5304 TCGA-E1-5322 TCGA-FG-5962 TCGA-FG-6688 TCGA-FG-6691 
        0.56        41.13       130.78        47.77        18.77        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7643 TCGA-FG-8182 TCGA-FG-A4MU TCGA-FG-A4MW 
       18.44        15.35        20.09        13.68        10.72        18.38 
TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7473 TCGA-HT-7477 TCGA-HT-7688 TCGA-HT-7860 
       10.78         5.72        16.54        24.26        31.69         0.49 
TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8110 TCGA-HT-8564 
        3.72        16.24        63.55        12.23        13.78        15.72 
TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 
        0.23         0.13         0.07        27.35         5.33        16.14 
TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HW-A5KK 
       21.40        17.65         2.43        10.52        15.35        12.76 
TCGA-KT-A7W1 TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A72U TCGA-QH-A6CS TCGA-QH-A6CV 
       14.40         2.30         4.11         0.16        19.33        14.53 
TCGA-QH-A6CX TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-RY-A845 TCGA-S9-A6TY 
       12.23         1.91        16.50         5.03        19.59        31.33 
TCGA-S9-A6U0 TCGA-S9-A6WM TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 
       22.95        19.86        36.13        22.32         7.13        20.02 
TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84H TCGA-TM-A84M 
       10.39        49.45        34.78        24.92        30.44        24.79 
TCGA-TQ-A7RH TCGA-VW-A8FI TCGA-WY-A85E 
       15.98         8.05        20.81 

$`AMP PEAK  6(7P11.2) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-6290 
        4.70        18.15        10.62        64.64         0.10        17.95 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 TCGA-DB-5274 
        8.48         7.56         8.02         7.40        81.96        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       47.93        72.92        50.17        44.52        36.56        78.28 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       18.84        30.21        46.72        39.78        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       31.63        24.20        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5143 
       17.88        30.74        16.18        19.96        31.82        14.40 
TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US 
        8.02        42.05        27.81        17.19        54.25        13.12 
TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 
        3.45        18.02        14.56        17.46        13.38         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
      182.33        18.94        17.49        15.16        52.11        22.42 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6408 TCGA-DU-6542 
       75.16        46.06        65.75        87.45       114.08         7.73 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7018 TCGA-DU-7019 
       62.96       156.23       138.28        14.99        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
       10.36        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8164 TCGA-DU-8167 
       60.30        23.31        41.98         2.76        21.40        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       14.17        14.24        15.12         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
        7.23         5.98         7.13        21.30        17.98       124.50 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
       42.31        23.51        44.42        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YV 
       57.93       134.27        78.21        95.57        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 
       36.82        32.35        14.33         0.23         0.20        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-7636 TCGA-FG-7638 
       34.36        36.82        14.93        24.99        17.88        22.55 
TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       20.61        12.95        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       22.52        32.61        38.27        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 
       36.66        48.69        20.45        13.58        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 
        6.67        11.54        40.11         0.13         0.03         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42         6.54         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 
        0.76        44.68         6.05        42.74         0.10        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 
       39.48        19.23        39.09         0.23        50.63        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 
       11.28        31.43         1.64         9.40         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       33.01         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R7 
        0.23        29.59        34.19        28.27        26.04        20.22 
TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B 
        0.10         2.70        16.93         1.81        16.83        17.52 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       17.82        20.35        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F1 
       14.40         0.23         6.71         1.64         2.37         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        7.63         0.76         1.28        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ 
       15.85        14.04        14.83        13.61         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-QH-A870 
       10.29        14.53        16.34        16.73        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
        9.90        28.08         2.07        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 
       18.77        37.84        34.49        28.70        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IY 
       15.91        18.61        15.16        14.07         7.92        23.51 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02       169.84        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84C 
       18.71        11.97        48.33        49.32        48.39        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O 
       59.05        40.64        28.08        24.16        40.83        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RW TCGA-VM-A8C8 
       25.38        18.61        14.93        23.80        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       37.05        16.01        23.21        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       39.88        43.40        45.80        46.88        37.71 

  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                       211.17                        182.33 
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                        16.50                         19.59 
[1] "0.1 - 211.2 (16.5)" "0.0 - 182.3 (19.6)"
[1] "hr=" "3"  
D6V2, continuous
D6V3, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P11.2) MUTATED    56  61
  AMP PEAK  6(7P11.2) WILD-TYPE 150 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P11.2) MUTATED     56   61
  AMP PEAK  6(7P11.2) WILD-TYPE  150  205
        clus
vv       AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE
  FEMALE                          56                           150
  MALE                            61                           205
[1] 2 2
[1] FALSE
D6V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  6(7P11.2) MUTATED            52               31                34
  AMP PEAK  6(7P11.2) WILD-TYPE         124               87               144
D6V5, multiclass
                   clus
vv                  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE
  ASTROCYTOMA                                52                           124
  OLIGOASTROCYTOMA                           31                            87
  OLIGODENDROGLIOMA                          34                           144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P11.2) MUTATED    26  91
  AMP PEAK  6(7P11.2) WILD-TYPE  66 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P11.2) MUTATED     26   91
  AMP PEAK  6(7P11.2) WILD-TYPE   66  289
     clus
vv    AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE
  NO                           26                            66
  YES                          91                           289
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(7P11.2) MUTATED                                  1     2
  AMP PEAK  6(7P11.2) WILD-TYPE                                0     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(7P11.2) MUTATED                           7   106
  AMP PEAK  6(7P11.2) WILD-TYPE                         8   331
D6V7, multiclass
                                  clus
vv                                 AMP PEAK  6(7P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                    106
                                  clus
vv                                 AMP PEAK  6(7P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                      331
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P11.2) MUTATED     5 106
  AMP PEAK  6(7P11.2) WILD-TYPE  13 313
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P11.2) MUTATED      5  106
  AMP PEAK  6(7P11.2) WILD-TYPE   13  313
                        clus
vv                       AMP PEAK  6(7P11.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         106
                        clus
vv                       AMP PEAK  6(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           313
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(7Q31.2) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(7Q31.2) MUTATED   117  47
  AMP PEAK  7(7Q31.2) WILD-TYPE 259  47
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                          164                           306 
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                           47                            47 
$`AMP PEAK  7(7Q31.2) MUTATED`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
        4.70         7.69        43.89        21.01         9.96         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5277 
       17.69        23.84        12.43         6.61       122.73        50.86 
TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A64O TCGA-DB-A64X 
       46.42        30.21        39.78        37.45        25.48        18.51 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT TCGA-DH-A7UV 
        8.02        30.21        27.81        17.19        13.38        18.61 
TCGA-DU-5849 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 
       14.56         8.45         6.81        17.49       211.17        49.02 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       65.75         1.22         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 
       16.83        94.52         7.96        11.47       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7292 
       14.99       105.21         6.54         8.84       117.40         7.96 
TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 
       25.91        41.98        23.74        20.68        19.13        16.96 
TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S6 
       12.59         4.96         3.65         5.65        12.20        77.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA 
       11.41        26.76         7.13        21.30       124.50        77.88 
TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5322 TCGA-F6-A8O4 
        7.50         0.56        50.14        41.13       130.78         0.20 
TCGA-FG-5962 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       47.77        36.82        18.77        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7643 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-A4MU TCGA-FG-A4MW 
       15.35        20.09        13.68        16.01        10.72        18.38 
TCGA-FG-A60L TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A87Q TCGA-HT-7473 TCGA-HT-7475 
       16.41        10.78        48.69         5.72        16.54        17.42 
TCGA-HT-7477 TCGA-HT-7604 TCGA-HT-7610 TCGA-HT-7688 TCGA-HT-7693 TCGA-HT-7860 
       24.26       122.47        56.09        31.69        17.52         0.49 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8108 
        3.72        11.28        16.24        63.55        12.23         2.50 
TCGA-HT-8110 TCGA-HT-8114 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R7 
       13.78        34.19        15.72         0.23         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A619 
        0.07        27.35         5.33         1.81        16.14        21.40 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EZ 
        4.31        17.82        20.35        14.40         0.23         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A72U TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A6CS 
        4.11         5.88         0.16         9.01        13.61        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA 
       14.83        14.53        12.23        10.29         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A870 TCGA-RY-A845 TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6WM 
        5.03        12.99        19.59        31.33        22.95        19.86 
TCGA-S9-A6WO TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW 
       18.61        36.13        22.32         7.13        20.02        15.06 
TCGA-S9-A7QY TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA 
       28.37       169.84        10.39        49.45        48.33        34.78 
TCGA-TM-A84B TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84M TCGA-TQ-A7RH TCGA-VW-A7QS 
       24.92        30.44        40.83        24.79        15.98        23.21 
TCGA-VW-A8FI TCGA-WY-A85E 
        8.05        20.81 

$`AMP PEAK  7(7Q31.2) WILD-TYPE`
TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-6290 
       18.15        10.62        64.64        40.18         0.10        17.95 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 TCGA-DB-5274 
        8.48         7.56         8.02         7.40        81.96        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       47.93        72.92        50.17        44.52        36.56        78.28 
TCGA-DB-A4XA TCGA-DB-A4XC TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       18.84        46.72        33.57        72.95        31.63        24.20 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       30.12         5.98        31.40        27.45        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       14.40        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66F 
       19.96        31.82        30.31        14.40        42.05        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 
       54.25        13.12         3.45        18.02        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
       13.38       182.33        18.94        15.16        52.11        22.42 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 
       75.16        46.06        87.45       114.08         7.73        62.96 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7294 TCGA-DU-7298 
       90.77        30.67        26.30        10.36        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8158 
       44.02        62.01        60.30        23.31         2.76         5.10 
TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TS 
       14.60        21.40        15.48        14.17        14.24        15.12 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A7T6 TCGA-DU-A7TB 
        8.65         2.70         7.23         5.98        17.98        42.31 
TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       23.51        44.42        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       78.21        95.57        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6689 TCGA-FG-7636 
       14.33         0.23        25.48        34.36        14.93        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8187 TCGA-FG-8188 
       22.55        20.61        12.95        14.24        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       22.52        32.61        38.27        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A710 
       17.82        15.02        16.44        22.26        28.54        36.66 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       20.45        13.58        27.52         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7478 
       40.11         0.13         0.03         3.75         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
        5.03        29.85        23.18         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       22.06        45.99        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 
       14.96         0.10         0.10         2.96         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 
       39.48        19.23        39.09         0.23        50.63        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       31.43         1.64         9.40         0.10        37.87        33.01 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 
        6.25         0.10         0.46         5.56         0.23        29.59 
TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A618 
       28.27        26.04         0.10         2.70        16.93        16.83 
TCGA-HT-A61B TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
       17.52        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL 
       35.90        21.70        21.60        19.59        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EW TCGA-P5-A5EX 
       20.71        19.00        42.77        14.40         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X 
        2.37         7.63         0.76         1.28        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
       11.64         0.20        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 
       14.04        13.61         2.20         9.17        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       16.73        11.08        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A847 
       30.87         5.46         9.90        28.08         2.07        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ 
       62.17        87.12        18.77        37.84        34.49        28.70 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IS 
       84.99        31.10        15.91        15.16        14.07         7.92 
TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QZ 
       23.51         8.19         2.04        17.03        13.12        13.02 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I 
       49.32        48.39        16.18        59.05        40.64        28.08 
TCGA-TM-A84J TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.16        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-W9-A837 TCGA-WH-A86K 
       35.93        23.47        37.05        16.01        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 

  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                       211.17                        182.33 
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                       17.305                        19.925 
[1] "0.1 - 211.2 (17.3)" "0.0 - 182.3 (19.9)"
[1] "hr=" "2"  
D7V2, continuous
D7V3, binary
                               cls
clus                              0   1
  AMP PEAK  7(7Q31.2) MUTATED    82  82
  AMP PEAK  7(7Q31.2) WILD-TYPE 124 184
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q31.2) MUTATED     82   82
  AMP PEAK  7(7Q31.2) WILD-TYPE  124  184
        clus
vv       AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE
  FEMALE                          82                           124
  MALE                            82                           184
[1] 2 2
[1] FALSE
D7V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  7(7Q31.2) MUTATED            69               45                50
  AMP PEAK  7(7Q31.2) WILD-TYPE         107               73               128
D7V5, multiclass
                   clus
vv                  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE
  ASTROCYTOMA                                69                           107
  OLIGOASTROCYTOMA                           45                            73
  OLIGODENDROGLIOMA                          50                           128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                               cls
clus                              0   1
  AMP PEAK  7(7Q31.2) MUTATED    36 128
  AMP PEAK  7(7Q31.2) WILD-TYPE  56 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q31.2) MUTATED     36  128
  AMP PEAK  7(7Q31.2) WILD-TYPE   56  252
     clus
vv    AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE
  NO                           36                            56
  YES                         128                           252
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(7Q31.2) MUTATED                                  1     4
  AMP PEAK  7(7Q31.2) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(7Q31.2) MUTATED                           9   149
  AMP PEAK  7(7Q31.2) WILD-TYPE                         6   288
D7V7, multiclass
                                  clus
vv                                 AMP PEAK  7(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                    149
                                  clus
vv                                 AMP PEAK  7(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                      288
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                               cls
clus                              0   1
  AMP PEAK  7(7Q31.2) MUTATED     6 153
  AMP PEAK  7(7Q31.2) WILD-TYPE  12 266
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q31.2) MUTATED      6  153
  AMP PEAK  7(7Q31.2) WILD-TYPE   12  266
                        clus
vv                       AMP PEAK  7(7Q31.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         153
                        clus
vv                       AMP PEAK  7(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           266
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(7Q32.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(7Q32.3) MUTATED   122  48
  AMP PEAK  8(7Q32.3) WILD-TYPE 254  46
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                          170                           300 
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                           48                            46 
$`AMP PEAK  8(7Q32.3) MUTATED`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
        4.70         7.69        43.89        21.01         9.96         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5277 
       17.69        23.84        12.43         6.61       122.73        50.86 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A64O 
       78.28        46.42        30.21        39.78        37.45        25.48 
TCGA-DB-A64X TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT 
       18.51         8.02        30.21        27.81        17.19        13.38 
TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5872 TCGA-DU-6392 
       18.61        14.56         8.45         6.81        17.49       211.17 
TCGA-DU-6395 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       49.02        65.75         1.22         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7008 
       19.89        16.83        94.52         7.96        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      138.28        14.99       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7292 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 
       90.77         7.96        25.91        41.98         2.76        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT 
       14.60        20.68        19.13        16.96        12.59         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L 
        3.65         5.65        12.20        77.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ 
        7.13        21.30       124.50        77.88         7.50         0.56 
TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5322 TCGA-E1-A7Z6 TCGA-F6-A8O4 TCGA-FG-5962 
       50.14        41.13       130.78        32.35         0.20        47.77 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       36.82        18.77        24.99        23.97        18.44        15.35 
TCGA-FG-7643 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A60L 
       20.09        13.68        16.01        10.72        18.38        16.41 
TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A87Q TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7477 
       10.78        48.69         5.72        16.54        17.42        24.26 
TCGA-HT-7604 TCGA-HT-7610 TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7860 
      122.47        56.09        31.69         2.96        17.52         0.49 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8108 
        3.72        11.28        16.24        63.55        12.23         2.50 
TCGA-HT-8110 TCGA-HT-8114 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R9 
       13.78        34.19        15.72         0.23         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A619 TCGA-HT-A61C 
       27.35         5.33         1.81        16.14        21.40        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7495 
        2.43        10.52        15.35        11.05         0.10         4.31 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KM TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EZ 
       17.82        20.35        20.71        14.40         0.23         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A72U TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A6CS 
        4.11         5.88         0.16         9.01        13.61        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA 
       14.83        14.53        12.23        10.29         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A870 TCGA-RY-A845 TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6WM 
        5.03        12.99        19.59        31.33        22.95        19.86 
TCGA-S9-A6WO TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW 
       18.61        36.13        22.32         7.13        20.02        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A7C4 
       13.12        28.37       169.84        10.39        49.45        48.33 
TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84H TCGA-TM-A84M TCGA-TQ-A7RH TCGA-VW-A7QS 
       34.78        24.92        30.44        24.79        15.98        23.21 
TCGA-VW-A8FI TCGA-WY-A85E 
        8.05        20.81 

$`AMP PEAK  8(7Q32.3) WILD-TYPE`
TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-6290 
       18.15        10.62        64.64        40.18         0.10        17.95 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 TCGA-DB-5274 
        8.48         7.56         8.02         7.40        81.96        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4XA 
       47.93        72.92        50.17        44.52        36.56        18.84 
TCGA-DB-A4XC TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P 
       46.72        33.57        72.95        31.63        24.20        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66F TCGA-DH-A7UR 
       31.82        30.31        14.40        42.05        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       13.12         3.45        18.02        17.46         6.74        13.38 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 
      182.33        18.94        15.16        52.11        22.42        75.16 
TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7018 
       46.06        87.45       114.08         7.73        62.96        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       26.30        10.36        94.32        18.94        44.02        62.01 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-8158 TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 
       60.30        23.31         5.10        21.40        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 
       14.24        15.12         8.65         2.70         7.23         5.98 
TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5303 TCGA-E1-5305 
       17.98        42.31        23.51        44.42        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YV 
       57.93       134.27        78.21        95.57        75.02        32.45 
TCGA-E1-A7YW TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6689 
       36.82        14.33         0.23        25.48        34.36        14.93 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8187 
       17.88        22.55        20.61        12.95        14.24        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY 
       14.96        22.52        32.61        38.27        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       14.76        17.82        15.02        16.44        22.26        28.54 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       36.66        20.45        13.58        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7476 
       11.54        40.11         0.13         0.03         3.75         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 
        4.01         5.03        29.85        23.18         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
        3.16        22.06        45.99        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7694 TCGA-HT-7695 
        0.10        14.96         0.10         0.10         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 
       39.48        19.23        39.09         0.23        50.63        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       31.43         1.64         9.40         0.10        37.87        33.01 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 
        6.25         0.10         0.46         5.56         0.23        29.59 
TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 
       28.27        26.04        20.22         0.10         2.70        16.93 
TCGA-HT-A618 TCGA-HT-A61B TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       16.83        17.52        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK 
       40.18        35.90        21.70        21.60        19.59        12.76 
TCGA-HW-A5KL TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EW TCGA-P5-A5EX 
       20.81        19.00        42.77        14.40         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X 
        2.37         7.63         0.76         1.28        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
       11.64         0.20        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 
       14.04        13.61         2.20         9.17        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       16.73        11.08        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A847 
       30.87         5.46         9.90        28.08         2.07        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ 
       62.17        87.12        18.77        37.84        34.49        28.70 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        69.50        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IS 
       84.99        31.10        15.91        15.16        14.07         7.92 
TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QZ TCGA-S9-A7R3 
       23.51         8.19         2.04        17.03        13.02        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C5 
       30.05        98.63        31.59        18.71        11.97        49.32 
TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J 
       48.39        16.18        59.05        40.64        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       40.83        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-W9-A837 TCGA-WH-A86K 
       35.93        23.47        37.05        16.01        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 

  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                       211.17                        182.33 
  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE 
                       17.075                        20.025 
[1] "0.1 - 211.2 (17.1)" "0.0 - 182.3 (20.0)"
[1] "hr=" "1.9"
D8V2, continuous
D8V3, binary
                               cls
clus                              0   1
  AMP PEAK  8(7Q32.3) MUTATED    86  84
  AMP PEAK  8(7Q32.3) WILD-TYPE 120 182
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q32.3) MUTATED     86   84
  AMP PEAK  8(7Q32.3) WILD-TYPE  120  182
        clus
vv       AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE
  FEMALE                          86                           120
  MALE                            84                           182
[1] 2 2
[1] FALSE
D8V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  8(7Q32.3) MUTATED            71               47                52
  AMP PEAK  8(7Q32.3) WILD-TYPE         105               71               126
D8V5, multiclass
                   clus
vv                  AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE
  ASTROCYTOMA                                71                           105
  OLIGOASTROCYTOMA                           47                            71
  OLIGODENDROGLIOMA                          52                           126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                               cls
clus                              0   1
  AMP PEAK  8(7Q32.3) MUTATED    38 132
  AMP PEAK  8(7Q32.3) WILD-TYPE  54 248
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q32.3) MUTATED     38  132
  AMP PEAK  8(7Q32.3) WILD-TYPE   54  248
     clus
vv    AMP PEAK  8(7Q32.3) MUTATED AMP PEAK  8(7Q32.3) WILD-TYPE
  NO                           38                            54
  YES                         132                           248
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(7Q32.3) MUTATED                                  1     4
  AMP PEAK  8(7Q32.3) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(7Q32.3) MUTATED                           9   155
  AMP PEAK  8(7Q32.3) WILD-TYPE                         6   282
D8V7, multiclass
                                  clus
vv                                 AMP PEAK  8(7Q32.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                    155
                                  clus
vv                                 AMP PEAK  8(7Q32.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                      282
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK  8(7Q32.3) MUTATED     6 158
  AMP PEAK  8(7Q32.3) WILD-TYPE  12 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q32.3) MUTATED      6  158
  AMP PEAK  8(7Q32.3) WILD-TYPE   12  261
                        clus
vv                       AMP PEAK  8(7Q32.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         158
                        clus
vv                       AMP PEAK  8(7Q32.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           261
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(8Q24.13) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(8Q24.13) MUTATED    75  18
  AMP PEAK  9(8Q24.13) WILD-TYPE 301  76
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                            93                            377 
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                            18                             76 
$`AMP PEAK  9(8Q24.13) MUTATED`
TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-DB-5277 
       18.15        40.18        17.95        12.43         8.48        50.86 
TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A64X TCGA-DH-5143 
       78.28        30.21        39.78        37.45        18.51        14.40 
TCGA-DH-A669 TCGA-DH-A66G TCGA-DH-A7UT TCGA-DU-5871 TCGA-DU-6399 TCGA-DU-6407 
       30.21        17.19        13.38        18.94        65.75        94.52 
TCGA-DU-6408 TCGA-DU-7010 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7304 
      114.08        14.99         8.84       117.40        90.77        23.31 
TCGA-DU-8158 TCGA-DU-8163 TCGA-DU-8167 TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S7 
        5.10        20.68        15.48        15.12         5.65         7.23 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TC TCGA-E1-5303 TCGA-E1-5304 
       17.98       124.50        77.88        23.51        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-A7YW TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6691 
       79.99        57.93        36.82        47.77        34.36        23.97 
TCGA-FG-7634 TCGA-FG-8188 TCGA-FG-A4MT TCGA-FG-A4MY TCGA-FG-A6J3 TCGA-FG-A70Y 
       15.35        14.96        38.27        23.70        22.26        28.54 
TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-7482 
       16.54        17.42         6.54        24.26        40.34       106.95 
TCGA-HT-7604 TCGA-HT-7689 TCGA-HT-7855 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-8011 
      122.47        14.96        19.23        23.61         3.68        16.24 
TCGA-HT-8013 TCGA-HT-8106 TCGA-HT-8111 TCGA-HT-A5R7 TCGA-HT-A614 TCGA-HT-A616 
       63.55         0.10         0.23        20.22         2.70         1.81 
TCGA-HT-A74J TCGA-HT-A74O TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72W 
       10.52         0.10         5.88         7.63         0.76        10.42 
TCGA-QH-A6CW TCGA-QH-A6XA TCGA-RY-A83Z TCGA-S9-A6TU TCGA-S9-A6TY TCGA-S9-A6U6 
       13.61        16.50         9.90        87.12        31.33        16.08 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A7QW TCGA-S9-A7QX 
       80.12        32.45        18.61        15.16        15.06        13.12 
TCGA-TM-A7CF TCGA-TM-A84H TCGA-TM-A84Q TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       48.39        30.44        25.38        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8CA TCGA-WY-A858 
       43.04        13.51        43.96 

$`AMP PEAK  9(8Q24.13) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 
        4.70         7.69        43.89        10.62        64.64         0.10 
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6667 
       21.01         9.96         6.38        17.69        23.84         7.56 
TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 
        8.02         7.40         6.61       122.73        81.96        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 
       47.93        72.92        50.17        44.52        36.56        46.42 
TCGA-DB-A4XA TCGA-DB-A4XC TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       18.84        46.72        33.57        72.95        31.63        24.20 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O 
       29.23        14.40        12.10        11.24        17.88        30.74 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A66B 
       16.18        19.96        31.82        30.31         8.02        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV 
       27.81        17.19        54.25        13.12         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        6.81       182.33        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 
       22.42        49.02        75.16        46.06         1.22        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6410 
        7.04        11.64       133.74        19.89        16.83         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 
        7.73        11.47        62.96       156.23       138.28       105.21 
TCGA-DU-7012 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
        6.54        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 
       18.94        44.02        62.01        25.91        60.30        41.98 
TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
        2.76        23.74        14.60        21.40        19.13        16.96 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY 
       14.17        14.24        12.59         4.96         3.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        8.65         2.70        77.98         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7TB TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
        7.13        21.30        42.31         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       50.14       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 
       32.45        32.35        14.33         0.23         0.20        25.48 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6692 TCGA-FG-7636 
       36.82        18.77        14.93        24.99        18.44        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MU TCGA-FG-A4MW 
       16.01        20.09        22.52        32.61        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.71        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7478 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 
        0.03         3.75         6.38        75.19        95.93       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 
        4.01         5.03        29.85        23.18         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        31.69         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 
       17.52         6.90        14.53        39.48        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 
       50.63         0.49        37.15         0.33         0.13         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 
       35.47         3.72        11.28        31.43         1.64         9.40 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 
        0.10        37.87        33.01        12.23         6.25         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        2.50         5.56        13.78        29.59        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA 
       15.72         0.23        26.04         0.13         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        0.10         5.33        16.93        16.14        16.83        21.40 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 
       17.52        17.65         2.43        15.35        11.05        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       19.89         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        1.28         0.16        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       19.33        14.83        14.53        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XC 
       10.29        14.53        16.34        16.73         1.91         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
       30.87         5.46        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U0 
       62.17        18.77        37.84        34.49        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       17.62        23.64        32.61        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
      106.39        69.50        72.59        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.91        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY 
        7.13        20.02         8.19         2.04        17.03        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I 
       34.78        24.92        16.18        59.05        40.64        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S 
       24.16        40.83        24.79        33.24        18.61        14.93 
TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       30.08         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A859 
       16.01        23.21         8.05        51.06        13.32        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                        124.50                         211.17 
  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE 
                         20.22                          18.44 
[1] "0.1 - 124.5 (20.2)" "0.0 - 211.2 (18.4)"
[1] "hr=" "1.2"
D9V2, continuous
D9V3, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.13) MUTATED    36  57
  AMP PEAK  9(8Q24.13) WILD-TYPE 170 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.13) MUTATED     36   57
  AMP PEAK  9(8Q24.13) WILD-TYPE  170  209
        clus
vv       AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE
  FEMALE                           36                            170
  MALE                             57                            209
[1] 2 2
[1] FALSE
D9V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK  9(8Q24.13) MUTATED            45               27                21
  AMP PEAK  9(8Q24.13) WILD-TYPE         131               91               157
D9V5, multiclass
                   clus
vv                  AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE
  ASTROCYTOMA                                 45                            131
  OLIGOASTROCYTOMA                            27                             91
  OLIGODENDROGLIOMA                           21                            157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.13) MUTATED    18  75
  AMP PEAK  9(8Q24.13) WILD-TYPE  74 305
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.13) MUTATED     18   75
  AMP PEAK  9(8Q24.13) WILD-TYPE   74  305
     clus
vv    AMP PEAK  9(8Q24.13) MUTATED AMP PEAK  9(8Q24.13) WILD-TYPE
  NO                            18                             74
  YES                           75                            305
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(8Q24.13) MUTATED                                  0     0
  AMP PEAK  9(8Q24.13) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(8Q24.13) MUTATED                           3    87
  AMP PEAK  9(8Q24.13) WILD-TYPE                        12   350
D9V7, multiclass
                                  clus
vv                                 AMP PEAK  9(8Q24.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      87
                                  clus
vv                                 AMP PEAK  9(8Q24.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.13) MUTATED     5  82
  AMP PEAK  9(8Q24.13) WILD-TYPE  13 337
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.13) MUTATED      5   82
  AMP PEAK  9(8Q24.13) WILD-TYPE   13  337
                        clus
vv                       AMP PEAK  9(8Q24.13) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           82
                        clus
vv                       AMP PEAK  9(8Q24.13) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            337
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(9Q34.3) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(9Q34.3) MUTATED    36   7
  AMP PEAK 10(9Q34.3) WILD-TYPE 340  87
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                           43                           427 
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                            7                            87 
$`AMP PEAK 10(9Q34.3) MUTATED`
TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6290 TCGA-CS-6665 TCGA-DB-A4XE TCGA-DB-A64R 
        9.96         6.38        17.95        12.43        37.45        31.40 
TCGA-DB-A64X TCGA-DH-5142 TCGA-DU-7010 TCGA-DU-7298 TCGA-DU-8158 TCGA-DU-8161 
       18.51        30.31        14.99        18.94         5.10        23.74 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8168 TCGA-DU-A5TT TCGA-DU-A76O TCGA-E1-5302 
       21.40        19.13        14.17         4.96         7.13        50.14 
TCGA-E1-5304 TCGA-FG-A4MY TCGA-FG-A60K TCGA-FG-A6J3 TCGA-FG-A87N TCGA-HT-7468 
       41.13        23.70        17.82        22.26        13.58         6.67 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7483 TCGA-HT-7601 TCGA-HT-7686 TCGA-HT-7873 
       24.26         6.38       172.77         5.03        42.74        23.61 
TCGA-HT-A5RB TCGA-HT-A617 TCGA-HT-A61B TCGA-HT-A74J TCGA-HW-8319 TCGA-S9-A6TW 
        0.10        16.14        17.52        10.52        21.70        37.84 
TCGA-S9-A6WH TCGA-S9-A6WM TCGA-S9-A7QW TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84T 
       32.45        19.86        15.06        59.05        30.44        23.80 
TCGA-WY-A85E 
       20.81 

$`AMP PEAK 10(9Q34.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6666 
       40.18         0.10        21.01        17.69        23.84         8.48 
TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 
        7.56         8.02         7.40         6.61       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 
       75.25        47.93        72.92        50.86        50.17        44.52 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        46.42        18.84        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O 
       39.78        33.57        72.95        31.63        24.20        25.48 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
       30.12         5.98        27.45        27.81        29.23        14.40 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       31.82        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
       11.47        62.96       156.23       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
        7.96        94.32        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8166 
       23.31        41.98         2.76        14.60        20.68        16.96 
TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW 
       15.48        14.24        12.59        15.12         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       11.41        26.76        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5303 
       42.31        23.51         7.50        44.42         0.56        67.46 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ 
       10.72        18.38        18.71        14.76        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       16.44        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
        5.72        27.52         0.10        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7479 
        0.03        16.54         3.75        17.42         6.54        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 
       75.19        95.93       106.95         4.01        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
        0.76        44.68         6.05         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59        34.19        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 
        0.13        20.22         0.07        27.35         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H 
       16.93         1.81        16.83        21.40        17.65         2.43 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18        35.90         4.31        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       18.77        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL 
      106.39        69.50        72.59        80.12        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       17.03        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       16.18        40.64        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RH TCGA-TQ-A7RW 
       33.24        25.38        18.61        14.93        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D 
       37.71 

  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                       172.77                        211.17 
  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE 
                        19.13                         18.61 
[1] "0.1 - 172.8 (19.1)" "0.0 - 211.2 (18.6)"
[1] "hr=" "1"  
D10V2, continuous
D10V3, binary
                               cls
clus                              0   1
  AMP PEAK 10(9Q34.3) MUTATED    24  19
  AMP PEAK 10(9Q34.3) WILD-TYPE 182 247
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(9Q34.3) MUTATED     24   19
  AMP PEAK 10(9Q34.3) WILD-TYPE  182  247
        clus
vv       AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE
  FEMALE                          24                           182
  MALE                            19                           247
[1] 2 2
[1] FALSE
D10V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 10(9Q34.3) MUTATED            23               11                 9
  AMP PEAK 10(9Q34.3) WILD-TYPE         153              107               169
D10V5, multiclass
                   clus
vv                  AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE
  ASTROCYTOMA                                23                           153
  OLIGOASTROCYTOMA                           11                           107
  OLIGODENDROGLIOMA                           9                           169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                               cls
clus                              0   1
  AMP PEAK 10(9Q34.3) MUTATED    10  33
  AMP PEAK 10(9Q34.3) WILD-TYPE  82 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(9Q34.3) MUTATED     10   33
  AMP PEAK 10(9Q34.3) WILD-TYPE   82  347
     clus
vv    AMP PEAK 10(9Q34.3) MUTATED AMP PEAK 10(9Q34.3) WILD-TYPE
  NO                           10                            82
  YES                          33                           347
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(9Q34.3) MUTATED                                  1     1
  AMP PEAK 10(9Q34.3) WILD-TYPE                                0     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(9Q34.3) MUTATED                           1    38
  AMP PEAK 10(9Q34.3) WILD-TYPE                        14   399
D10V7, multiclass
                                  clus
vv                                 AMP PEAK 10(9Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     38
                                  clus
vv                                 AMP PEAK 10(9Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                      399
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                               cls
clus                              0   1
  AMP PEAK 10(9Q34.3) MUTATED     3  37
  AMP PEAK 10(9Q34.3) WILD-TYPE  15 382
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(9Q34.3) MUTATED      3   37
  AMP PEAK 10(9Q34.3) WILD-TYPE   15  382
                        clus
vv                       AMP PEAK 10(9Q34.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          37
                        clus
vv                       AMP PEAK 10(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           382
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(10P15.3) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 11(10P15.3) MUTATED    53  13
  AMP PEAK 11(10P15.3) WILD-TYPE 323  81
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                            66                            404 
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                            13                             81 
$`AMP PEAK 11(10P15.3) MUTATED`
TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5270 
       18.15        40.18        12.43         8.48         7.56       122.73 
TCGA-DB-5277 TCGA-DB-A4XE TCGA-DB-A75M TCGA-DH-A66B TCGA-DH-A7UU TCGA-DH-A7UV 
       50.86        37.45        17.88        42.05         3.45        18.61 
TCGA-DU-5871 TCGA-DU-6396 TCGA-DU-6408 TCGA-DU-7014 TCGA-DU-7019 TCGA-DU-7299 
       18.94        75.16       114.08       117.40        26.30        44.02 
TCGA-DU-7304 TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TW TCGA-E1-5303 TCGA-E1-5304 
       23.31        12.59        15.12         5.65        67.46        41.13 
TCGA-E1-5322 TCGA-E1-A7YW TCGA-FG-6691 TCGA-FG-8185 TCGA-FG-A4MY TCGA-FG-A60L 
      130.78        36.82        23.97        14.24        23.70        16.41 
TCGA-FG-A70Y TCGA-HT-7470 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7479 TCGA-HT-7482 
       28.54        40.11        16.54         6.54        40.34       106.95 
TCGA-HT-7483 TCGA-HT-7688 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-8106 TCGA-HT-8111 
      172.77        31.69        23.61         3.68         0.10         0.23 
TCGA-HT-8114 TCGA-HT-A74O TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-8321 TCGA-IK-7675 
       34.19         0.10         8.32        35.90        19.59        19.00 
TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A72X TCGA-QH-A6XA TCGA-RY-A845 TCGA-S9-A6U0 
        2.30         5.88        13.25        16.50        19.59        22.95 
TCGA-S9-A7IS TCGA-S9-A7J0 TCGA-S9-A89Z TCGA-TM-A7CA TCGA-TM-A84H TCGA-TQ-A7RH 
        7.92        20.02        11.97        34.78        30.44        15.98 
TCGA-VM-A8C8 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85E 
       43.04        13.32        43.96        39.88        43.40        20.81 

$`AMP PEAK 11(10P15.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 
        4.70         7.69        43.89        10.62        64.64         0.10 
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
       21.01         9.96         6.38        17.69        23.84        17.95 
TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        8.02         7.40         6.61        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       18.84        30.21        46.72        39.78        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       11.24        30.74        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       14.40         8.02        30.21        27.81        17.19        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       54.25        13.12        13.38        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 
        6.74        13.38         8.45         6.81       182.33        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 
       15.16       211.17        52.11        22.42        49.02        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       19.89        16.83        94.52         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
        8.84        90.77        30.67        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 
       18.94        62.01        25.91        60.30        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TT TCGA-DU-A5TU 
       16.96        15.48        14.17        14.24         4.96         3.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
       11.41        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       50.14        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       75.02        32.45        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       24.99        18.44        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       20.09        12.95        13.68        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
       14.76        17.82        15.02        16.44        22.26        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 
        0.10         6.67        11.54         0.13         0.03         3.75 
TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7485 
       17.42        24.26         6.38        75.19        95.93         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
        0.23        50.63         0.49        37.15         0.33         0.13 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
       12.23         6.25         0.46         2.50         5.56        13.78 
TCGA-HT-8113 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
       16.93         1.81        16.14        16.83        21.40        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 
       17.65         2.43        10.52        15.35        11.05        29.92 
TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.89        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 
       17.82        20.35        12.76        20.81        20.71        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        4.11         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.34        16.73         1.91         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
        9.90        28.08         2.07        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 
       18.77        37.84        34.49        31.33        28.70        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 
       36.13        22.32        23.51         7.13         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       49.45        48.33        49.32        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       59.05        40.64        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RW 
       33.24        25.38        18.61        14.93        23.80        26.99 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A85B 
       37.05        16.01        23.21         8.05        51.06        45.80 
TCGA-WY-A85C TCGA-WY-A85D 
       46.88        37.71 

  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                        172.77                         211.17 
  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE 
                         21.88                          18.00 
[1] "0.1 - 172.8 (21.9)" "0.0 - 211.2 (18.0)"
[1] "hr=" "1.3"
D11V2, continuous
D11V3, binary
                                cls
clus                               0   1
  AMP PEAK 11(10P15.3) MUTATED    24  42
  AMP PEAK 11(10P15.3) WILD-TYPE 182 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10P15.3) MUTATED     24   42
  AMP PEAK 11(10P15.3) WILD-TYPE  182  224
        clus
vv       AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE
  FEMALE                           24                            182
  MALE                             42                            224
[1] 2 2
[1] FALSE
D11V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 11(10P15.3) MUTATED            34               23                 9
  AMP PEAK 11(10P15.3) WILD-TYPE         142               95               169
D11V5, multiclass
                   clus
vv                  AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE
  ASTROCYTOMA                                 34                            142
  OLIGOASTROCYTOMA                            23                             95
  OLIGODENDROGLIOMA                            9                            169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                                cls
clus                               0   1
  AMP PEAK 11(10P15.3) MUTATED    18  48
  AMP PEAK 11(10P15.3) WILD-TYPE  74 332
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10P15.3) MUTATED     18   48
  AMP PEAK 11(10P15.3) WILD-TYPE   74  332
     clus
vv    AMP PEAK 11(10P15.3) MUTATED AMP PEAK 11(10P15.3) WILD-TYPE
  NO                            18                             74
  YES                           48                            332
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(10P15.3) MUTATED                                  0     0
  AMP PEAK 11(10P15.3) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(10P15.3) MUTATED                           2    63
  AMP PEAK 11(10P15.3) WILD-TYPE                        13   374
D11V7, multiclass
                                  clus
vv                                 AMP PEAK 11(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      63
                                  clus
vv                                 AMP PEAK 11(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    13
  WHITE                                                       374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                                cls
clus                               0   1
  AMP PEAK 11(10P15.3) MUTATED     5  54
  AMP PEAK 11(10P15.3) WILD-TYPE  13 365
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10P15.3) MUTATED      5   54
  AMP PEAK 11(10P15.3) WILD-TYPE   13  365
                        clus
vv                       AMP PEAK 11(10P15.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           54
                        clus
vv                       AMP PEAK 11(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            365
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(11Q24.1) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(11Q24.1) MUTATED    65  17
  AMP PEAK 12(11Q24.1) WILD-TYPE 311  77
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                            82                            388 
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                            17                             77 
$`AMP PEAK 12(11Q24.1) MUTATED`
TCGA-CS-5396 TCGA-DB-5277 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
        9.96        50.86        46.42        30.21        46.72        39.78 
TCGA-DB-A64L TCGA-DB-A64Q TCGA-DB-A64V TCGA-DB-A75L TCGA-DH-5144 TCGA-DH-A66D 
       24.20         5.98        29.23        11.24         8.02        27.81 
TCGA-DH-A7UT TCGA-DU-5852 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-6392 
       13.38         6.74         6.81       182.33        18.94       211.17 
TCGA-DU-6393 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6407 TCGA-DU-7015 TCGA-DU-7018 
       52.11        46.06         1.22        94.52        90.77        30.67 
TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-A5TT 
       18.94        25.91        23.31        41.98         2.76         4.96 
TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-E1-5304 TCGA-E1-5318 TCGA-FG-5962 
        5.65         7.23         5.98        41.13        78.21        47.77 
TCGA-FG-7634 TCGA-FG-8191 TCGA-FG-A60L TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7601 
       15.35        32.61        16.41        40.11         3.75         5.03 
TCGA-HT-7604 TCGA-HT-7607 TCGA-HT-7676 TCGA-HT-7684 TCGA-HT-7688 TCGA-HT-7693 
      122.47         3.16         0.16         6.05        31.69        17.52 
TCGA-HT-8109 TCGA-HT-A74H TCGA-HT-A74K TCGA-HW-7490 TCGA-HW-8319 TCGA-HW-8321 
        5.56         2.43        15.35        19.23        21.70        19.59 
TCGA-P5-A5EV TCGA-P5-A72W TCGA-QH-A65S TCGA-QH-A65X TCGA-QH-A6CZ TCGA-QH-A6X9 
        0.23        10.42         2.53        15.85         9.17         1.91 
TCGA-RY-A840 TCGA-RY-A845 TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TY TCGA-S9-A6WD 
       28.08        19.59        87.12        37.84        31.33        69.50 
TCGA-S9-A6WH TCGA-S9-A6WN TCGA-S9-A7IZ TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R8 
       32.45        15.91         7.13        28.37        13.02        31.59 
TCGA-S9-A89Z TCGA-TM-A84B TCGA-TM-A84I TCGA-TM-A84J TCGA-TQ-A7RW TCGA-VM-A8C8 
       11.97        24.92        28.08        24.16        26.99        43.04 
TCGA-VM-A8CA TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85E 
       13.51        45.80        46.88        20.81 

$`AMP PEAK 12(11Q24.1) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XE 
       50.17        44.52        36.56        78.28        18.84        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64R 
       33.57        72.95        31.63        25.48        30.12        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75M 
       27.45        27.81        14.40        18.51        12.10        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       30.74        16.18        19.96        31.82        30.31        14.40 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       30.21        42.05        17.19        17.19        54.25        13.12 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
        3.45        18.61        18.02        14.56        17.46        13.38 
TCGA-DU-5854 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
        8.45        17.49        15.16        22.42        49.02        75.16 
TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       65.75        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       16.83       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 
      117.40        26.30        10.36         7.96        94.32        44.02 
TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       62.01        60.30         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       12.59        15.12         3.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
       77.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        0.56        50.14        67.46        79.99        57.93       134.27 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       14.33         0.23         0.20        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 
       18.77        14.93        24.99        23.97        18.44        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MT TCGA-FG-A4MU 
       16.01        20.09        14.96        22.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A6IZ 
       18.38        18.71        23.70        14.76        17.82        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        22.26        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7476 
       11.54         0.13         0.03        16.54        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 
      172.77         4.01        29.85        23.18         4.57        17.29 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 
       16.24         0.76        44.68        42.74         0.10        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         0.10         2.96         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.10         0.46         2.50        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
       16.93         1.81        16.14        16.83        21.40        17.52 
TCGA-HT-A61C TCGA-HT-A74J TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       17.65        10.52        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8322 
        8.32        40.18        35.90         4.31        21.60        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40        14.40         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       12.62        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
       12.23         2.20        10.29        14.53        16.34        16.73 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A843 
       32.65        59.38        30.87         5.46         9.90         2.07 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U0 
       30.67        62.17        18.77        34.49        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL 
        5.85       106.39        72.59        80.12        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       19.86        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       22.32        23.51        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       15.06        13.12       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       98.63        18.71        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L 
       48.39        16.18        59.05        40.64        30.44        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       15.98        30.08         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85D 
       43.96        39.88        43.40        37.71 

  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                          0.16                           0.03 
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                        211.17                         172.77 
  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE 
                        21.255                         18.265 
[1] "0.2 - 211.2 (21.3)" "0.0 - 172.8 (18.3)"
[1] "hr=" "1"  
D12V2, continuous
D12V3, binary
                                cls
clus                               0   1
  AMP PEAK 12(11Q24.1) MUTATED    39  43
  AMP PEAK 12(11Q24.1) WILD-TYPE 167 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11Q24.1) MUTATED     39   43
  AMP PEAK 12(11Q24.1) WILD-TYPE  167  223
        clus
vv       AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE
  FEMALE                           39                            167
  MALE                             43                            223
[1] 2 2
[1] FALSE
D12V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 12(11Q24.1) MUTATED            30               17                35
  AMP PEAK 12(11Q24.1) WILD-TYPE         146              101               143
D12V5, multiclass
                   clus
vv                  AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE
  ASTROCYTOMA                                 30                            146
  OLIGOASTROCYTOMA                            17                            101
  OLIGODENDROGLIOMA                           35                            143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                                cls
clus                               0   1
  AMP PEAK 12(11Q24.1) MUTATED    15  67
  AMP PEAK 12(11Q24.1) WILD-TYPE  77 313
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11Q24.1) MUTATED     15   67
  AMP PEAK 12(11Q24.1) WILD-TYPE   77  313
     clus
vv    AMP PEAK 12(11Q24.1) MUTATED AMP PEAK 12(11Q24.1) WILD-TYPE
  NO                            15                             77
  YES                           67                            313
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(11Q24.1) MUTATED                                  0     0
  AMP PEAK 12(11Q24.1) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(11Q24.1) MUTATED                           3    76
  AMP PEAK 12(11Q24.1) WILD-TYPE                        12   361
D12V7, multiclass
                                  clus
vv                                 AMP PEAK 12(11Q24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      76
                                  clus
vv                                 AMP PEAK 12(11Q24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       361
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                                cls
clus                               0   1
  AMP PEAK 12(11Q24.1) MUTATED     2  73
  AMP PEAK 12(11Q24.1) WILD-TYPE  16 346
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11Q24.1) MUTATED      2   73
  AMP PEAK 12(11Q24.1) WILD-TYPE   16  346
                        clus
vv                       AMP PEAK 12(11Q24.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           73
                        clus
vv                       AMP PEAK 12(11Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            346
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(12P13.32) MUTATION ANALYSIS
D13V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 13(12P13.32) MUTATED    45  19
  AMP PEAK 13(12P13.32) WILD-TYPE 331  75
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                             64                             406 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                             19                              75 
$`AMP PEAK 13(12P13.32) MUTATED`
TCGA-CS-4943 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A4XB 
       18.15        81.96        47.93        50.86        78.28        30.21 
TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A64P TCGA-DH-A669 TCGA-DU-6395 TCGA-DU-6396 
       46.72        37.45        30.12        30.21        49.02        75.16 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6403 TCGA-DU-6408 TCGA-DU-7007 TCGA-DU-7008 
       65.75         1.22        11.64       114.08        62.96       156.23 
TCGA-DU-7299 TCGA-DU-7304 TCGA-DU-8165 TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A5TT 
       44.02        23.31        19.13        14.24        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5303 TCGA-E1-5304 
        3.65        12.20       124.50        77.88        67.46        41.13 
TCGA-E1-A7YW TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-8182 
       36.82        36.82        24.99        23.97        15.35        13.68 
TCGA-FG-8185 TCGA-FG-8191 TCGA-FG-A6J3 TCGA-FG-A711 TCGA-HT-7469 TCGA-HT-7473 
       14.24        32.61        22.26        48.69        11.54        16.54 
TCGA-HT-7478 TCGA-HT-7604 TCGA-HT-7686 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7884 
        6.38       122.47        42.74        23.61         3.68        11.28 
TCGA-HT-8018 TCGA-HT-A614 TCGA-HW-A5KM TCGA-QH-A6CV TCGA-RY-A83Z TCGA-S9-A6UA 
       37.87         2.70        20.71        14.53         9.90         5.85 
TCGA-S9-A6WO TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QX TCGA-S9-A7R7 TCGA-TM-A84I 
       18.61         7.13        20.02        13.12        98.63        28.08 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85B TCGA-WY-A85E 
       43.96        39.88        45.80        20.81 

$`AMP PEAK 13(12P13.32) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
        6.61       122.73        75.25        72.92        50.17        44.52 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       36.56        46.42        18.84        39.78        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       31.63        24.20        25.48         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       17.88        30.74        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       14.40         8.02        42.05        27.81        17.19        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       54.25        13.12        13.38         3.45        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 
       22.42        46.06        87.45         7.04       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7009 
       16.83        94.52         7.96         7.73        11.47       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       62.01        25.91        60.30        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74        14.60        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TR TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       14.17        12.59         5.65         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       17.98        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       50.14        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
      130.78        75.02        32.45        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6689 
        0.20        47.77        25.48        34.36        18.77        14.93 
TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       18.44        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MT TCGA-FG-A4MU 
       16.01        20.09        14.96        22.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
       15.02        16.44        28.54        10.78        36.66        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 
       13.58         5.72        27.52         0.10         6.67        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.13         0.03         3.75        17.42         6.54        24.26 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
        5.03        29.85        23.18         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 
        0.16        16.24         0.76        44.68         6.05         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 
       50.63         0.49        37.15         0.33         0.13         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
       35.47         3.72        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
       63.55         0.10        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 
       20.22         0.07        27.35         0.10         5.33        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C 
        1.81        16.14        16.83        21.40        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       19.89         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.81        19.00        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW 
       12.62        15.85        14.04        19.33        14.83        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       31.10        19.86        15.91        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
        7.92        22.32        23.51         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       15.06        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       30.05        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       40.64        30.44        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85D 
       13.32        43.40        46.88        37.71 

  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                           1.22                            0.03 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                         156.23                          211.17 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                         26.535                          17.880 
[1] "1.2 - 156.2 (26.5)" "0.0 - 211.2 (17.9)"
[1] "hr=" "1.1"
D13V2, continuous
D13V3, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED    23  41
  AMP PEAK 13(12P13.32) WILD-TYPE 183 225
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED     23   41
  AMP PEAK 13(12P13.32) WILD-TYPE  183  225
        clus
vv       AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  FEMALE                            23                             183
  MALE                              41                             225
[1] 2 2
[1] FALSE
D13V4, continuous
                                 vv
clus                              ASTROCYTOMA OLIGOASTROCYTOMA
  AMP PEAK 13(12P13.32) MUTATED            29               18
  AMP PEAK 13(12P13.32) WILD-TYPE         147              100
                                 vv
clus                              OLIGODENDROGLIOMA
  AMP PEAK 13(12P13.32) MUTATED                  17
  AMP PEAK 13(12P13.32) WILD-TYPE               161
D13V5, multiclass
                   clus
vv                  AMP PEAK 13(12P13.32) MUTATED
  ASTROCYTOMA                                  29
  OLIGOASTROCYTOMA                             18
  OLIGODENDROGLIOMA                            17
                   clus
vv                  AMP PEAK 13(12P13.32) WILD-TYPE
  ASTROCYTOMA                                   147
  OLIGOASTROCYTOMA                              100
  OLIGODENDROGLIOMA                             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED    18  46
  AMP PEAK 13(12P13.32) WILD-TYPE  74 334
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED     18   46
  AMP PEAK 13(12P13.32) WILD-TYPE   74  334
     clus
vv    AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  NO                             18                              74
  YES                            46                             334
[1] 2 2
[1] FALSE
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(12P13.32) MUTATED                                  0     1
  AMP PEAK 13(12P13.32) WILD-TYPE                                1     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(12P13.32) MUTATED                           2    61
  AMP PEAK 13(12P13.32) WILD-TYPE                        13   376
D13V7, multiclass
                                  clus
vv                                 AMP PEAK 13(12P13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    2
  WHITE                                                       61
                                  clus
vv                                 AMP PEAK 13(12P13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     13
  WHITE                                                        376
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED     1  57
  AMP PEAK 13(12P13.32) WILD-TYPE  17 362
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED      1   57
  AMP PEAK 13(12P13.32) WILD-TYPE   17  362
                        clus
vv                       AMP PEAK 13(12P13.32) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            57
                        clus
vv                       AMP PEAK 13(12P13.32) WILD-TYPE
  HISPANIC OR LATINO                                  17
  NOT HISPANIC OR LATINO                             362
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(12Q14.1) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(12Q14.1) MUTATED    18  16
  AMP PEAK 14(12Q14.1) WILD-TYPE 358  78
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            34                            436 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            16                             78 
$`AMP PEAK 14(12Q14.1) MUTATED`
TCGA-CS-4941 TCGA-CS-6665 TCGA-DH-A669 TCGA-DU-6400 TCGA-DU-6403 TCGA-DU-7010 
        7.69        12.43        30.21         1.22        11.64        14.99 
TCGA-DU-7013 TCGA-DU-7298 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A7TA 
        8.84        18.94        19.13         4.96        12.20        77.88 
TCGA-E1-5305 TCGA-E1-5318 TCGA-E1-A7YV TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-A6J3 
       79.99        78.21        32.45        15.35        17.88        22.26 
TCGA-FG-A70Z TCGA-HT-8563 TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A61B TCGA-IK-7675 
       10.78        28.27         5.33         2.70        17.52        19.00 
TCGA-P5-A5EZ TCGA-P5-A72U TCGA-QH-A6CV TCGA-S9-A6UA TCGA-S9-A7IZ TCGA-S9-A7R2 
        2.30         0.16        14.53         5.85         7.13        10.39 
TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84I TCGA-VW-A8FI 
       49.45        24.92        28.08         8.05 

$`AMP PEAK 14(12Q14.1) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31        14.40         8.02        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
       87.45         7.04       133.74        19.89        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
      114.08         7.96         7.73        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      138.28       105.21         6.54       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 
       26.30        10.36         7.96        94.32        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74        14.60        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW 
       14.17        14.24        12.59        15.12         3.65         5.65 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TB 
       26.76         7.13        21.30        17.98       124.50        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       23.51         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       41.13        57.93       134.27        95.57       130.78        75.02 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       23.97        18.44        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y 
       14.76        17.82        16.41        15.02        16.44        28.54 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       34.19        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.07        27.35         0.10        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       16.83        21.40        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 
       17.82        20.35        12.76        20.81        20.71        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W 
        4.11         5.88         7.63         0.76         1.28        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       16.34        16.73         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
        5.46         9.90        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       98.24        95.93       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       28.37        13.02       169.84        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59        18.71        11.97        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J 
       48.39        16.18        59.05        40.64        30.44        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       23.21        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                          0.16                           0.03 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                         79.99                         211.17 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                        14.760                         18.805 
[1] "0.2 - 80.0 (14.8)"  "0.0 - 211.2 (18.8)"
[1] "hr=" "4.1"
D14V2, continuous
D14V3, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q14.1) MUTATED    16  18
  AMP PEAK 14(12Q14.1) WILD-TYPE 190 248
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q14.1) MUTATED     16   18
  AMP PEAK 14(12Q14.1) WILD-TYPE  190  248
        clus
vv       AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  FEMALE                           16                            190
  MALE                             18                            248
[1] 2 2
[1] FALSE
D14V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 14(12Q14.1) MUTATED            20                5                 9
  AMP PEAK 14(12Q14.1) WILD-TYPE         156              113               169
D14V5, multiclass
                   clus
vv                  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  ASTROCYTOMA                                 20                            156
  OLIGOASTROCYTOMA                             5                            113
  OLIGODENDROGLIOMA                            9                            169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q14.1) MUTATED     4  30
  AMP PEAK 14(12Q14.1) WILD-TYPE  88 350
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q14.1) MUTATED      4   30
  AMP PEAK 14(12Q14.1) WILD-TYPE   88  350
     clus
vv    AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  NO                             4                             88
  YES                           30                            350
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(12Q14.1) MUTATED                                  0     1
  AMP PEAK 14(12Q14.1) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(12Q14.1) MUTATED                           2    31
  AMP PEAK 14(12Q14.1) WILD-TYPE                        13   406
D14V7, multiclass
                                  clus
vv                                 AMP PEAK 14(12Q14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      31
                                  clus
vv                                 AMP PEAK 14(12Q14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    13
  WHITE                                                       406
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q14.1) MUTATED     1  33
  AMP PEAK 14(12Q14.1) WILD-TYPE  17 386
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q14.1) MUTATED      1   33
  AMP PEAK 14(12Q14.1) WILD-TYPE   17  386
                        clus
vv                       AMP PEAK 14(12Q14.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           33
                        clus
vv                       AMP PEAK 14(12Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                 17
  NOT HISPANIC OR LATINO                            386
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(13Q34) MUTATION ANALYSIS
D15V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 15(13Q34) MUTATED    18   2
  AMP PEAK 15(13Q34) WILD-TYPE 358  92
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          20                          450 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                           2                           92 
$`AMP PEAK 15(13Q34) MUTATED`
TCGA-DB-5277 TCGA-DU-5853 TCGA-DU-7015 TCGA-DU-7301 TCGA-DU-A5TT TCGA-DU-A5TU 
       50.86        13.38        90.77        25.91         4.96         3.65 
TCGA-DU-A5TY TCGA-HT-7476 TCGA-HT-7604 TCGA-HT-7611 TCGA-HT-7688 TCGA-HT-7873 
       12.20         6.54       122.47        57.60        31.69        23.61 
TCGA-HT-8563 TCGA-HT-A5R7 TCGA-QH-A65S TCGA-QH-A6X9 TCGA-S9-A89Z TCGA-TM-A7C3 
       28.27        20.22         2.53         1.91        11.97        49.45 
TCGA-TM-A84T TCGA-VM-A8CA 
       23.80        13.51 

$`AMP PEAK 15(13Q34) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84       117.40        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 
        7.96        94.32        18.94        44.02        62.01        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 
       14.24        12.59        15.12         5.65         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.50        44.42         0.56        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
       75.02        32.45        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       29.85        23.18         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       45.99        56.09         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 
        0.76        44.68         6.05        42.74         0.10        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59        34.19        15.72         0.23        26.04         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C 
        1.81        16.14        16.83        21.40        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 
        2.43        10.52        15.35        11.05         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       19.89         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        5.88         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23         2.20         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.34        16.73        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C4 TCGA-TM-A7C5 
       30.05        98.63        31.59        18.71        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       30.44        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       25.38        18.61        14.93        15.98        26.99        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       30.08         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                        1.91                         0.03 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                      122.47                       211.17 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                      21.915                       18.610 
[1] "1.9 - 122.5 (21.9)" "0.0 - 211.2 (18.6)"
[1] "hr=" "2.2"
D15V2, continuous
D15V3, binary
                              cls
clus                             0   1
  AMP PEAK 15(13Q34) MUTATED     8  13
  AMP PEAK 15(13Q34) WILD-TYPE 198 253
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(13Q34) MUTATED      8   13
  AMP PEAK 15(13Q34) WILD-TYPE  198  253
        clus
vv       AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE
  FEMALE                          8                          198
  MALE                           13                          253
[1] 2 2
[1] FALSE
D15V4, continuous
                              vv
clus                           ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 15(13Q34) MUTATED            10                5                 6
  AMP PEAK 15(13Q34) WILD-TYPE         166              113               172
D15V5, multiclass
                   clus
vv                  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE
  ASTROCYTOMA                               10                          166
  OLIGOASTROCYTOMA                           5                          113
  OLIGODENDROGLIOMA                          6                          172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                              cls
clus                             0   1
  AMP PEAK 15(13Q34) MUTATED     5  16
  AMP PEAK 15(13Q34) WILD-TYPE  87 364
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(13Q34) MUTATED      5   16
  AMP PEAK 15(13Q34) WILD-TYPE   87  364
     clus
vv    AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE
  NO                           5                           87
  YES                         16                          364
[1] 2 2
[1] FALSE
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(13Q34) MUTATED                                  0     0
  AMP PEAK 15(13Q34) WILD-TYPE                                1     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(13Q34) MUTATED                           1    19
  AMP PEAK 15(13Q34) WILD-TYPE                        14   418
D15V7, multiclass
                                  clus
vv                                 AMP PEAK 15(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 1
  WHITE                                                    19
                                  clus
vv                                 AMP PEAK 15(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     418
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                              cls
clus                             0   1
  AMP PEAK 15(13Q34) MUTATED     1  19
  AMP PEAK 15(13Q34) WILD-TYPE  17 400
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(13Q34) MUTATED      1   19
  AMP PEAK 15(13Q34) WILD-TYPE   17  400
                        clus
vv                       AMP PEAK 15(13Q34) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         19
                        clus
vv                       AMP PEAK 15(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               17
  NOT HISPANIC OR LATINO                          400
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(15Q26.3) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(15Q26.3) MUTATED     7   8
  AMP PEAK 16(15Q26.3) WILD-TYPE 369  86
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            15                            455 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                             8                             86 
$`AMP PEAK 16(15Q26.3) MUTATED`
TCGA-CS-4943 TCGA-CS-6666 TCGA-DB-5277 TCGA-DU-5852 TCGA-DU-7306 TCGA-E1-5304 
       18.15         8.48        50.86         6.74        41.98        41.13 
TCGA-E1-A7YV TCGA-FG-A4MY TCGA-HT-7470 TCGA-HT-8108 TCGA-HW-8319 TCGA-S9-A6UA 
       32.45        23.70        40.11         2.50        21.70         5.85 
TCGA-S9-A7IS TCGA-S9-A7IZ TCGA-TM-A84B 
        7.92         7.13        24.92 

$`AMP PEAK 16(15Q26.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95        12.43         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       44.52        36.56        78.28        46.42        18.84        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       46.72        39.78        37.45        33.57        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       24.20        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       17.88        30.74        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       18.02        14.56        17.46        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       23.31         2.76         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA 
       26.76         7.13        21.30        17.98       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
      130.78        75.02        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        25.48        34.36        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       10.72        18.38        18.71        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        6.67        11.54         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 
       33.01        12.23         6.25         0.10         0.46         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.83        21.40        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18        35.90         4.31        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35        12.76        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        1.28         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        9.01        13.61        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       36.13        22.32        23.51        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        30.05        98.63        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       11.97        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       23.80        15.98        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                          2.50                           0.03 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                         50.86                         211.17 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                         21.70                          18.61 
[1] "2.5 - 50.9 (21.7)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "4.1"
D16V2, continuous
D16V3, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.3) MUTATED     7   8
  AMP PEAK 16(15Q26.3) WILD-TYPE 199 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.3) MUTATED      7    8
  AMP PEAK 16(15Q26.3) WILD-TYPE  199  258
        clus
vv       AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE
  FEMALE                            7                            199
  MALE                              8                            258
[1] 2 2
[1] FALSE
D16V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 16(15Q26.3) MUTATED             9                4                 2
  AMP PEAK 16(15Q26.3) WILD-TYPE         167              114               176
D16V5, multiclass
                   clus
vv                  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE
  ASTROCYTOMA                                  9                            167
  OLIGOASTROCYTOMA                             4                            114
  OLIGODENDROGLIOMA                            2                            176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.3) MUTATED     4  11
  AMP PEAK 16(15Q26.3) WILD-TYPE  88 369
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.3) MUTATED      4   11
  AMP PEAK 16(15Q26.3) WILD-TYPE   88  369
     clus
vv    AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE
  NO                             4                             88
  YES                           11                            369
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(15Q26.3) MUTATED                                  0     0
  AMP PEAK 16(15Q26.3) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(15Q26.3) MUTATED                           0    15
  AMP PEAK 16(15Q26.3) WILD-TYPE                        15   422
D16V7, multiclass
                                  clus
vv                                 AMP PEAK 16(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      15
                                  clus
vv                                 AMP PEAK 16(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       422
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.3) MUTATED     1  13
  AMP PEAK 16(15Q26.3) WILD-TYPE  17 406
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.3) MUTATED      1   13
  AMP PEAK 16(15Q26.3) WILD-TYPE   17  406
                        clus
vv                       AMP PEAK 16(15Q26.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           13
                        clus
vv                       AMP PEAK 16(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                 17
  NOT HISPANIC OR LATINO                            406
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(17Q25.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(17Q25.1) MUTATED    26  13
  AMP PEAK 17(17Q25.1) WILD-TYPE 350  81
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                            39                            431 
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                            13                             81 
$`AMP PEAK 17(17Q25.1) MUTATED`
TCGA-CS-6665 TCGA-DB-A4XB TCGA-DB-A4XF TCGA-DB-A64P TCGA-DB-A64Q TCGA-DH-5140 
       12.43        30.21        33.57        30.12         5.98        19.96 
TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-6399 TCGA-DU-7010 TCGA-DU-7013 TCGA-DU-7304 
       30.21        17.19        65.75        14.99         8.84        23.31 
TCGA-DU-A6S7 TCGA-E1-5304 TCGA-E1-A7YO TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-7634 
        7.23        41.13        75.02         0.20        47.77        15.35 
TCGA-FG-A60J TCGA-FG-A87Q TCGA-HT-7477 TCGA-HT-8010 TCGA-HT-A61C TCGA-IK-7675 
       14.76         5.72        24.26         1.64        17.65        19.00 
TCGA-QH-A6CV TCGA-RY-A840 TCGA-S9-A6TS TCGA-S9-A6U1 TCGA-S9-A6UA TCGA-S9-A6WG 
       14.53        28.08        62.17        17.62         5.85        80.12 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A7J0 TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84M 
       31.10        19.86        20.02        59.05        30.44        24.79 
TCGA-VM-A8CA TCGA-VM-A8CH TCGA-VW-A8FI 
       13.51        23.47         8.05 

$`AMP PEAK 17(17Q25.1) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A4XH 
       18.84        46.72        39.78        37.45        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       24.20        25.48        31.40        27.45        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O 
       14.40        18.51        12.10        11.24        17.88        30.74 
TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B 
       16.18        31.82        30.31        14.40         8.02        42.05 
TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       27.81        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7014 
       62.96       156.23       138.28       105.21         6.54       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 
       18.94        44.02        62.01        25.91        60.30        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       15.12         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
        2.70        77.98         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
        7.50        44.42         0.56        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YV 
       57.93       134.27        78.21        95.57       130.78        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5963 TCGA-FG-5964 
       36.82        32.35        14.33         0.23        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60K 
       38.27        10.72        18.38        18.71        23.70        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 
       36.66        48.69        20.45        13.58        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       16.83        21.40        17.52         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 
       17.82        20.35        12.76        20.81        20.71        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       19.33        14.83        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 
       59.38        30.87         5.46         9.90         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       30.67        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       28.70        22.95        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI 
       95.93       106.39        69.50        72.59        32.45        84.99 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       22.32        23.51         7.13         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O 
       16.18        40.64        28.08        24.16        40.83        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VV-A829 
       43.04        30.08         0.10         7.89        35.93        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       16.01        23.21        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                          0.20                           0.03 
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                         80.12                         211.17 
  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE 
                         19.96                          18.61 
[1] "0.2 - 80.1 (20.0)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "2.2"
D17V2, continuous
D17V3, binary
                                cls
clus                               0   1
  AMP PEAK 17(17Q25.1) MUTATED    15  24
  AMP PEAK 17(17Q25.1) WILD-TYPE 191 242
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(17Q25.1) MUTATED     15   24
  AMP PEAK 17(17Q25.1) WILD-TYPE  191  242
        clus
vv       AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE
  FEMALE                           15                            191
  MALE                             24                            242
[1] 2 2
[1] FALSE
D17V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 17(17Q25.1) MUTATED            19                6                14
  AMP PEAK 17(17Q25.1) WILD-TYPE         157              112               164
D17V5, multiclass
                   clus
vv                  AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE
  ASTROCYTOMA                                 19                            157
  OLIGOASTROCYTOMA                             6                            112
  OLIGODENDROGLIOMA                           14                            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                                cls
clus                               0   1
  AMP PEAK 17(17Q25.1) MUTATED     6  33
  AMP PEAK 17(17Q25.1) WILD-TYPE  86 347
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(17Q25.1) MUTATED      6   33
  AMP PEAK 17(17Q25.1) WILD-TYPE   86  347
     clus
vv    AMP PEAK 17(17Q25.1) MUTATED AMP PEAK 17(17Q25.1) WILD-TYPE
  NO                             6                             86
  YES                           33                            347
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(17Q25.1) MUTATED                                  0     2
  AMP PEAK 17(17Q25.1) WILD-TYPE                                1     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(17Q25.1) MUTATED                           0    34
  AMP PEAK 17(17Q25.1) WILD-TYPE                        15   403
D17V7, multiclass
                                  clus
vv                                 AMP PEAK 17(17Q25.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      34
                                  clus
vv                                 AMP PEAK 17(17Q25.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       403
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                                cls
clus                               0   1
  AMP PEAK 17(17Q25.1) MUTATED     2  33
  AMP PEAK 17(17Q25.1) WILD-TYPE  16 386
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(17Q25.1) MUTATED      2   33
  AMP PEAK 17(17Q25.1) WILD-TYPE   16  386
                        clus
vv                       AMP PEAK 17(17Q25.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           33
                        clus
vv                       AMP PEAK 17(17Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            386
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(19P13.3) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(19P13.3) MUTATED    96  23
  AMP PEAK 18(19P13.3) WILD-TYPE 280  71
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                           119                            351 
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                            23                             71 
$`AMP PEAK 18(19P13.3) MUTATED`
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6668 TCGA-DB-5274 
       21.01         9.96        17.69        23.84         8.02        75.25 
TCGA-DB-5278 TCGA-DB-A4XD TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P 
       50.17        39.78        72.95        31.63        24.20        30.12 
TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A75L TCGA-DH-5141 TCGA-DH-5142 
       31.40        27.81        14.40        11.24        31.82        30.31 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F TCGA-DH-A7UU TCGA-DU-5854 TCGA-DU-5874 
        8.02        30.21        17.19         3.45         8.45        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6406 
       52.11        22.42        46.06         1.22         7.04        16.83 
TCGA-DU-7009 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7306 
      138.28        90.77        26.30        18.94        62.01        41.98 
TCGA-DU-8164 TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A7TJ TCGA-E1-5304 
       21.40         8.65        77.98        11.41         0.56        41.13 
TCGA-E1-5318 TCGA-E1-A7YO TCGA-FG-5962 TCGA-FG-6692 TCGA-FG-7638 TCGA-FG-7643 
       78.21        75.02        47.77        18.44        22.55        20.09 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A60K 
       16.01        20.09        14.96        10.72        18.38        17.82 
TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A87Q TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7472 
       28.54        36.66         5.72         6.67        11.54         0.03 
TCGA-HT-7480 TCGA-HT-7483 TCGA-HT-7605 TCGA-HT-7608 TCGA-HT-7681 TCGA-HT-7687 
       75.19       172.77         4.57        22.06        44.68         0.10 
TCGA-HT-7695 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7875 TCGA-HT-7882 TCGA-HT-8012 
       14.53         0.49        23.61         0.33         3.72         9.40 
TCGA-HT-8104 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A61B TCGA-HW-7495 
       12.23        27.35         5.33        16.93        17.52         4.31 
TCGA-HW-8322 TCGA-KT-A7W1 TCGA-P5-A5F0 TCGA-P5-A72U TCGA-P5-A730 TCGA-QH-A65X 
       17.82        14.40         4.11         0.16         0.20        15.85 
TCGA-QH-A6CV TCGA-QH-A6CZ TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML 
       14.53         9.17         5.03        11.08        88.83        94.03 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-S9-A6TV TCGA-S9-A6TX 
       59.38        30.87         5.46        28.08        18.77        34.49 
TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WM 
       31.33        23.64       106.39        72.59        32.45        19.86 
TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C3 
        7.13         8.19         2.04        13.02       169.84        49.45 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84Q TCGA-VM-A8CA 
       48.39        24.92        40.64        24.79        25.38        13.51 
TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VW-A7QS TCGA-W9-A837 TCGA-WY-A85E 
        0.10        35.93        23.21        51.06        20.81 

$`AMP PEAK 18(19P13.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5397 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 
       40.18         0.10         6.38        17.95        12.43         8.48 
TCGA-CS-6667 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 
        7.56         7.40         6.61       122.73        81.96        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        50.86        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64O 
       18.84        30.21        46.72        37.45        33.57        25.48 
TCGA-DB-A64Q TCGA-DB-A64S TCGA-DB-A64V TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75M 
        5.98        27.45        29.23        18.51        12.10        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D 
       30.74        16.18        19.96        14.40        42.05        27.81 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5847 
       17.19        54.25        13.12        13.38        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 
       14.56        17.46         6.74        13.38         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 
       18.94        17.49       211.17        49.02        75.16        65.75 
TCGA-DU-6401 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6407 TCGA-DU-6408 
       87.45        11.64       133.74        19.89        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 
        7.96         7.73        11.47        62.96       156.23        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7290 
      105.21         6.54         8.84       117.40        30.67        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
        7.96        94.32        44.02        25.91        60.30        23.31 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 
        2.76         5.10        23.74        14.60        20.68        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S3 TCGA-DU-A6S7 
        4.96         3.65         5.65        12.20         2.70         7.23 
TCGA-DU-A6S8 TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
        5.98        26.76         7.13        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-E1-5302 
       77.88        42.31        23.51         7.50        44.42        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 
       67.46        79.99        57.93       134.27        95.57       130.78 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       25.48        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 
       23.97        15.35        17.88        20.61        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY 
       14.24        22.52        32.61        38.27        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
       14.76        16.41        15.02        16.44        22.26        10.78 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7470 
       48.69        20.45        13.58        27.52         0.10        40.11 
TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.13        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7601 
        6.38        40.34        95.93       106.95         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7609 
       29.85        23.18       122.47        17.29         3.16        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        0.76         6.05        42.74        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7854 TCGA-HT-7855 
        0.10         2.96        17.52         6.90        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7874 TCGA-HT-7877 TCGA-HT-7879 
       39.09         0.23        50.63        37.15         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        5.33        35.47        11.28        31.43         1.64        16.24 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 
       63.55         0.10        37.87        33.01         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 
       20.22         0.07         0.10         2.70         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       16.83        21.40        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KJ 
       40.18        35.90        21.70        21.60        19.59        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 
        0.23         6.71         1.64         2.37         2.30         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        7.63         0.76         1.28        10.42        13.25        11.64 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        9.01        13.61        15.16         2.53        12.62        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 
       19.33        14.83        13.61        12.23         2.20        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A870 
       14.53        16.34        16.73         1.91        16.50        12.99 
TCGA-R8-A6MO TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
       32.65         9.90         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U5 
       87.12        37.84        28.70        22.95        17.62        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WD TCGA-S9-A6WG 
       16.08        98.24        95.93         5.85        69.50        80.12 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J3 
       36.13         7.92        22.32        23.51        20.02        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       15.06        13.12        28.37        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 
       98.63        31.59        18.71        11.97        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       34.78        16.18        59.05        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       40.83        33.24        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CH TCGA-VV-A829 
       26.99        43.04        30.08         7.89        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       16.01         8.05        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       45.80        46.88        37.71 

  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                        172.77                         211.17 
  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE 
                         20.09                          18.15 
[1] "0.0 - 172.8 (20.1)" "0.1 - 211.2 (18.1)"
[1] "hr=" "1.1"
D18V2, continuous
D18V3, binary
                                cls
clus                               0   1
  AMP PEAK 18(19P13.3) MUTATED    51  69
  AMP PEAK 18(19P13.3) WILD-TYPE 155 197
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(19P13.3) MUTATED     51   69
  AMP PEAK 18(19P13.3) WILD-TYPE  155  197
        clus
vv       AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE
  FEMALE                           51                            155
  MALE                             69                            197
[1] 2 2
[1] FALSE
D18V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 18(19P13.3) MUTATED            24               27                69
  AMP PEAK 18(19P13.3) WILD-TYPE         152               91               109
D18V5, multiclass
                   clus
vv                  AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE
  ASTROCYTOMA                                 24                            152
  OLIGOASTROCYTOMA                            27                             91
  OLIGODENDROGLIOMA                           69                            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                                cls
clus                               0   1
  AMP PEAK 18(19P13.3) MUTATED    21  99
  AMP PEAK 18(19P13.3) WILD-TYPE  71 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(19P13.3) MUTATED     21   99
  AMP PEAK 18(19P13.3) WILD-TYPE   71  281
     clus
vv    AMP PEAK 18(19P13.3) MUTATED AMP PEAK 18(19P13.3) WILD-TYPE
  NO                            21                             71
  YES                           99                            281
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(19P13.3) MUTATED                                  0     2
  AMP PEAK 18(19P13.3) WILD-TYPE                                1     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(19P13.3) MUTATED                           5   109
  AMP PEAK 18(19P13.3) WILD-TYPE                        10   328
D18V7, multiclass
                                  clus
vv                                 AMP PEAK 18(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                     109
                                  clus
vv                                 AMP PEAK 18(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       328
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                                cls
clus                               0   1
  AMP PEAK 18(19P13.3) MUTATED     5 108
  AMP PEAK 18(19P13.3) WILD-TYPE  13 311
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(19P13.3) MUTATED      5  108
  AMP PEAK 18(19P13.3) WILD-TYPE   13  311
                        clus
vv                       AMP PEAK 18(19P13.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          108
                        clus
vv                       AMP PEAK 18(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            311
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(19P13.2) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(19P13.2) MUTATED    88  23
  AMP PEAK 19(19P13.2) WILD-TYPE 288  71
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                           111                            359 
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                            23                             71 
$`AMP PEAK 19(19P13.2) MUTATED`
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6668 TCGA-DB-5274 
       21.01         9.96        17.69        23.84         8.02        75.25 
TCGA-DB-5278 TCGA-DB-A4XD TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64R 
       50.17        39.78        72.95        24.20        30.12        31.40 
TCGA-DB-A75L TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F 
       11.24        31.82        30.31         8.02        30.21        17.19 
TCGA-DU-5854 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 
        8.45        15.16        52.11        22.42        46.06         1.22 
TCGA-DU-6402 TCGA-DU-6406 TCGA-DU-7009 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7298 
        7.04        16.83       138.28        90.77        26.30        18.94 
TCGA-DU-7306 TCGA-DU-8164 TCGA-DU-A5TT TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A76K 
       41.98        21.40         4.96         8.65        77.98        11.41 
TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5304 TCGA-E1-5318 TCGA-E1-A7YO TCGA-FG-5962 
        7.50         0.56        41.13        78.21        75.02        47.77 
TCGA-FG-6692 TCGA-FG-7638 TCGA-FG-7643 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       18.44        22.55        20.09        16.01        20.09        14.96 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A60K TCGA-FG-A710 TCGA-FG-A87Q TCGA-HT-7468 
       10.72        18.38        17.82        36.66         5.72         6.67 
TCGA-HT-7469 TCGA-HT-7480 TCGA-HT-7605 TCGA-HT-7608 TCGA-HT-7681 TCGA-HT-7687 
       11.54        75.19         4.57        22.06        44.68         0.10 
TCGA-HT-7695 TCGA-HT-7860 TCGA-HT-7875 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8012 
       14.53         0.49         0.33         3.72        16.24         9.40 
TCGA-HT-8104 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A61B TCGA-HW-7495 
       12.23        27.35         5.33        16.93        17.52         4.31 
TCGA-HW-8322 TCGA-KT-A7W1 TCGA-P5-A5F0 TCGA-P5-A72U TCGA-P5-A730 TCGA-QH-A65X 
       17.82        14.40         4.11         0.16         0.20        15.85 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CZ TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK 
       14.83        14.53         9.17         5.03        11.08        88.83 
TCGA-R8-A6ML TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-S9-A6TV 
       94.03        59.38        30.87         5.46        28.08        18.77 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WH 
       34.49        31.33        23.64       106.39        72.59        32.45 
TCGA-S9-A6WM TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C3 
       19.86         8.19         2.04        13.02       169.84        49.45 
TCGA-TM-A84B TCGA-TM-A84G TCGA-TM-A84L TCGA-TM-A84M TCGA-VM-A8CA TCGA-VM-A8CB 
       24.92        40.64        40.83        24.79        13.51         0.10 
TCGA-VM-A8CE TCGA-VW-A7QS TCGA-W9-A837 
       35.93        23.21        51.06 

$`AMP PEAK 19(19P13.2) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5397 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 
       40.18         0.10         6.38        17.95        12.43         8.48 
TCGA-CS-6667 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 
        7.56         7.40         6.61       122.73        81.96        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        50.86        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XH 
       18.84        30.21        46.72        37.45        33.57        31.63 
TCGA-DB-A64O TCGA-DB-A64Q TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
       25.48         5.98        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       18.51        12.10        17.88        30.74        16.18        19.96 
TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       14.40        42.05        27.81        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
        6.74        13.38         6.81       182.33        18.94        17.49 
TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6403 
      211.17        49.02        75.16        65.75        87.45        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
      133.74        19.89        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       11.47        62.96       156.23        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
        8.84       117.40        30.67        10.36         7.96        94.32 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 
       44.02        62.01        25.91        60.30        23.31         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 
        5.10        23.74        14.60        20.68        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU 
       15.48        14.17        14.24        12.59        15.12         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76L 
        5.65        12.20         2.70         7.23         5.98        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
        7.13        21.30        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       23.51        44.42        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
      134.27        95.57       130.78        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       14.33         0.23         0.20        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 
       18.77        14.93        24.99        23.97        15.35        17.88 
TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8189 TCGA-FG-8191 
       20.61        12.95        13.68        14.24        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ 
       38.27        18.71        23.70        14.76        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A713 
       16.44        22.26        28.54        10.78        48.69        20.45 
TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
       13.58        27.52         0.10        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       40.34        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7609 
       29.85        23.18       122.47        17.29         3.16        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        0.76         6.05        42.74        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7854 TCGA-HT-7855 
        0.10         2.96        17.52         6.90        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7877 
       39.09         0.23        50.63        23.61        37.15         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        3.68         5.33        35.47        11.28        31.43         1.64 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 
       63.55         0.10        37.87        33.01         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 
       20.22         0.07         0.10         2.70         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       16.83        21.40        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KJ 
       40.18        35.90        21.70        21.60        19.59        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 
        0.23         6.71         1.64         2.37         2.30         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        7.63         0.76         1.28        10.42        13.25        11.64 
TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z 
        9.01        13.61        15.16         2.53        12.62        14.04 
TCGA-QH-A6CS TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 
       19.33        13.61        12.23         2.20        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A870 TCGA-R8-A6MO 
       16.34        16.73         1.91        16.50        12.99        32.65 
TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
        9.90         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TW TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U5 TCGA-S9-A6U6 
       37.84        28.70        22.95        17.62        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WD TCGA-S9-A6WG TCGA-S9-A6WI 
       98.24        95.93         5.85        69.50        80.12        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       31.10        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J3 
        7.92        22.32        23.51         7.13        20.02        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       15.06        13.12        28.37        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 
       98.63        31.59        18.71        11.97        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I 
       34.78        48.39        16.18        59.05        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.16        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CH 
       15.98        26.99        43.04        30.08         7.89        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       37.05        16.01         8.05        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                        169.84                         211.17 
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                         18.77                          18.61 
[1] "0.1 - 169.8 (18.8)" "0.0 - 211.2 (18.6)"
[1] "hr=" "1.1"
D19V2, continuous
D19V3, binary
                                cls
clus                               0   1
  AMP PEAK 19(19P13.2) MUTATED    44  69
  AMP PEAK 19(19P13.2) WILD-TYPE 162 197
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(19P13.2) MUTATED     44   69
  AMP PEAK 19(19P13.2) WILD-TYPE  162  197
        clus
vv       AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  FEMALE                           44                            162
  MALE                             69                            197
[1] 2 2
[1] FALSE
D19V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 19(19P13.2) MUTATED            22               23                68
  AMP PEAK 19(19P13.2) WILD-TYPE         154               95               110
D19V5, multiclass
                   clus
vv                  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  ASTROCYTOMA                                 22                            154
  OLIGOASTROCYTOMA                            23                             95
  OLIGODENDROGLIOMA                           68                            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                                cls
clus                               0   1
  AMP PEAK 19(19P13.2) MUTATED    21  92
  AMP PEAK 19(19P13.2) WILD-TYPE  71 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(19P13.2) MUTATED     21   92
  AMP PEAK 19(19P13.2) WILD-TYPE   71  288
     clus
vv    AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  NO                            21                             71
  YES                           92                            288
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(19P13.2) MUTATED                                  0     2
  AMP PEAK 19(19P13.2) WILD-TYPE                                1     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(19P13.2) MUTATED                           5   102
  AMP PEAK 19(19P13.2) WILD-TYPE                        10   335
D19V7, multiclass
                                  clus
vv                                 AMP PEAK 19(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                     102
                                  clus
vv                                 AMP PEAK 19(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                                cls
clus                               0   1
  AMP PEAK 19(19P13.2) MUTATED     5 102
  AMP PEAK 19(19P13.2) WILD-TYPE  13 317
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(19P13.2) MUTATED      5  102
  AMP PEAK 19(19P13.2) WILD-TYPE   13  317
                        clus
vv                       AMP PEAK 19(19P13.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          102
                        clus
vv                       AMP PEAK 19(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            317
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(XP11.22) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(XP11.22) MUTATED    35   6
  AMP PEAK 20(XP11.22) WILD-TYPE 341  88
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                            41                            429 
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                             6                             88 
$`AMP PEAK 20(XP11.22) MUTATED`
TCGA-CS-6665 TCGA-CS-6667 TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A75L TCGA-DH-A66B 
       12.43         7.56        50.86        78.28        11.24        42.05 
TCGA-DU-5871 TCGA-DU-6407 TCGA-DU-7014 TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A5TT 
       18.94        94.52       117.40        14.24        15.12         4.96 
TCGA-E1-5302 TCGA-E1-5318 TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-A713 TCGA-FG-A87N 
       50.14        78.21        17.88        14.24        20.45        13.58 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7609 TCGA-HT-7688 TCGA-HT-7689 
       17.42         6.54        24.26        45.99        31.69        14.96 
TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-A616 TCGA-HT-A74J TCGA-HT-A74O 
       63.55        12.23         0.10         1.81        10.52         0.10 
TCGA-HW-7493 TCGA-HW-8321 TCGA-P5-A5EZ TCGA-P5-A72W TCGA-QH-A6CV TCGA-RY-A83Z 
       35.90        19.59         2.30        10.42        14.53         9.90 
TCGA-S9-A7QX TCGA-VM-A8C8 TCGA-WY-A859 TCGA-WY-A85B TCGA-WY-A85E 
       13.12        43.04        39.88        45.80        20.81 

$`AMP PEAK 20(XP11.22) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       23.84        17.95         8.48         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       44.52        36.56        46.42        18.84        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       39.78        37.45        33.57        72.95        31.63        24.20 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O 
       29.23        14.40        18.51        12.10        17.88        30.74 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       16.18        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       30.21        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 
        6.74        13.38         8.45         6.81       182.33        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
      133.74        19.89        16.83       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TR TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       14.17        12.59         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
        7.13        21.30        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 
       23.51         7.50        44.42         0.56        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       79.99        57.93       134.27        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        25.48        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 
       24.99        23.97        18.44        15.35        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       20.09        12.95        13.68        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87Q 
       22.26        28.54        10.78        36.66        48.69         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        0.03        16.54         3.75         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 
        0.76        44.68         6.05        42.74         0.10         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 
        0.10        37.87        33.01         6.25         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A617 
       27.35         0.10         5.33         2.70        16.93        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74K 
       16.83        21.40        17.52        17.65         2.43        15.35 
TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
       11.05        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
        4.31        21.70        21.60        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
        0.23         6.71         1.64         2.37         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z 
        7.63         0.76         1.28         0.16        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX 
       15.85        14.04        19.33        14.83        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 
       94.03        32.65        59.38        30.87         5.46        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       36.13         7.92        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ 
        8.19         2.04        17.03        15.06        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       28.08        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C9 
       18.61        14.93        23.80        15.98        26.99        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85D 
       43.40        46.88        37.71 

  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                        117.40                         211.17 
  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE 
                         17.42                          18.71 
[1] "0.1 - 117.4 (17.4)" "0.0 - 211.2 (18.7)"
[1] "hr=" "1.4"
D20V2, continuous
D20V3, binary
                                cls
clus                               0   1
  AMP PEAK 20(XP11.22) MUTATED    18  23
  AMP PEAK 20(XP11.22) WILD-TYPE 188 243
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(XP11.22) MUTATED     18   23
  AMP PEAK 20(XP11.22) WILD-TYPE  188  243
        clus
vv       AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE
  FEMALE                           18                            188
  MALE                             23                            243
[1] 2 2
[1] FALSE
D20V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 20(XP11.22) MUTATED            24                9                 8
  AMP PEAK 20(XP11.22) WILD-TYPE         152              109               170
D20V5, multiclass
                   clus
vv                  AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE
  ASTROCYTOMA                                 24                            152
  OLIGOASTROCYTOMA                             9                            109
  OLIGODENDROGLIOMA                            8                            170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                                cls
clus                               0   1
  AMP PEAK 20(XP11.22) MUTATED    11  30
  AMP PEAK 20(XP11.22) WILD-TYPE  81 350
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(XP11.22) MUTATED     11   30
  AMP PEAK 20(XP11.22) WILD-TYPE   81  350
     clus
vv    AMP PEAK 20(XP11.22) MUTATED AMP PEAK 20(XP11.22) WILD-TYPE
  NO                            11                             81
  YES                           30                            350
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(XP11.22) MUTATED                                  0     2
  AMP PEAK 20(XP11.22) WILD-TYPE                                1     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(XP11.22) MUTATED                           1    38
  AMP PEAK 20(XP11.22) WILD-TYPE                        14   399
D20V7, multiclass
                                  clus
vv                                 AMP PEAK 20(XP11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      38
                                  clus
vv                                 AMP PEAK 20(XP11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       399
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                                cls
clus                               0   1
  AMP PEAK 20(XP11.22) MUTATED     1  36
  AMP PEAK 20(XP11.22) WILD-TYPE  17 383
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(XP11.22) MUTATED      1   36
  AMP PEAK 20(XP11.22) WILD-TYPE   17  383
                        clus
vv                       AMP PEAK 20(XP11.22) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           36
                        clus
vv                       AMP PEAK 20(XP11.22) WILD-TYPE
  HISPANIC OR LATINO                                 17
  NOT HISPANIC OR LATINO                            383
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(XP11.22) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(XP11.22) MUTATED    46  11
  AMP PEAK 21(XP11.22) WILD-TYPE 330  83
  AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE 
                            57                            413 
  AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE 
                            11                             83 
$`AMP PEAK 21(XP11.22) MUTATED`
TCGA-CS-4938 TCGA-CS-6665 TCGA-CS-6667 TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A75L 
        4.70        12.43         7.56        50.86        78.28        11.24 
TCGA-DH-A66B TCGA-DU-5871 TCGA-DU-6396 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6542 
       42.05        18.94        75.16        87.45        94.52         7.73 
TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TS 
       62.96        14.99       117.40        15.48        14.24        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-E1-5302 TCGA-E1-5307 TCGA-E1-5318 TCGA-FG-7636 
        4.96         3.65        50.14        57.93        78.21        17.88 
TCGA-FG-8185 TCGA-FG-A4MY TCGA-FG-A713 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7609 
       14.24        23.70        20.45         6.54        24.26        45.99 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7902 TCGA-HT-8013 
       31.69        14.96        19.23         0.23        31.43        63.55 
TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A74J TCGA-HT-A74O 
       12.23         0.10         1.81        16.83        10.52         0.10 
TCGA-HW-7493 TCGA-HW-8321 TCGA-P5-A5EZ TCGA-P5-A72W TCGA-P5-A733 TCGA-QH-A6CV 
       35.90        19.59         2.30        10.42        13.61        14.53 
TCGA-S9-A7IZ TCGA-S9-A7QX TCGA-S9-A89V TCGA-TM-A84Q TCGA-VM-A8C8 TCGA-WY-A858 
        7.13        13.12        18.71        25.38        43.04        43.96 
TCGA-WY-A859 TCGA-WY-A85B TCGA-WY-A85E 
       39.88        45.80        20.81 

$`AMP PEAK 21(XP11.22) WILD-TYPE`
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        7.69        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       17.95         8.48         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
       81.96        75.25        47.93        72.92        50.17        44.52 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       36.56        46.42        18.84        30.21        46.72        39.78 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O 
       37.45        33.57        72.95        31.63        24.20        25.48 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       30.12         5.98        31.40        27.45        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       14.40        18.51        12.10        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 
       13.38         8.45         6.81       182.33        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 
      211.17        52.11        22.42        49.02        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
        1.22         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 
      114.08         7.96        11.47       156.23       138.28       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8168 
       14.60        20.68        21.40        19.13        16.96        14.17 
TCGA-DU-A5TR TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       12.59         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 
       44.42         0.56        67.46        41.13        79.99       134.27 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       15.35        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       10.72        18.38        18.71        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       48.69        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       17.42         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7611 
        4.57        17.29         3.16        22.06        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        6.05        42.74         0.10         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7858 
       17.52         6.90        14.53        39.48        39.09        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 
        5.33        35.47         3.72        11.28         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 
        9.40         0.10        37.87        33.01         6.25         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        27.35         0.10         5.33         2.70        16.93 
TCGA-HT-A617 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74K 
       16.14        21.40        17.52        17.65         2.43        15.35 
TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
       11.05        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
        4.31        21.70        21.60        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
        0.23         6.71         1.64         2.37         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z 
        7.63         0.76         1.28         0.16        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        0.20         9.01        15.16         2.53        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       14.04        19.33        14.83        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 
       36.13         7.92        22.32        23.51        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        2.04        17.03        15.06        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        99.06        30.05        98.63        31.59        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       40.83        24.79        33.24        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       15.98        26.99        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85D 
       51.06        13.32        43.40        46.88        37.71 

  AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE 
                        117.40                         211.17 
  AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE 
                         18.71                          18.61 
[1] "0.1 - 117.4 (18.7)" "0.0 - 211.2 (18.6)"
[1] "hr=" "1"  
D21V2, continuous
D21V3, binary
                                cls
clus                               0   1
  AMP PEAK 21(XP11.22) MUTATED    30  27
  AMP PEAK 21(XP11.22) WILD-TYPE 176 239
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(XP11.22) MUTATED     30   27
  AMP PEAK 21(XP11.22) WILD-TYPE  176  239
        clus
vv       AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE
  FEMALE                           30                            176
  MALE                             27                            239
[1] 2 2
[1] FALSE
D21V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  AMP PEAK 21(XP11.22) MUTATED            35               13                 9
  AMP PEAK 21(XP11.22) WILD-TYPE         141              105               169
D21V5, multiclass
                   clus
vv                  AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE
  ASTROCYTOMA                                 35                            141
  OLIGOASTROCYTOMA                            13                            105
  OLIGODENDROGLIOMA                            9                            169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                                cls
clus                               0   1
  AMP PEAK 21(XP11.22) MUTATED    13  44
  AMP PEAK 21(XP11.22) WILD-TYPE  79 336
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(XP11.22) MUTATED     13   44
  AMP PEAK 21(XP11.22) WILD-TYPE   79  336
     clus
vv    AMP PEAK 21(XP11.22) MUTATED AMP PEAK 21(XP11.22) WILD-TYPE
  NO                            13                             79
  YES                           44                            336
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(XP11.22) MUTATED                                  0     1
  AMP PEAK 21(XP11.22) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(XP11.22) MUTATED                           1    55
  AMP PEAK 21(XP11.22) WILD-TYPE                        14   382
D21V7, multiclass
                                  clus
vv                                 AMP PEAK 21(XP11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      55
                                  clus
vv                                 AMP PEAK 21(XP11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       382
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                                cls
clus                               0   1
  AMP PEAK 21(XP11.22) MUTATED     2  50
  AMP PEAK 21(XP11.22) WILD-TYPE  16 369
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(XP11.22) MUTATED      2   50
  AMP PEAK 21(XP11.22) WILD-TYPE   16  369
                        clus
vv                       AMP PEAK 21(XP11.22) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           50
                        clus
vv                       AMP PEAK 21(XP11.22) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            369
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK  1(1P36.32) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.32) MUTATED   158  32
  DEL PEAK  1(1P36.32) WILD-TYPE 218  62
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                           190                            280 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            32                             62 
$`DEL PEAK  1(1P36.32) MUTATED`
TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-CS-6670 TCGA-DB-5274 
       64.64         0.10         9.96         8.02         6.61        75.25 
TCGA-DB-5275 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH 
       47.93        50.17        44.52        18.84        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U 
       24.20        25.48        30.12         5.98        31.40        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A669 
       29.23        14.40        12.10        31.82         8.02        30.21 
TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5852 TCGA-DU-5870 
       17.19        54.25        13.12        14.56         6.74       182.33 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 
       17.49        15.16        52.11        22.42        75.16        46.06 
TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6405 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7009 
        1.22         7.04        19.89         7.96        11.47       138.28 
TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7294 TCGA-DU-7300 TCGA-DU-7302 
      117.40        30.67        10.36        94.32        62.01        60.30 
TCGA-DU-8158 TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A6S2 TCGA-DU-A6S3 
        5.10        21.40        15.48        14.17         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TG TCGA-E1-5311 
       77.98         5.98        21.30        17.98        44.42       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 
       78.21        95.57        75.02        14.33         0.23        47.77 
TCGA-FG-5964 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8185 
       34.36        18.44        15.35        22.55        20.61        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 
       16.01        20.09        22.52        17.82        15.02        16.44 
TCGA-FG-A710 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7477 
       36.66        20.45         0.10         6.67         0.13        24.26 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7616 
       75.19        95.93         4.57         3.16        22.06         0.23 
TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7692 TCGA-HT-7694 
       14.27        16.24        44.68         0.10         2.96         6.90 
TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       14.53        39.09         0.23        37.15         0.33         0.13 
TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-8109 TCGA-HT-8113 
       35.47         1.64         9.40         6.25         5.56        29.59 
TCGA-HT-A4DV TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A619 
       26.04         0.07        27.35        16.93        16.14        21.40 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 
       17.65         2.43        15.35        11.05        29.92        19.89 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-IK-8125 TCGA-KT-A74X 
       40.18         4.31        17.82        20.35        42.77        14.40 
TCGA-P5-A5EX TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        1.64         4.11         0.76        11.64         0.20         9.01 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV 
       15.16        12.62        15.85        14.04        14.83        14.53 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XC 
        2.20         9.17        14.53        16.34        16.73         5.03 
TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       11.08        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A6TX 
        5.46        28.08        30.67        62.17        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       31.33        23.64        32.61       106.39        69.50        72.59 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP 
       32.45        84.99        31.10        19.86        15.91        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       14.07        36.13        23.51         8.19         2.04        17.03 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M 
       28.37        13.02       169.84        49.32        40.64        24.79 
TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       33.24        18.61        14.93        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VV-A829 TCGA-VW-A7QS TCGA-W9-A837 
       35.93        37.05        23.21        51.06 

$`DEL PEAK  1(1P36.32) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        10.62        40.18 
TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 
       21.01         6.38        17.69        23.84        17.95        12.43 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5276 
        8.48         7.56         7.40       122.73        81.96        72.92 
TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC 
       50.86        36.56        78.28        46.42        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64S TCGA-DB-A64X TCGA-DB-A75L 
       39.78        37.45        33.57        27.45        18.51        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 
       17.88        30.74        16.18        19.96        30.31        14.40 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       42.05        27.81        17.19        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5871 
       18.02        17.46        13.38         8.45         6.81        18.94 
TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6403 TCGA-DU-6404 
      211.17        49.02        65.75        87.45        11.64       133.74 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 
       16.83        94.52       114.08         7.73        62.96       156.23 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7019 
       14.99       105.21         6.54         8.84        90.77        26.30 
TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 
        7.96        18.94        44.02        25.91        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 
        2.76        23.74        14.60        20.68        19.13        16.96 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 
       12.20         7.23        11.41        26.76         7.13       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5302 
       77.88        42.31        23.51         7.50         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5322 TCGA-E1-A7YV 
       67.46        41.13        79.99        57.93       130.78        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 
       36.82        32.35         0.20        25.48        36.82        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7636 TCGA-FG-7643 TCGA-FG-8181 
       14.93        24.99        23.97        17.88        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       13.68        14.96        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y 
       18.71        23.70        14.76        16.41        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7469 
       10.78        48.69        13.58         5.72        27.52        11.54 
TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
       40.11         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
        6.38        40.34       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7610 
       29.85        23.18       122.47        17.29        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 
       57.60         0.16         0.76         6.05        42.74        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7855 
       14.96         0.10         0.10        17.52        39.48        19.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7882 
       50.63         0.49        23.61         3.68         5.33         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
       11.28        31.43        16.24        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8110 
       33.01        12.23         0.10         0.46         2.50        13.78 
TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 
        0.23        34.19        28.27        15.72         0.23         0.13 
TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 
       20.22         0.10         5.33         2.70         1.81        16.83 
TCGA-HT-A61B TCGA-HT-A74J TCGA-HT-A74O TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 
       17.52        10.52         0.10         8.32        19.23        35.90 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       21.70        21.60        19.59        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ 
       19.00        14.40         0.23         6.71         2.37         2.30 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        5.88         7.63         1.28         0.16        10.42        13.25 
TCGA-P5-A733 TCGA-QH-A65S TCGA-QH-A6CS TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6X3 
       13.61         2.53        19.33        13.61        12.23        10.29 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A870 TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 
        1.91        16.50        12.99         9.90         2.07        19.59 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U6 
       87.12        18.77        28.70        22.95        17.62        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WO TCGA-S9-A7IS 
       98.24        95.93         5.85        80.12        18.61         7.92 
TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R2 
       22.32         7.13        20.02        15.06        13.12        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       49.45        48.33        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84Q 
       59.05        30.44        28.08        24.16        40.83        25.38 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CH 
       23.80        15.98        26.99        43.04        30.08        23.47 
TCGA-VV-A86M TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       16.01         8.05        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                        182.33                         211.17 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                        18.525                         18.710 
[1] "0.1 - 182.3 (18.5)" "0.0 - 211.2 (18.7)"
[1] "hr=" "1.4"
D22V2, continuous
D22V3, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED    88 103
  DEL PEAK  1(1P36.32) WILD-TYPE 118 163
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     88  103
  DEL PEAK  1(1P36.32) WILD-TYPE  118  163
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  FEMALE                           88                            118
  MALE                            103                            163
[1] 2 2
[1] FALSE
D22V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  1(1P36.32) MUTATED            19               41               131
  DEL PEAK  1(1P36.32) WILD-TYPE         157               77                47
D22V5, multiclass
                   clus
vv                  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  ASTROCYTOMA                                 19                            157
  OLIGOASTROCYTOMA                            41                             77
  OLIGODENDROGLIOMA                          131                             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED    28 163
  DEL PEAK  1(1P36.32) WILD-TYPE  64 217
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     28  163
  DEL PEAK  1(1P36.32) WILD-TYPE   64  217
     clus
vv    DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  NO                            28                             64
  YES                          163                            217
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.32) MUTATED                                  1     5
  DEL PEAK  1(1P36.32) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.32) MUTATED                           5   174
  DEL PEAK  1(1P36.32) WILD-TYPE                        10   263
D22V7, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                     174
                                  clus
vv                                 DEL PEAK  1(1P36.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       263
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED     6 171
  DEL PEAK  1(1P36.32) WILD-TYPE  12 248
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      6  171
  DEL PEAK  1(1P36.32) WILD-TYPE   12  248
                        clus
vv                       DEL PEAK  1(1P36.32) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          171
                        clus
vv                       DEL PEAK  1(1P36.32) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            248
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK  2(1P32.3) MUTATION ANALYSIS
D23V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P32.3) MUTATED   153  27
  DEL PEAK  2(1P32.3) WILD-TYPE 223  67
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                          180                           290 
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                           27                            67 
$`DEL PEAK  2(1P32.3) MUTATED`
TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-CS-6670 TCGA-DB-5274 
       64.64         0.10         9.96         8.02         6.61        75.25 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       50.17        44.52        18.84        72.95        31.63        24.20 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V 
       25.48        30.12         5.98        31.40        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A75K TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F 
       14.40        12.10        31.82         8.02        30.21        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 
       54.25        13.12        14.56       182.33        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7014 
       22.42        46.06         1.22         7.96       138.28       117.40 
TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-8158 TCGA-DU-8161 
       30.67        94.32        62.01        60.30         5.10        23.74 
TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       21.40        15.48        14.17         8.65         2.70        77.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TG 
        5.98        11.41        26.76        21.30        17.98        44.42 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-EZ-7264 
      134.27        78.21        95.57       130.78        75.02        14.33 
TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 
        0.23        47.77        34.36        15.35        22.55        20.61 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A60K TCGA-FG-A6IZ 
       14.24        16.01        20.09        22.52        17.82        15.02 
TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A713 TCGA-FG-A87Q TCGA-HT-7467 TCGA-HT-7468 
       16.44        36.66        20.45         5.72         0.10         6.67 
TCGA-HT-7471 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 
        0.13        75.19        95.93         4.57         3.16        22.06 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7692 
        0.23        14.27        16.24        44.68         0.10         2.96 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7874 
        6.90        14.53        39.09         0.23         0.49        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8105 
        0.33         0.13        35.47         1.64         9.40         6.25 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R9 
        5.56        13.78        29.59         0.23        26.04         0.07 
TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74K 
       16.93        16.14        21.40        17.65         2.43        15.35 
TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8322 
       11.05        29.92        19.89        40.18         4.31        17.82 
TCGA-HW-A5KJ TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5F0 TCGA-P5-A72Z 
       20.35        42.77        14.40         1.64         4.11        11.64 
TCGA-P5-A730 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU 
        0.20        15.16        12.62        15.85        14.04        14.83 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X 
        2.20         9.17        14.53        16.34        16.73        11.08 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A840 TCGA-RY-A847 TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 
       28.08        30.67        37.84        34.49        31.33        23.64 
TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI 
       32.61       106.39        69.50        72.59        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IY 
       31.10        15.91        15.16        14.07        36.13        23.51 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.19         2.04        17.03        28.37        13.02       169.84 
TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S 
       49.32        40.64        24.79        33.24        18.61        14.93 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VV-A829 TCGA-VW-A7QS TCGA-W9-A837 
       13.51         0.10        35.93        37.05        23.21        51.06 

$`DEL PEAK  2(1P32.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        10.62        40.18 
TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 
       21.01         6.38        17.69        23.84        17.95        12.43 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 
        8.48         7.56         7.40       122.73        81.96        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB 
       72.92        50.86        36.56        78.28        46.42        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64S TCGA-DB-A64X 
       46.72        39.78        37.45        33.57        27.45        18.51 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 
       11.24        17.88        30.74        16.18        19.96        30.31 
TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT TCGA-DH-A7UU 
       14.40        42.05        27.81        17.19        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.61        18.02        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6396 
        6.81        18.94        17.49       211.17        49.02        75.16 
TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       65.75        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       16.83        94.52       114.08         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      156.23        14.99       105.21         6.54         8.84        90.77 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 
       26.30        10.36         7.96        18.94        44.02        25.91 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 
       23.31        41.98         2.76        14.60        20.68        19.13 
TCGA-DU-8166 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       16.96        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A76O TCGA-DU-A7T8 TCGA-DU-A7TA 
        5.65        12.20         7.23         7.13       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       42.31        23.51         7.50         0.56        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       41.13        79.99        57.93        32.45        36.82        32.35 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
        0.20        25.48        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       23.97        18.44        17.88        20.09        12.95        13.68 
TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       14.96        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       23.70        14.76        16.41        22.26        28.54        10.78 
TCGA-FG-A711 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 
       48.69        13.58        27.52        11.54        40.11         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       40.34       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       23.18       122.47        17.29        45.99        56.09        57.60 
TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 
        0.16         0.76         6.05        42.74        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 
        0.10         0.10        17.52        39.48        19.23        50.63 
TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
       23.61         3.68         5.33         3.72        11.28        31.43 
TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 
        0.10         0.46         2.50         0.23        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       15.72         0.13        20.22        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A74J TCGA-HT-A74O 
        2.70         1.81        16.83        17.52        10.52         0.10 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
        8.32        19.23        35.90        21.70        21.60        19.59 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EV 
       12.76        20.81        20.71        19.00        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        6.71         2.37         2.30         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A731 TCGA-P5-A733 
        1.28         0.16        10.42        13.25         9.01        13.61 
TCGA-QH-A65S TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6X3 
        2.53        19.33        14.53        13.61        12.23        10.29 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A870 TCGA-RY-A83Z TCGA-RY-A843 
        1.91        16.50         5.03        12.99         9.90         2.07 
TCGA-RY-A845 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U0 
       19.59        62.17        87.12        18.77        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WG 
       17.62        16.08        98.24        95.93         5.85        80.12 
TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 
       19.86        18.61         7.92        22.32         7.13        20.02 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       15.06        13.12        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA 
       31.59        18.71        11.97        49.45        48.33        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I 
       48.39        24.92        16.18        59.05        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84Q TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       24.16        40.83        25.38        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A8FI 
       43.04        30.08         7.89        23.47        16.01         8.05 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E 
       37.71        20.81 

  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                       182.33                        211.17 
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                       18.725                        18.660 
[1] "0.1 - 182.3 (18.7)" "0.0 - 211.2 (18.7)"
[1] "hr=" "1.7"
D23V2, continuous
D23V3, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P32.3) MUTATED    82  99
  DEL PEAK  2(1P32.3) WILD-TYPE 124 167
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P32.3) MUTATED     82   99
  DEL PEAK  2(1P32.3) WILD-TYPE  124  167
        clus
vv       DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE
  FEMALE                          82                           124
  MALE                            99                           167
[1] 2 2
[1] FALSE
D23V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  2(1P32.3) MUTATED            13               37               131
  DEL PEAK  2(1P32.3) WILD-TYPE         163               81                47
D23V5, multiclass
                   clus
vv                  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE
  ASTROCYTOMA                                13                           163
  OLIGOASTROCYTOMA                           37                            81
  OLIGODENDROGLIOMA                         131                            47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P32.3) MUTATED    23 158
  DEL PEAK  2(1P32.3) WILD-TYPE  69 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P32.3) MUTATED     23  158
  DEL PEAK  2(1P32.3) WILD-TYPE   69  222
     clus
vv    DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE
  NO                           23                            69
  YES                         158                           222
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P32.3) MUTATED                                  1     4
  DEL PEAK  2(1P32.3) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P32.3) MUTATED                           4   166
  DEL PEAK  2(1P32.3) WILD-TYPE                        11   271
D23V7, multiclass
                                  clus
vv                                 DEL PEAK  2(1P32.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                    166
                                  clus
vv                                 DEL PEAK  2(1P32.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                      271
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P32.3) MUTATED     6 162
  DEL PEAK  2(1P32.3) WILD-TYPE  12 257
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P32.3) MUTATED      6  162
  DEL PEAK  2(1P32.3) WILD-TYPE   12  257
                        clus
vv                       DEL PEAK  2(1P32.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         162
                        clus
vv                       DEL PEAK  2(1P32.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           257
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK  3(1Q43) MUTATION ANALYSIS
D24V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  3(1Q43) MUTATED    18   9
  DEL PEAK  3(1Q43) WILD-TYPE 358  85
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         27                         443 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          9                          85 
$`DEL PEAK  3(1Q43) MUTATED`
TCGA-DU-5871 TCGA-DU-6396 TCGA-DU-6542 TCGA-DU-7015 TCGA-DU-8158 TCGA-DU-8161 
       18.94        75.16         7.73        90.77         5.10        23.74 
TCGA-DU-A5TS TCGA-DU-A7TA TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5322 TCGA-E1-A7YV 
       15.12        77.88        44.42        50.14       130.78        32.45 
TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-A6J3 TCGA-HT-7857 TCGA-HT-8109 TCGA-HT-8113 
       17.88        14.24        22.26         0.23         5.56        29.59 
TCGA-HT-A619 TCGA-P5-A5F4 TCGA-QH-A65S TCGA-QH-A6CW TCGA-S9-A6WI TCGA-S9-A7R1 
       21.40         0.76         2.53        13.61        84.99       169.84 
TCGA-TM-A84I TCGA-TM-A84T TCGA-TQ-A7RW 
       28.08        23.80        26.99 

$`DEL PEAK  3(1Q43) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        50.86        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       33.57        72.95        31.63        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       13.38         3.45        18.61        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 
        6.74        13.38         8.45         6.81       182.33        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 
       15.16       211.17        52.11        22.42        49.02        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 
       19.89        16.83        94.52       114.08         7.96        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84       117.40        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       23.31        41.98         2.76        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       21.30        17.98       124.50        42.31        23.51         7.50 
TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        0.56        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
       78.21        95.57        75.02        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 
       22.55        20.61        20.09        12.95        13.68        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       15.02        16.44        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       20.45        13.58         5.72        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 
        6.90        14.53        39.48        19.23        39.09        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8110 
       12.23         6.25         0.10         0.46         2.50        13.78 
TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
        0.23        34.19        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B 
        2.70        16.93         1.81        16.14        16.83        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        4.11         5.88         7.63         1.28         0.16        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       12.62        15.85        14.04        19.33        14.83        14.53 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       32.45        31.10        19.86        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       28.37        13.02        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        24.92        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       30.44        24.16        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RH TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       18.61        14.93        15.98        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        46.88        37.71        20.81 

  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                       0.23                        0.03 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                     169.84                      211.17 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                      23.74                       18.51 
[1] "0.2 - 169.8 (23.7)" "0.0 - 211.2 (18.5)"
[1] "hr=" "1.2"
D24V2, continuous
D24V3, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED    14  13
  DEL PEAK  3(1Q43) WILD-TYPE 192 253
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED     14   13
  DEL PEAK  3(1Q43) WILD-TYPE  192  253
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  FEMALE                        14                         192
  MALE                          13                         253
[1] 2 2
[1] FALSE
D24V4, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  3(1Q43) MUTATED             7               10                10
  DEL PEAK  3(1Q43) WILD-TYPE         169              108               168
D24V5, multiclass
                   clus
vv                  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  ASTROCYTOMA                               7                         169
  OLIGOASTROCYTOMA                         10                         108
  OLIGODENDROGLIOMA                        10                         168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED     5  22
  DEL PEAK  3(1Q43) WILD-TYPE  87 358
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      5   22
  DEL PEAK  3(1Q43) WILD-TYPE   87  358
     clus
vv    DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  NO                          5                          87
  YES                        22                         358
[1] 2 2
[1] FALSE
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(1Q43) MUTATED                                  0     1
  DEL PEAK  3(1Q43) WILD-TYPE                                1     7
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q43) MUTATED                           2    24
  DEL PEAK  3(1Q43) WILD-TYPE                        13   413
D24V7, multiclass
                                  clus
vv                                 DEL PEAK  3(1Q43) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                   24
                                  clus
vv                                 DEL PEAK  3(1Q43) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    413
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED     2  25
  DEL PEAK  3(1Q43) WILD-TYPE  16 394
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      2   25
  DEL PEAK  3(1Q43) WILD-TYPE   16  394
                        clus
vv                       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  HISPANIC OR LATINO                             2                          16
  NOT HISPANIC OR LATINO                        25                         394
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.3) MUTATED    51  17
  DEL PEAK  4(2Q37.3) WILD-TYPE 325  77
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           68                           402 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           17                            77 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-CS-4943 TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5270 TCGA-DB-5277 TCGA-DB-5281 
       18.15         6.38         8.48       122.73        50.86        78.28 
TCGA-DB-A64P TCGA-DH-5142 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A7UR TCGA-DU-5855 
       30.12        30.31        30.21        42.05        54.25         6.81 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 
       49.02        75.16        94.52       114.08         7.73        62.96 
TCGA-DU-7008 TCGA-DU-7014 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8167 TCGA-DU-A5TR 
      156.23       117.40        23.31        41.98        15.48        12.59 
TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A7T6 TCGA-E1-5304 TCGA-F6-A8O4 
       15.12         5.65         7.23        17.98        41.13         0.20 
TCGA-FG-A6J3 TCGA-HT-7473 TCGA-HT-7477 TCGA-HT-7601 TCGA-HT-7606 TCGA-HT-7690 
       22.26        16.54        24.26         5.03        17.29         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-8013 TCGA-HT-A5RB TCGA-HT-A618 
        2.96        17.52        19.23        63.55         0.10        16.83 
TCGA-HT-A61B TCGA-HW-7493 TCGA-HW-8321 TCGA-IK-7675 TCGA-P5-A5EW TCGA-P5-A5F6 
       17.52        35.90        19.59        19.00         6.71         1.28 
TCGA-P5-A72W TCGA-P5-A733 TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6X3 TCGA-QH-A6X9 
       10.42        13.61        14.53        13.61        10.29         1.91 
TCGA-RY-A83Z TCGA-RY-A845 TCGA-S9-A6U6 TCGA-S9-A6WG TCGA-S9-A6WQ TCGA-S9-A7J0 
        9.90        19.59        16.08        80.12        14.07        20.02 
TCGA-S9-A89Z TCGA-TM-A7CA TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q 
       11.97        34.78        28.08        40.83        33.24        25.38 
TCGA-TQ-A7RH TCGA-TQ-A7RW 
       15.98        26.99 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
        0.10        21.01         9.96        17.69        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5273 
       12.43         7.56         8.02         7.40         6.61        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       75.25        47.93        72.92        50.17        44.52        36.56 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       46.42        18.84        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64Q 
       33.57        72.95        31.63        24.20        25.48         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       31.82        14.40         8.02        27.81        17.19        17.19 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 
       13.12        13.38         3.45        18.61        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 
       17.46         6.74        13.38         8.45       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 
       17.49        15.16       211.17        52.11        22.42        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7009 TCGA-DU-7010 
       19.89        16.83         7.96        11.47       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       25.91        60.30         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        19.13        16.96        14.17        14.24 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        4.96         3.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       95.57       130.78        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       14.33         0.23        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z 
       17.82        16.41        15.02        16.44        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 
       95.93       106.95       172.77         4.01        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
      122.47         4.57         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7691 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 
        0.10         6.90        14.53        39.48        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
        1.64        16.24         9.40         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A619 
        5.33         2.70        16.93         1.81        16.14        21.40 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        40.18         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.70        21.60        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EX 
       20.71        42.77        14.40        14.40         0.23         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-QH-A65R 
        0.16        13.25        11.64         0.20         9.01        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
       12.23         2.20         9.17        14.53        16.34        16.73 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 
       32.65        59.38        30.87         5.46        28.08         2.07 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       15.16        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       169.84        10.39        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF 
       31.59        18.71        49.45        48.33        49.32        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J 
       24.92        16.18        59.05        40.64        30.44        24.16 
TCGA-TM-A84M TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 
       24.79        18.61        14.93        23.80        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       39.88        43.40        45.80        46.88        37.71        20.81 

  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       156.23                        211.17 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       18.575                        18.660 
[1] "0.1 - 156.2 (18.6)" "0.0 - 211.2 (18.7)"
[1] "hr=" "1.2"
D25V2, continuous
D25V3, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    27  42
  DEL PEAK  4(2Q37.3) WILD-TYPE 179 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     27   42
  DEL PEAK  4(2Q37.3) WILD-TYPE  179  224
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                          27                           179
  MALE                            42                           224
[1] 2 2
[1] FALSE
D25V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  4(2Q37.3) MUTATED            32               21                16
  DEL PEAK  4(2Q37.3) WILD-TYPE         144               97               162
D25V5, multiclass
                   clus
vv                  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  ASTROCYTOMA                                32                           144
  OLIGOASTROCYTOMA                           21                            97
  OLIGODENDROGLIOMA                          16                           162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    16  53
  DEL PEAK  4(2Q37.3) WILD-TYPE  76 327
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     16   53
  DEL PEAK  4(2Q37.3) WILD-TYPE   76  327
     clus
vv    DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  NO                           16                            76
  YES                          53                           327
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2Q37.3) MUTATED                                  0     2
  DEL PEAK  4(2Q37.3) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED                           2    64
  DEL PEAK  4(2Q37.3) WILD-TYPE                        13   373
D25V7, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     64
                                  clus
vv                                 DEL PEAK  4(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                      373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     5  63
  DEL PEAK  4(2Q37.3) WILD-TYPE  13 356
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      5   63
  DEL PEAK  4(2Q37.3) WILD-TYPE   13  356
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          63
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           356
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK  5(3P21.31) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  5(3P21.31) MUTATED    31  12
  DEL PEAK  5(3P21.31) WILD-TYPE 345  82
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            43                            427 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            12                             82 
$`DEL PEAK  5(3P21.31) MUTATED`
TCGA-DB-5275 TCGA-DB-5277 TCGA-DH-A66D TCGA-DU-6396 TCGA-DU-6542 TCGA-DU-7010 
       47.93        50.86        27.81        75.16         7.73        14.99 
TCGA-DU-7300 TCGA-DU-8168 TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A76R TCGA-DU-A7TA 
       62.01        14.17         4.96         3.65        21.30        77.88 
TCGA-E1-5304 TCGA-E1-5322 TCGA-E1-A7YV TCGA-E1-A7YW TCGA-HT-7469 TCGA-HT-7473 
       41.13       130.78        32.45        36.82        11.54        16.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7482 TCGA-HT-7606 TCGA-HT-7690 TCGA-HT-8111 
       24.26         6.38       106.95        17.29         0.10         0.23 
TCGA-HT-8564 TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A619 TCGA-IK-7675 TCGA-P5-A5F6 
       15.72        20.22        27.35        21.40        19.00         1.28 
TCGA-QH-A6X9 TCGA-S9-A6WG TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A89V TCGA-TM-A84H 
        1.91        80.12         7.13        20.02        18.71        30.44 
TCGA-TM-A84J TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VV-A829 TCGA-WY-A859 
       24.16        15.98        26.99        43.04        37.05        39.88 
TCGA-WY-A85E 
       20.81 

$`DEL PEAK  5(3P21.31) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 
        7.40         6.61       122.73        81.96        75.25        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66F 
       30.31        14.40         8.02        30.21        42.05        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       52.11        22.42        49.02        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
       94.52       114.08         7.96        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
      138.28       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       44.02        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TW 
       16.96        15.48        14.24        12.59        15.12         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TB 
       11.41        26.76         7.13        17.98       124.50        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       23.51         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO 
       79.99        57.93       134.27        78.21        95.57        75.02 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       32.35        14.33         0.23         0.20        47.77        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       22.26        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 
       13.58         5.72        27.52         0.10         6.67        40.11 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7479 
        0.13         0.03         3.75        17.42         6.54        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       75.19        95.93       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
       23.18       122.47         4.57         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
       14.96         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
       35.47         3.72        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59        34.19        28.27         0.23        26.04         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
        0.07         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.14        16.83        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA 
        9.17        10.29        14.53        16.34        16.73        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       19.59        30.67        62.17        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       69.50        72.59        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       22.32        23.51         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       30.05        98.63        31.59        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       40.64        28.08        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       18.61        14.93        23.80        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
        7.89        35.93        23.47        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       51.06        13.32        43.96        43.40        45.80        46.88 
TCGA-WY-A85D 
       37.71 

  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                        130.78                         211.17 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                         21.30                          18.38 
[1] "0.1 - 130.8 (21.3)" "0.0 - 211.2 (18.4)"
[1] "hr=" "1.4"
D26V2, continuous
D26V3, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED    20  24
  DEL PEAK  5(3P21.31) WILD-TYPE 186 242
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED     20   24
  DEL PEAK  5(3P21.31) WILD-TYPE  186  242
        clus
vv       DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  FEMALE                           20                            186
  MALE                             24                            242
[1] 2 2
[1] FALSE
D26V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  5(3P21.31) MUTATED            16               14                14
  DEL PEAK  5(3P21.31) WILD-TYPE         160              104               164
D26V5, multiclass
                   clus
vv                  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  ASTROCYTOMA                                 16                            160
  OLIGOASTROCYTOMA                            14                            104
  OLIGODENDROGLIOMA                           14                            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED    11  33
  DEL PEAK  5(3P21.31) WILD-TYPE  81 347
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED     11   33
  DEL PEAK  5(3P21.31) WILD-TYPE   81  347
     clus
vv    DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  NO                            11                             81
  YES                           33                            347
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(3P21.31) MUTATED                                  0     1
  DEL PEAK  5(3P21.31) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P21.31) MUTATED                           0    42
  DEL PEAK  5(3P21.31) WILD-TYPE                        15   395
D26V7, multiclass
                                  clus
vv                                 DEL PEAK  5(3P21.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      42
                                  clus
vv                                 DEL PEAK  5(3P21.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       395
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED     5  36
  DEL PEAK  5(3P21.31) WILD-TYPE  13 383
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED      5   36
  DEL PEAK  5(3P21.31) WILD-TYPE   13  383
                        clus
vv                       DEL PEAK  5(3P21.31) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           36
                        clus
vv                       DEL PEAK  5(3P21.31) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            383
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  6(3Q13.31) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  6(3Q13.31) MUTATED    22  13
  DEL PEAK  6(3Q13.31) WILD-TYPE 354  81
  DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE 
                            35                            435 
  DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE 
                            13                             81 
$`DEL PEAK  6(3Q13.31) MUTATED`
TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-5281 TCGA-DU-6402 TCGA-DU-6542 TCGA-DU-7007 
        8.48        50.86        78.28         7.04         7.73        62.96 
TCGA-DU-7014 TCGA-DU-7300 TCGA-DU-8167 TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A76K 
      117.40        62.01        15.48         3.65         5.65        11.41 
TCGA-DU-A76O TCGA-DU-A76R TCGA-E1-5302 TCGA-E1-A7YV TCGA-E1-A7Z6 TCGA-FG-5963 
        7.13        21.30        50.14        32.45        32.35        25.48 
TCGA-HT-7469 TCGA-HT-7603 TCGA-HT-7606 TCGA-HT-8111 TCGA-HT-8564 TCGA-HT-A619 
       11.54        23.18        17.29         0.23        15.72        21.40 
TCGA-HW-7489 TCGA-HW-8321 TCGA-IK-7675 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A733 
        8.32        19.59        19.00         7.63         1.28        13.61 
TCGA-S9-A6TV TCGA-TM-A84J TCGA-VM-A8C8 TCGA-WY-A85C TCGA-WY-A85E 
       18.77        24.16        43.04        46.88        20.81 

$`DEL PEAK  6(3Q13.31) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95        12.43         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       50.17        44.52        36.56        46.42        18.84        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       46.72        39.78        37.45        33.57        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       24.20        25.48        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       17.88        30.74        16.18        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
        1.22        87.45        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 
       94.52       114.08         7.96        11.47       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
       14.99       105.21         6.54         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74        14.60        20.68        21.40        19.13        16.96 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TY 
       14.17        14.24        12.59        15.12         4.96        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76L 
        8.65         2.70        77.98         7.23         5.98        26.76 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       44.42         0.56        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YW 
      134.27        78.21        95.57       130.78        75.02        36.82 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 
       14.33         0.23         0.20        47.77        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72        18.38        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        22.26        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
       27.52         0.10         6.67        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 
        5.03        29.85       122.47         4.57         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33        35.47         3.72        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS 
        5.56        13.78        29.59        34.19        28.27         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       26.04         0.13        20.22         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       17.52        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
        0.10        29.92        19.89        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
        4.31        21.70        21.60        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.81        20.71        42.77        14.40        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 
        0.76         0.16        10.42        13.25        11.64         0.20 
TCGA-P5-A731 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        9.01        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW 
        2.07        19.59        30.67        62.17        87.12        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        22.32        23.51         7.13        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04        17.03        15.06        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       28.08        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C9 TCGA-VM-A8CA 
       14.93        23.80        15.98        26.99        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85D 
       43.40        45.80        37.71 

  DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE 
                          0.23                           0.03 
  DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE 
                        117.40                         211.17 
  DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE 
                         19.00                          18.61 
[1] "0.2 - 117.4 (19.0)" "0.0 - 211.2 (18.6)"
[1] "hr=" "2.3"
D27V2, continuous
D27V3, binary
                                cls
clus                               0   1
  DEL PEAK  6(3Q13.31) MUTATED    12  23
  DEL PEAK  6(3Q13.31) WILD-TYPE 194 243
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q13.31) MUTATED     12   23
  DEL PEAK  6(3Q13.31) WILD-TYPE  194  243
        clus
vv       DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE
  FEMALE                           12                            194
  MALE                             23                            243
[1] 2 2
[1] FALSE
D27V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  6(3Q13.31) MUTATED            16                8                11
  DEL PEAK  6(3Q13.31) WILD-TYPE         160              110               167
D27V5, multiclass
                   clus
vv                  DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE
  ASTROCYTOMA                                 16                            160
  OLIGOASTROCYTOMA                             8                            110
  OLIGODENDROGLIOMA                           11                            167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                                cls
clus                               0   1
  DEL PEAK  6(3Q13.31) MUTATED     9  26
  DEL PEAK  6(3Q13.31) WILD-TYPE  83 354
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q13.31) MUTATED      9   26
  DEL PEAK  6(3Q13.31) WILD-TYPE   83  354
     clus
vv    DEL PEAK  6(3Q13.31) MUTATED DEL PEAK  6(3Q13.31) WILD-TYPE
  NO                             9                             83
  YES                           26                            354
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(3Q13.31) MUTATED                                  0     1
  DEL PEAK  6(3Q13.31) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3Q13.31) MUTATED                           1    33
  DEL PEAK  6(3Q13.31) WILD-TYPE                        14   404
D27V7, multiclass
                                  clus
vv                                 DEL PEAK  6(3Q13.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      33
                                  clus
vv                                 DEL PEAK  6(3Q13.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       404
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                                cls
clus                               0   1
  DEL PEAK  6(3Q13.31) MUTATED     2  30
  DEL PEAK  6(3Q13.31) WILD-TYPE  16 389
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q13.31) MUTATED      2   30
  DEL PEAK  6(3Q13.31) WILD-TYPE   16  389
                        clus
vv                       DEL PEAK  6(3Q13.31) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           30
                        clus
vv                       DEL PEAK  6(3Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            389
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  7(3Q29) MUTATION ANALYSIS
D28V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  7(3Q29) MUTATED    25  15
  DEL PEAK  7(3Q29) WILD-TYPE 351  79
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                         40                         430 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                         15                          79 
$`DEL PEAK  7(3Q29) MUTATED`
TCGA-CS-6290 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-5281 TCGA-DH-A7UU TCGA-DU-6395 
       17.95         8.48        50.86        78.28         3.45        49.02 
TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-8161 
       62.96        14.99       117.40        18.94        62.01        23.74 
TCGA-DU-8167 TCGA-DU-A5TU TCGA-DU-A76R TCGA-E1-5302 TCGA-E1-A7YV TCGA-FG-5963 
       15.48         3.65        21.30        50.14        32.45        25.48 
TCGA-FG-6691 TCGA-FG-A6J3 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7477 TCGA-HT-7604 
       23.97        22.26        40.11         0.03        24.26       122.47 
TCGA-HT-7688 TCGA-HT-8111 TCGA-HT-8564 TCGA-HT-A619 TCGA-IK-7675 TCGA-P5-A5F6 
       31.69         0.23        15.72        21.40        19.00         1.28 
TCGA-P5-A733 TCGA-QH-A65S TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A89Z TCGA-TM-A84B 
       13.61         2.53         7.13        20.02        11.97        24.92 
TCGA-TM-A84J TCGA-VM-A8C8 TCGA-WY-A859 TCGA-WY-A85C 
       24.16        43.04        39.88        46.88 

$`DEL PEAK  7(3Q29) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       23.84        12.43         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       44.52        36.56        46.42        18.84        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       39.78        37.45        33.57        72.95        31.63        24.20 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       29.23        14.40        18.51        12.10        11.24        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       30.74        16.18        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
        8.02        30.21        42.05        27.81        17.19        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 
       54.25        13.12        13.38        18.61        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       17.46         6.74        13.38         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
       18.94        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 
        7.96         7.73        11.47       156.23       138.28       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
        7.96        94.32        44.02        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       41.98         2.76         5.10        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       19.13        16.96        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        4.96         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T6 
        7.23         5.98        11.41        26.76         7.13        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        0.56        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 
       78.21        95.57       130.78        75.02        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 
       14.33         0.23         0.20        47.77        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       18.77        14.93        24.99        18.44        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       16.41        15.02        16.44        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        6.67        11.54         0.13        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
        6.54         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 
      172.77         4.01         5.03        29.85        23.18         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74         0.10        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        37.87        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 
        0.46         2.50         5.56        13.78        29.59        34.19 
TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       28.27         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       27.35         0.10         5.33         2.70        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.14        16.83        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
       15.16        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       22.32        23.51         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 
       30.05        98.63        31.59        18.71        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       49.32        34.78        48.39        16.18        59.05        40.64 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       30.44        28.08        40.83        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C9 
       18.61        14.93        23.80        15.98        26.99        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85D TCGA-WY-A85E 
       43.40        45.80        37.71        20.81 

  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                       0.03                        0.07 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                     122.47                      211.17 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                     23.000                      18.265 
[1] "0.0 - 122.5 (23.0)" "0.1 - 211.2 (18.3)"
[1] "hr=" "1.9"
D28V2, continuous
D28V3, binary
                             cls
clus                            0   1
  DEL PEAK  7(3Q29) MUTATED    16  24
  DEL PEAK  7(3Q29) WILD-TYPE 190 242
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED     16   24
  DEL PEAK  7(3Q29) WILD-TYPE  190  242
        clus
vv       DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  FEMALE                        16                         190
  MALE                          24                         242
[1] 2 2
[1] FALSE
D28V4, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  7(3Q29) MUTATED            21                7                12
  DEL PEAK  7(3Q29) WILD-TYPE         155              111               166
D28V5, multiclass
                   clus
vv                  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  ASTROCYTOMA                              21                         155
  OLIGOASTROCYTOMA                          7                         111
  OLIGODENDROGLIOMA                        12                         166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                             cls
clus                            0   1
  DEL PEAK  7(3Q29) MUTATED     9  31
  DEL PEAK  7(3Q29) WILD-TYPE  83 349
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED      9   31
  DEL PEAK  7(3Q29) WILD-TYPE   83  349
     clus
vv    DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  NO                          9                          83
  YES                        31                         349
[1] 2 2
[1] FALSE
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3Q29) MUTATED                                  0     1
  DEL PEAK  7(3Q29) WILD-TYPE                                1     7
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3Q29) MUTATED                           2    36
  DEL PEAK  7(3Q29) WILD-TYPE                        13   401
D28V7, multiclass
                                  clus
vv                                 DEL PEAK  7(3Q29) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                   36
                                  clus
vv                                 DEL PEAK  7(3Q29) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    401
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                             cls
clus                            0   1
  DEL PEAK  7(3Q29) MUTATED     2  34
  DEL PEAK  7(3Q29) WILD-TYPE  16 385
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED      2   34
  DEL PEAK  7(3Q29) WILD-TYPE   16  385
                        clus
vv                       DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  HISPANIC OR LATINO                             2                          16
  NOT HISPANIC OR LATINO                        34                         385
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  8(4Q34.3) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(4Q34.3) MUTATED   100  25
  DEL PEAK  8(4Q34.3) WILD-TYPE 276  69
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                          125                           345 
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                           25                            69 
$`DEL PEAK  8(4Q34.3) MUTATED`
TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5274 TCGA-DB-5275 
       18.15        64.64         8.48         7.56        75.25        47.93 
TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XE TCGA-DB-A4XH 
       50.86        44.52        78.28        18.84        37.45        31.63 
TCGA-DB-A64W TCGA-DB-A75O TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66G TCGA-DH-A7UV 
       14.40        30.74        30.21        42.05        17.19        18.61 
TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6399 TCGA-DU-6400 
       17.46        13.38        18.94        15.16        65.75         1.22 
TCGA-DU-6405 TCGA-DU-6410 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7018 
       19.89         7.96        62.96       156.23        14.99        30.67 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7309 TCGA-DU-8165 
       94.32        44.02        25.91        60.30         2.76        19.13 
TCGA-DU-8168 TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S3 
       14.17        12.59        15.12         3.65         5.65         2.70 
TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5303 
        5.98        21.30       124.50        77.88        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5322 TCGA-EZ-7264 
       41.13        79.99        57.93       134.27       130.78        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-7636 
        0.23         0.20        47.77        25.48        34.36        17.88 
TCGA-FG-7638 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L 
       22.55        14.24        14.96        23.70        14.76        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7468 
       15.02        16.44        22.26        20.45         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7480 
       11.54         0.13        16.54         6.54        24.26        75.19 
TCGA-HT-7677 TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-7856 TCGA-HT-8105 TCGA-HT-A5R7 
       16.24        31.69         2.96        39.09         6.25        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RC TCGA-HT-A616 TCGA-HT-A619 TCGA-HT-A74J TCGA-HT-A74K 
        0.07         5.33         1.81        21.40        10.52        15.35 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-8321 TCGA-IK-7675 
       19.89         8.32        40.18        35.90        19.59        19.00 
TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A733 TCGA-QH-A6X4 TCGA-QH-A6XA 
       42.77         0.23         2.30        13.61        14.53        16.50 
TCGA-RY-A83Z TCGA-S9-A6TW TCGA-S9-A6WD TCGA-S9-A6WL TCGA-S9-A6WP TCGA-S9-A7IS 
        9.90        37.84        69.50        31.10        15.16         7.92 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QY TCGA-S9-A89Z TCGA-TM-A7C4 
       23.51         7.13        20.02        28.37        11.97        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84R TCGA-TM-A84T TCGA-TQ-A7RW 
       49.32        34.78        48.39        18.61        23.80        26.99 
TCGA-VM-A8C8 TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85E 
       43.04        13.32        39.88        43.40        20.81 

$`DEL PEAK  8(4Q34.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 
        4.70         7.69        43.89        10.62        40.18         0.10 
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
       21.01         9.96         6.38        17.69        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 
       12.43         8.02         7.40         6.61       122.73        81.96 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC 
       72.92        50.17        36.56        46.42        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       39.78        33.57        72.95        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64X 
        5.98        31.40        27.45        27.81        29.23        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       12.10        11.24        17.88        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UR 
       30.31        14.40         8.02        27.81        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5852 
       13.12        13.38         3.45        18.02        14.56         6.74 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6393 
        8.45         6.81       182.33        17.49       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6402 
       22.42        49.02        75.16        46.06        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 
       11.64       133.74        16.83        94.52       114.08         7.73 
TCGA-DU-7006 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
       11.47       138.28       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7300 
       90.77        26.30        10.36         7.96        18.94        62.01 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       23.31        41.98         5.10        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TT TCGA-DU-A5TY 
       21.40        16.96        15.48        14.24         4.96        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
        8.65        77.98         7.23        11.41        26.76         7.13 
TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       17.98        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       78.21        95.57        75.02        32.45        36.82        32.35 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 
       15.35        20.61        20.09        12.95        13.68        16.01 
TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       20.09        22.52        32.61        38.27        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A60K TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       18.71        17.82        28.54        10.78        36.66        48.69 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7474 
       13.58         5.72        27.52        40.11         0.03         3.75 
TCGA-HT-7475 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
       17.42         6.38        40.34        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
        0.23        14.27         0.16         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 
       42.74         0.10        14.96         0.10         0.10        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7858 
        6.90        14.53        39.48        19.23         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
       12.23         0.10         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59        34.19        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 
       26.04         0.13        27.35         0.10         2.70        16.93 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74L 
       16.14        16.83        17.52        17.65         2.43        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7490 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        0.10        29.92        19.23         4.31        21.70        21.60 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A74X 
       17.82        20.35        12.76        20.81        20.71        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
       14.40         6.71         1.64         2.37         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
       11.64         0.20         9.01        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X5 TCGA-QH-A6X8 
       12.23         2.20         9.17        10.29        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
        1.91         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 
       32.65        59.38        30.87         5.46        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX 
       19.59        30.67        62.17        87.12        18.77        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE 
       16.08        98.24        95.93         5.85       106.39        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       80.12        32.45        84.99        19.86        15.91        18.61 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       14.07        36.13        22.32         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       15.06        13.12        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A84B 
       30.05        98.63        31.59        18.71        49.45        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84S TCGA-TQ-A7RH 
       40.83        24.79        33.24        25.38        14.93        15.98 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 
       37.05        16.01        23.21         8.05        51.06        43.96 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       45.80        46.88        37.71 

  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                       156.23                        211.17 
  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE 
                        19.89                         17.98 
[1] "0.1 - 156.2 (19.9)" "0.0 - 211.2 (18.0)"
[1] "hr=" "1.1"
D29V2, continuous
D29V3, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q34.3) MUTATED    53  72
  DEL PEAK  8(4Q34.3) WILD-TYPE 153 194
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.3) MUTATED     53   72
  DEL PEAK  8(4Q34.3) WILD-TYPE  153  194
        clus
vv       DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE
  FEMALE                          53                           153
  MALE                            72                           194
[1] 2 2
[1] FALSE
D29V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  8(4Q34.3) MUTATED            45               30                50
  DEL PEAK  8(4Q34.3) WILD-TYPE         131               88               128
D29V5, multiclass
                   clus
vv                  DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE
  ASTROCYTOMA                                45                           131
  OLIGOASTROCYTOMA                           30                            88
  OLIGODENDROGLIOMA                          50                           128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q34.3) MUTATED    30  95
  DEL PEAK  8(4Q34.3) WILD-TYPE  62 285
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.3) MUTATED     30   95
  DEL PEAK  8(4Q34.3) WILD-TYPE   62  285
     clus
vv    DEL PEAK  8(4Q34.3) MUTATED DEL PEAK  8(4Q34.3) WILD-TYPE
  NO                           30                            62
  YES                          95                           285
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(4Q34.3) MUTATED                                  0     3
  DEL PEAK  8(4Q34.3) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(4Q34.3) MUTATED                           2   119
  DEL PEAK  8(4Q34.3) WILD-TYPE                        13   318
D29V7, multiclass
                                  clus
vv                                 DEL PEAK  8(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                    119
                                  clus
vv                                 DEL PEAK  8(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   13
  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"
D29V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q34.3) MUTATED     5 112
  DEL PEAK  8(4Q34.3) WILD-TYPE  13 307
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.3) MUTATED      5  112
  DEL PEAK  8(4Q34.3) WILD-TYPE   13  307
                        clus
vv                       DEL PEAK  8(4Q34.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         112
                        clus
vv                       DEL PEAK  8(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           307
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  9(5P15.33) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  9(5P15.33) MUTATED    37   9
  DEL PEAK  9(5P15.33) WILD-TYPE 339  85
  DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE 
                            46                            424 
  DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE 
                             9                             85 
$`DEL PEAK  9(5P15.33) MUTATED`
TCGA-CS-4943 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5281 TCGA-DB-A4XC TCGA-DB-A4XE 
       18.15        47.93        72.92        78.28        46.72        37.45 
TCGA-DB-A4XH TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-6399 
       31.63        18.51        19.96        27.81        17.19        65.75 
TCGA-DU-7007 TCGA-DU-7306 TCGA-DU-8165 TCGA-DU-A7T6 TCGA-E1-5302 TCGA-E1-5304 
       62.96        41.98        19.13        17.98        50.14        41.13 
TCGA-E1-A7YV TCGA-FG-5962 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-A4MW TCGA-FG-A4MY 
       32.45        47.77        36.82        14.93        18.38        23.70 
TCGA-FG-A6J3 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7873 
       22.26         3.75        17.42        31.69        14.96        23.61 
TCGA-HT-7879 TCGA-HT-7884 TCGA-HT-8106 TCGA-HT-A614 TCGA-HT-A61B TCGA-HT-A74O 
        3.68        11.28         0.10         2.70        17.52         0.10 
TCGA-P5-A5F4 TCGA-P5-A72W TCGA-RY-A83Z TCGA-S9-A6TV TCGA-S9-A6WM TCGA-S9-A7IX 
        0.76        10.42         9.90        18.77        19.86        22.32 
TCGA-S9-A7R7 TCGA-TM-A84I TCGA-TQ-A7RH TCGA-WY-A859 
       98.63        28.08        15.98        39.88 

$`DEL PEAK  9(5P15.33) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5277 TCGA-DB-5278 
        6.61       122.73        81.96        75.25        50.86        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD 
       44.52        36.56        46.42        18.84        30.21        39.78 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       33.57        72.95        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K 
       31.40        27.45        27.81        29.23        14.40        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5142 
       11.24        17.88        30.74        16.18        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66F TCGA-DH-A7UR 
       14.40         8.02        30.21        42.05        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 
       13.12        13.38         3.45        18.61        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       17.46         6.74        13.38         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
       18.94        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       49.02        75.16        46.06         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.96         7.73        11.47       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8158 
       62.01        25.91        60.30        23.31         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74        14.60        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 
      130.78        75.02        36.82        32.35        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 
        0.20        25.48        34.36        18.77        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A60J 
       22.52        32.61        38.27        10.72        18.71        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z 
       17.82        16.41        15.02        16.44        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       16.54         6.54        24.26         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
       37.15         0.33         0.13         5.33        35.47         3.72 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 
       37.87        33.01        12.23         6.25         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        5.56        13.78         0.23        29.59        34.19        28.27 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        26.04         0.13        20.22         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
       27.35         0.10         5.33        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       16.83        21.40        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
       11.05        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U 
        2.30         4.11         5.88         7.63         1.28         0.16 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
       30.87         5.46        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       62.17        87.12        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       32.45        84.99        31.10        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.07        36.13         7.92        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04        17.03        15.06        13.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 
       13.02       169.84        10.39        99.06        30.05        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71        11.97        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
       14.93        23.80        26.99        43.04        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A85A 
       23.21         8.05        51.06        13.32        43.96        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE 
                         98.63                         211.17 
  DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE 
                         21.11                          18.23 
[1] "0.1 - 98.6 (21.1)"  "0.0 - 211.2 (18.2)"
[1] "hr=" "1"  
D30V2, continuous
D30V3, binary
                                cls
clus                               0   1
  DEL PEAK  9(5P15.33) MUTATED    18  28
  DEL PEAK  9(5P15.33) WILD-TYPE 188 238
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(5P15.33) MUTATED     18   28
  DEL PEAK  9(5P15.33) WILD-TYPE  188  238
        clus
vv       DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE
  FEMALE                           18                            188
  MALE                             28                            238
[1] 2 2
[1] FALSE
D30V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK  9(5P15.33) MUTATED            19               19                 8
  DEL PEAK  9(5P15.33) WILD-TYPE         157               99               170
D30V5, multiclass
                   clus
vv                  DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE
  ASTROCYTOMA                                 19                            157
  OLIGOASTROCYTOMA                            19                             99
  OLIGODENDROGLIOMA                            8                            170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                                cls
clus                               0   1
  DEL PEAK  9(5P15.33) MUTATED    15  31
  DEL PEAK  9(5P15.33) WILD-TYPE  77 349
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(5P15.33) MUTATED     15   31
  DEL PEAK  9(5P15.33) WILD-TYPE   77  349
     clus
vv    DEL PEAK  9(5P15.33) MUTATED DEL PEAK  9(5P15.33) WILD-TYPE
  NO                            15                             77
  YES                           31                            349
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(5P15.33) MUTATED                                  0     0
  DEL PEAK  9(5P15.33) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(5P15.33) MUTATED                           0    45
  DEL PEAK  9(5P15.33) WILD-TYPE                        15   392
D30V7, multiclass
                                  clus
vv                                 DEL PEAK  9(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      45
                                  clus
vv                                 DEL PEAK  9(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       392
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                                cls
clus                               0   1
  DEL PEAK  9(5P15.33) MUTATED     2  42
  DEL PEAK  9(5P15.33) WILD-TYPE  16 377
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(5P15.33) MUTATED      2   42
  DEL PEAK  9(5P15.33) WILD-TYPE   16  377
                        clus
vv                       DEL PEAK  9(5P15.33) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           42
                        clus
vv                       DEL PEAK  9(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            377
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK 10(5Q34) MUTATION ANALYSIS
D31V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 10(5Q34) MUTATED    42  18
  DEL PEAK 10(5Q34) WILD-TYPE 334  76
  DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE 
                         60                         410 
  DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE 
                         18                          76 
$`DEL PEAK 10(5Q34) MUTATED`
TCGA-CS-6665 TCGA-CS-6666 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A4XH 
       12.43         8.48        72.92        50.86        78.28        31.63 
TCGA-DB-A64X TCGA-DB-A75L TCGA-DH-5140 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G 
       18.51        11.24        19.96        42.05        27.81        17.19 
TCGA-DH-A7UU TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6408 TCGA-DU-7007 TCGA-DU-7010 
        3.45        65.75        87.45       114.08        62.96        14.99 
TCGA-DU-8165 TCGA-DU-A5TU TCGA-DU-A6S7 TCGA-DU-A7T6 TCGA-E1-5302 TCGA-E1-5304 
       19.13         3.65         7.23        17.98        50.14        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-FG-5963 TCGA-FG-7636 TCGA-FG-A6J3 TCGA-HT-7469 
       79.99        57.93        25.48        17.88        22.26        11.54 
TCGA-HT-7470 TCGA-HT-7477 TCGA-HT-7609 TCGA-HT-7879 TCGA-HT-7884 TCGA-HT-7902 
       40.11        24.26        45.99         3.68        11.28        31.43 
TCGA-HT-8106 TCGA-HT-A5R7 TCGA-HT-A614 TCGA-HT-A618 TCGA-HW-7489 TCGA-IK-7675 
        0.10        20.22         2.70        16.83         8.32        19.00 
TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A72X TCGA-QH-A65S TCGA-RY-A83Z TCGA-S9-A6TS 
        2.30         5.88        13.25         2.53         9.90        62.17 
TCGA-S9-A6TV TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A7IS TCGA-S9-A7R7 TCGA-S9-A89Z 
       18.77        19.86        18.61         7.92        98.63        11.97 
TCGA-TM-A7CF TCGA-TM-A84I TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85B TCGA-WY-A85D 
       48.39        28.08        13.32        39.88        45.80        37.71 

$`DEL PEAK 10(5Q34) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       23.84        17.95         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5278 TCGA-DB-5279 
      122.73        81.96        75.25        47.93        50.17        44.52 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       36.56        46.42        18.84        30.21        46.72        39.78 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       37.45        33.57        72.95        24.20        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5142 
       12.10        17.88        30.74        16.18        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US 
       14.40         8.02        30.21        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       13.38        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       46.06         1.22         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 
       16.83        94.52         7.96         7.73        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
      138.28       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74        14.60        20.68        21.40 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        4.96         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5303 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       67.46       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       47.77        34.36        36.82        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       23.97        18.44        15.35        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7472 
        5.72        27.52         0.10         6.67         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42         6.54         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       22.06        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        5.33        35.47         3.72         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       34.19        28.27        15.72         0.23        26.04         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 
        0.07        27.35         0.10         5.33        16.93         1.81 
TCGA-HT-A617 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.14        21.40        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 
       15.35        11.05         0.10        29.92        19.89        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 
       17.82        20.35        12.76        20.81        20.71        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       14.40        14.40         0.23         6.71         1.64         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
        4.11         7.63         0.76         1.28         0.16        10.42 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65V 
       11.64         0.20         9.01        13.61        15.16        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
       15.85        14.04        19.33        14.83        14.53        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TW 
       28.08         2.07        19.59        30.67        87.12        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        16.08        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY 
       15.91        15.16        14.07        36.13        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       30.05        31.59        18.71        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       34.78        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       24.16        40.83        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 
       14.93        23.80        15.98        26.99        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A85A 
       16.01        23.21         8.05        51.06        43.96        43.40 
TCGA-WY-A85C TCGA-WY-A85E 
       46.88        20.81 

  DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE 
                       0.10                        0.03 
  DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE 
                     114.08                      211.17 
  DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE 
                     19.495                      18.410 
[1] "0.1 - 114.1 (19.5)" "0.0 - 211.2 (18.4)"
[1] "hr=" "1.5"
D31V2, continuous
D31V3, binary
                             cls
clus                            0   1
  DEL PEAK 10(5Q34) MUTATED    27  33
  DEL PEAK 10(5Q34) WILD-TYPE 179 233
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(5Q34) MUTATED     27   33
  DEL PEAK 10(5Q34) WILD-TYPE  179  233
        clus
vv       DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE
  FEMALE                        27                         179
  MALE                          33                         233
[1] 2 2
[1] FALSE
D31V4, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 10(5Q34) MUTATED            39               12                 9
  DEL PEAK 10(5Q34) WILD-TYPE         137              106               169
D31V5, multiclass
                   clus
vv                  DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE
  ASTROCYTOMA                              39                         137
  OLIGOASTROCYTOMA                         12                         106
  OLIGODENDROGLIOMA                         9                         169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                             cls
clus                            0   1
  DEL PEAK 10(5Q34) MUTATED    16  44
  DEL PEAK 10(5Q34) WILD-TYPE  76 336
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(5Q34) MUTATED     16   44
  DEL PEAK 10(5Q34) WILD-TYPE   76  336
     clus
vv    DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE
  NO                         16                          76
  YES                        44                         336
[1] 2 2
[1] FALSE
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(5Q34) MUTATED                                  0     0
  DEL PEAK 10(5Q34) WILD-TYPE                                1     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(5Q34) MUTATED                           0    60
  DEL PEAK 10(5Q34) WILD-TYPE                        15   377
D31V7, multiclass
                                  clus
vv                                 DEL PEAK 10(5Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                   60
                                  clus
vv                                 DEL PEAK 10(5Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                    377
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                             cls
clus                            0   1
  DEL PEAK 10(5Q34) MUTATED     1  56
  DEL PEAK 10(5Q34) WILD-TYPE  17 363
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(5Q34) MUTATED      1   56
  DEL PEAK 10(5Q34) WILD-TYPE   17  363
                        clus
vv                       DEL PEAK 10(5Q34) MUTATED DEL PEAK 10(5Q34) WILD-TYPE
  HISPANIC OR LATINO                             1                          17
  NOT HISPANIC OR LATINO                        56                         363
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK 11(6P25.3) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(6P25.3) MUTATED    26  17
  DEL PEAK 11(6P25.3) WILD-TYPE 350  77
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                           43                           427 
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                           17                            77 
$`DEL PEAK 11(6P25.3) MUTATED`
TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64O 
        6.38         8.48        50.86        33.57        31.63        25.48 
TCGA-DH-A669 TCGA-DH-A66G TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6407 TCGA-DU-8158 
       30.21        17.19         1.22         7.04        94.52         5.10 
TCGA-DU-8161 TCGA-DU-A7T6 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-A70Y 
       23.74        17.98        25.48        36.82        24.99        28.54 
TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-7873 TCGA-HT-7884 TCGA-HT-8564 TCGA-HT-A4DS 
        2.96        19.23        23.61        11.28        15.72         0.23 
TCGA-HT-A614 TCGA-HT-A617 TCGA-HT-A74L TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8322 
        2.70        16.14        11.05        19.23        35.90        17.82 
TCGA-IK-7675 TCGA-P5-A5EZ TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A6CS TCGA-QH-A6CX 
       19.00         2.30         0.76         1.28        19.33        12.23 
TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A7IS TCGA-TM-A7CF TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.77        28.70         7.92        48.39        26.99        43.04 
TCGA-VM-A8CD 
        7.89 

$`DEL PEAK 11(6P25.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         9.96        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95        12.43         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       44.52        36.56        78.28        46.42        18.84        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P 
       46.72        39.78        37.45        72.95        24.20        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       18.51        12.10        11.24        17.88        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B 
       19.96        31.82        30.31        14.40         8.02        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       27.81        17.19        54.25        13.12        13.38         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       65.75        87.45        11.64       133.74        19.89        16.83 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
      114.08         7.96         7.73        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      138.28        14.99       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
       41.98         2.76        14.60        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       21.30       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       44.42         0.56        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6691 TCGA-FG-6692 
       47.77        34.36        18.77        14.93        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       32.61        38.27        10.72        18.38        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 
        0.10        17.52         6.90        14.53        39.48        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
        0.23        50.63         0.49        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 
        3.68         5.33        35.47         3.72        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV 
       13.78         0.23        29.59        34.19        28.27        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C 
       16.93         1.81        16.83        21.40        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
        2.43        10.52        15.35         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
        8.32        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X 
       20.35        12.76        20.81        20.71        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 
       14.40         0.23         6.71         1.64         2.37         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        5.88         7.63         0.16        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CY 
       15.85        14.04        14.83        14.53        13.61         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW 
        2.07        19.59        30.67        62.17        87.12        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       34.49        31.33        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX 
       15.91        18.61        15.16        14.07        36.13        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        30.05        98.63        31.59        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C 
       49.45        48.33        49.32        34.78        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       59.05        40.64        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
       15.98        30.08        13.51         0.10        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                         0.23                          0.03 
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                        94.52                        211.17 
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                        18.77                         18.61 
[1] "0.2 - 94.5 (18.8)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "3.7"
D32V2, continuous
D32V3, binary
                               cls
clus                              0   1
  DEL PEAK 11(6P25.3) MUTATED    20  24
  DEL PEAK 11(6P25.3) WILD-TYPE 186 242
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P25.3) MUTATED     20   24
  DEL PEAK 11(6P25.3) WILD-TYPE  186  242
        clus
vv       DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE
  FEMALE                          20                           186
  MALE                            24                           242
[1] 2 2
[1] FALSE
D32V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 11(6P25.3) MUTATED            21                9                14
  DEL PEAK 11(6P25.3) WILD-TYPE         155              109               164
D32V5, multiclass
                   clus
vv                  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE
  ASTROCYTOMA                                21                           155
  OLIGOASTROCYTOMA                            9                           109
  OLIGODENDROGLIOMA                          14                           164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                               cls
clus                              0   1
  DEL PEAK 11(6P25.3) MUTATED     9  35
  DEL PEAK 11(6P25.3) WILD-TYPE  83 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P25.3) MUTATED      9   35
  DEL PEAK 11(6P25.3) WILD-TYPE   83  345
     clus
vv    DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE
  NO                            9                            83
  YES                          35                           345
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(6P25.3) MUTATED                                  1     0
  DEL PEAK 11(6P25.3) WILD-TYPE                                0     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6P25.3) MUTATED                           0    43
  DEL PEAK 11(6P25.3) WILD-TYPE                        15   394
D32V7, multiclass
                                  clus
vv                                 DEL PEAK 11(6P25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     43
                                  clus
vv                                 DEL PEAK 11(6P25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   15
  WHITE                                                      394
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(6P25.3) MUTATED     3  38
  DEL PEAK 11(6P25.3) WILD-TYPE  15 381
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P25.3) MUTATED      3   38
  DEL PEAK 11(6P25.3) WILD-TYPE   15  381
                        clus
vv                       DEL PEAK 11(6P25.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          38
                        clus
vv                       DEL PEAK 11(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           381
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK 12(6Q22.31) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 12(6Q22.31) MUTATED    45  23
  DEL PEAK 12(6Q22.31) WILD-TYPE 331  71
  DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE 
                            68                            402 
  DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE 
                            23                             71 
$`DEL PEAK 12(6Q22.31) MUTATED`
TCGA-CS-4944 TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5280 TCGA-DB-A4XF TCGA-DB-A4XH 
       10.62         6.38         8.48        36.56        33.57        31.63 
TCGA-DB-A64O TCGA-DB-A75M TCGA-DH-A669 TCGA-DH-A66B TCGA-DU-5847 TCGA-DU-5855 
       25.48        17.88        30.21        42.05        18.02         6.81 
TCGA-DU-5872 TCGA-DU-6400 TCGA-DU-6405 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7012 
       17.49         1.22        19.89         7.73        11.47         6.54 
TCGA-DU-7014 TCGA-DU-7298 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-A7T6 TCGA-DU-A7TC 
      117.40        18.94         5.10        23.74        17.98        23.51 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-FG-5963 TCGA-FG-7636 TCGA-FG-8191 
       41.13        79.99        57.93        25.48        17.88        32.61 
TCGA-FG-A4MT TCGA-FG-A6J3 TCGA-FN-7833 TCGA-HT-7475 TCGA-HT-7606 TCGA-HT-7688 
       38.27        22.26        27.52        17.42        17.29        31.69 
TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-7884 TCGA-HT-8564 TCGA-HT-A4DS 
       14.96         2.96        19.23        11.28        15.72         0.23 
TCGA-HT-A5RB TCGA-HT-A617 TCGA-HT-A619 TCGA-HW-A5KK TCGA-P5-A5EV TCGA-P5-A5EZ 
        0.10        16.14        21.40        12.76         0.23         2.30 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-QH-A6CS TCGA-QH-A6CX 
        7.63         0.76         1.28        10.42        19.33        12.23 
TCGA-QH-A870 TCGA-RY-A83Z TCGA-S9-A6TZ TCGA-S9-A6U6 TCGA-S9-A7IS TCGA-S9-A7R2 
       12.99         9.90        28.70        16.08         7.92        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A7CF TCGA-TM-A84Q TCGA-TQ-A7RW TCGA-VM-A8C8 
       99.06        31.59        48.39        25.38        26.99        43.04 
TCGA-VM-A8CD TCGA-WY-A85B 
        7.89        45.80 

$`DEL PEAK 12(6Q22.31) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
        0.10        21.01         9.96        17.69        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       12.43         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 
       81.96        75.25        47.93        72.92        50.86        50.17 
TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       44.52        78.28        46.42        18.84        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q 
       39.78        37.45        72.95        24.20        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       12.10        11.24        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       30.31        14.40         8.02        27.81        17.19        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 
       54.25        13.12        13.38         3.45        18.61        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 
       17.46         6.74        13.38         8.45       182.33        18.94 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       46.06        65.75        87.45         7.04        11.64       133.74 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7007 TCGA-DU-7008 
       16.83        94.52       114.08         7.96        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
      138.28        14.99       105.21         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 
       26.30        10.36         7.96        94.32        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 
       25.91        60.30        23.31        41.98         2.76        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA 
       11.41        26.76         7.13        21.30       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       42.31         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV 
      134.27        78.21        95.57       130.78        75.02        32.45 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       36.82        32.35        14.33         0.23         0.20        47.77 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       18.44        15.35        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       16.41        15.02        16.44        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-HT-7467 TCGA-HT-7468 
       48.69        20.45        13.58         5.72         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       11.54        40.11         0.13         0.03        16.54         3.75 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
      122.47         4.57         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 
       44.68         6.05        42.74         0.10         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 
       17.52         6.90        14.53        39.48        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 
        3.68         5.33        35.47         3.72        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV 
       13.78         0.23        29.59        34.19        28.27        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 
        0.13        20.22         0.07        27.35         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       16.93         1.81        16.83        17.52        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM 
       21.60        19.59        17.82        20.35        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX 
       19.00        42.77        14.40        14.40         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z 
        2.37         4.11         5.88         0.16        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CY 
       15.85        14.04        14.83        14.53        13.61         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
       16.50         5.03        11.08        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       59.38        30.87         5.46        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U8 
       31.33        22.95        17.62        23.64        32.61        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       15.16        14.07        36.13        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V 
       28.37        13.02       169.84        30.05        98.63        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B 
       11.97        49.45        48.33        49.32        34.78        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       16.18        59.05        40.64        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       40.83        24.79        33.24        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
       15.98        30.08        13.51         0.10        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.96        39.88        43.40        46.88        37.71        20.81 

  DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE 
                        117.40                         211.17 
  DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE 
                         17.88                          18.77 
[1] "0.1 - 117.4 (17.9)" "0.0 - 211.2 (18.8)"
[1] "hr=" "2.8"
D33V2, continuous
D33V3, binary
                                cls
clus                               0   1
  DEL PEAK 12(6Q22.31) MUTATED    32  37
  DEL PEAK 12(6Q22.31) WILD-TYPE 174 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(6Q22.31) MUTATED     32   37
  DEL PEAK 12(6Q22.31) WILD-TYPE  174  229
        clus
vv       DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE
  FEMALE                           32                            174
  MALE                             37                            229
[1] 2 2
[1] FALSE
D33V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 12(6Q22.31) MUTATED            44               11                14
  DEL PEAK 12(6Q22.31) WILD-TYPE         132              107               164
D33V5, multiclass
                   clus
vv                  DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE
  ASTROCYTOMA                                 44                            132
  OLIGOASTROCYTOMA                            11                            107
  OLIGODENDROGLIOMA                           14                            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                                cls
clus                               0   1
  DEL PEAK 12(6Q22.31) MUTATED    16  53
  DEL PEAK 12(6Q22.31) WILD-TYPE  76 327
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(6Q22.31) MUTATED     16   53
  DEL PEAK 12(6Q22.31) WILD-TYPE   76  327
     clus
vv    DEL PEAK 12(6Q22.31) MUTATED DEL PEAK 12(6Q22.31) WILD-TYPE
  NO                            16                             76
  YES                           53                            327
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(6Q22.31) MUTATED                                  1     1
  DEL PEAK 12(6Q22.31) WILD-TYPE                                0     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6Q22.31) MUTATED                           3    64
  DEL PEAK 12(6Q22.31) WILD-TYPE                        12   373
D33V7, multiclass
                                  clus
vv                                 DEL PEAK 12(6Q22.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      64
                                  clus
vv                                 DEL PEAK 12(6Q22.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                                cls
clus                               0   1
  DEL PEAK 12(6Q22.31) MUTATED     3  60
  DEL PEAK 12(6Q22.31) WILD-TYPE  15 359
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(6Q22.31) MUTATED      3   60
  DEL PEAK 12(6Q22.31) WILD-TYPE   15  359
                        clus
vv                       DEL PEAK 12(6Q22.31) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           60
                        clus
vv                       DEL PEAK 12(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            359
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 13(6Q24.3) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(6Q24.3) MUTATED    48  23
  DEL PEAK 13(6Q24.3) WILD-TYPE 328  71
  DEL PEAK 13(6Q24.3) MUTATED DEL PEAK 13(6Q24.3) WILD-TYPE 
                           71                           399 
  DEL PEAK 13(6Q24.3) MUTATED DEL PEAK 13(6Q24.3) WILD-TYPE 
                           23                            71 
$`DEL PEAK 13(6Q24.3) MUTATED`
TCGA-CS-4944 TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5280 TCGA-DB-A4XF TCGA-DB-A4XH 
       10.62         6.38         8.48        36.56        33.57        31.63 
TCGA-DB-A64O TCGA-DB-A75M TCGA-DH-A669 TCGA-DH-A66B TCGA-DU-5847 TCGA-DU-5855 
       25.48        17.88        30.21        42.05        18.02         6.81 
TCGA-DU-5872 TCGA-DU-6400 TCGA-DU-6405 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7012 
       17.49         1.22        19.89         7.73        11.47         6.54 
TCGA-DU-7014 TCGA-DU-7298 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-A7T6 TCGA-DU-A7TC 
      117.40        18.94         5.10        23.74        17.98        23.51 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5322 TCGA-FG-5963 TCGA-FG-7636 
       41.13        79.99        57.93       130.78        25.48        17.88 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A6J3 TCGA-FN-7833 TCGA-HT-7472 TCGA-HT-7475 
       32.61        38.27        22.26        27.52         0.03        17.42 
TCGA-HT-7606 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-7884 
       17.29        31.69        14.96         2.96        19.23        11.28 
TCGA-HT-8108 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RB TCGA-HT-A617 
        2.50        28.27        15.72         0.23         0.10        16.14 
TCGA-HT-A619 TCGA-HW-A5KK TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F2 TCGA-P5-A5F4 
       21.40        12.76         0.23         2.30         7.63         0.76 
TCGA-P5-A5F6 TCGA-P5-A72W TCGA-QH-A6CS TCGA-QH-A6CX TCGA-QH-A870 TCGA-S9-A6TZ 
        1.28        10.42        19.33        12.23        12.99        28.70 
TCGA-S9-A6U6 TCGA-S9-A7IS TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A7CF TCGA-TM-A84Q 
       16.08         7.92        99.06        31.59        48.39        25.38 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8CD TCGA-VV-A86M TCGA-WY-A85B 
       26.99        43.04         7.89        16.01        45.80 

$`DEL PEAK 13(6Q24.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
        0.10        21.01         9.96        17.69        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       12.43         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 
       81.96        75.25        47.93        72.92        50.86        50.17 
TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       44.52        78.28        46.42        18.84        30.21        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q 
       39.78        37.45        72.95        24.20        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       12.10        11.24        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       30.31        14.40         8.02        27.81        17.19        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 
       54.25        13.12        13.38         3.45        18.61        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 
       17.46         6.74        13.38         8.45       182.33        18.94 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       46.06        65.75        87.45         7.04        11.64       133.74 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7007 TCGA-DU-7008 
       16.83        94.52       114.08         7.96        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
      138.28        14.99       105.21         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 
       26.30        10.36         7.96        94.32        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 
       25.91        60.30        23.31        41.98         2.76        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA 
       11.41        26.76         7.13        21.30       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       42.31         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW 
      134.27        78.21        95.57        75.02        32.45        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 
       32.35        14.33         0.23         0.20        47.77        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       15.35        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MU 
       14.24        16.01        20.09        14.96        22.52        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       15.02        16.44        28.54        10.78        36.66        48.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       20.45        13.58         5.72         0.10         6.67        11.54 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7477 
       40.11         0.13        16.54         3.75         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 
       42.74         0.10         0.10         0.10        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       14.53        39.48        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
       35.47         3.72        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.10         0.46         5.56        13.78         0.23        29.59 
TCGA-HT-8114 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
       34.19        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B 
        5.33         2.70        16.93         1.81        16.83        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A72U 
        6.71         1.64         2.37         4.11         5.88         0.16 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV 
        2.53        12.62        15.85        14.04        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       13.61         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK 
       16.73         1.91        16.50         5.03        11.08        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z 
       94.03        32.65        59.38        30.87         5.46         9.90 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU 
       28.08         2.07        19.59        30.67        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6U1 
       18.77        37.84        34.49        31.33        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       23.64        32.61        98.24        95.93         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       22.32        23.51         7.13        20.02         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       10.39        30.05        98.63        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       48.33        49.32        34.78        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-VM-A8C9 
       33.24        18.61        14.93        23.80        15.98        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VW-A7QS 
       13.51         0.10        35.93        23.47        37.05        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  DEL PEAK 13(6Q24.3) MUTATED DEL PEAK 13(6Q24.3) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK 13(6Q24.3) MUTATED DEL PEAK 13(6Q24.3) WILD-TYPE 
                       130.78                        211.17 
  DEL PEAK 13(6Q24.3) MUTATED DEL PEAK 13(6Q24.3) WILD-TYPE 
                        17.88                         18.77 
[1] "0.0 - 130.8 (17.9)" "0.1 - 211.2 (18.8)"
[1] "hr=" "2.4"
D34V2, continuous
D34V3, binary
                               cls
clus                              0   1
  DEL PEAK 13(6Q24.3) MUTATED    35  37
  DEL PEAK 13(6Q24.3) WILD-TYPE 171 229
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(6Q24.3) MUTATED     35   37
  DEL PEAK 13(6Q24.3) WILD-TYPE  171  229
        clus
vv       DEL PEAK 13(6Q24.3) MUTATED DEL PEAK 13(6Q24.3) WILD-TYPE
  FEMALE                          35                           171
  MALE                            37                           229
[1] 2 2
[1] FALSE
D34V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 13(6Q24.3) MUTATED            44               12                16
  DEL PEAK 13(6Q24.3) WILD-TYPE         132              106               162
D34V5, multiclass
                   clus
vv                  DEL PEAK 13(6Q24.3) MUTATED DEL PEAK 13(6Q24.3) WILD-TYPE
  ASTROCYTOMA                                44                           132
  OLIGOASTROCYTOMA                           12                           106
  OLIGODENDROGLIOMA                          16                           162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(6Q24.3) MUTATED    17  55
  DEL PEAK 13(6Q24.3) WILD-TYPE  75 325
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(6Q24.3) MUTATED     17   55
  DEL PEAK 13(6Q24.3) WILD-TYPE   75  325
     clus
vv    DEL PEAK 13(6Q24.3) MUTATED DEL PEAK 13(6Q24.3) WILD-TYPE
  NO                           17                            75
  YES                          55                           325
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(6Q24.3) MUTATED                                  1     1
  DEL PEAK 13(6Q24.3) WILD-TYPE                                0     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(6Q24.3) MUTATED                           3    66
  DEL PEAK 13(6Q24.3) WILD-TYPE                        12   371
D34V7, multiclass
                                  clus
vv                                 DEL PEAK 13(6Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     66
                                  clus
vv                                 DEL PEAK 13(6Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                      371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(6Q24.3) MUTATED     4  62
  DEL PEAK 13(6Q24.3) WILD-TYPE  14 357
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(6Q24.3) MUTATED      4   62
  DEL PEAK 13(6Q24.3) WILD-TYPE   14  357
                        clus
vv                       DEL PEAK 13(6Q24.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          62
                        clus
vv                       DEL PEAK 13(6Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           357
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 14(7P22.3) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(7P22.3) MUTATED    12   7
  DEL PEAK 14(7P22.3) WILD-TYPE 364  87
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           19                           451 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                            7                            87 
$`DEL PEAK 14(7P22.3) MUTATED`
TCGA-CS-5393 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-7304 TCGA-DU-A6S7 TCGA-DU-A76R 
       40.18        46.06        65.75        23.31         7.23        21.30 
TCGA-FG-8188 TCGA-FN-7833 TCGA-HT-7470 TCGA-HT-7477 TCGA-HW-A5KL TCGA-P5-A5F2 
       14.96        27.52        40.11        24.26        20.81         7.63 
TCGA-P5-A5F6 TCGA-QH-A6CX TCGA-S9-A6TS TCGA-S9-A7R3 TCGA-TM-A84G TCGA-TM-A84H 
        1.28        12.23        62.17        99.06        40.64        30.44 
TCGA-VW-A7QS 
       23.21 

$`DEL PEAK 14(7P22.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       50.86        50.17        44.52        36.56        78.28        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       12.10        11.24        17.88        30.74        16.18        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        13.12        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45        18.61        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       60.30        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K 
       12.20         8.65         2.70        77.98         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       26.76         7.13        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       23.51         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       14.24        16.01        20.09        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72        18.38        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        22.26        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-HT-7467 
       36.66        48.69        20.45        13.58         5.72         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        6.67        11.54         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42         6.54         6.38        40.34        75.19        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      122.47         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        26.04         0.13        20.22         0.07        27.35 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        16.93         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J 
       16.83        21.40        17.52        17.65         2.43        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       15.35        11.05         0.10        29.92        19.89         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KM TCGA-IK-7675 
       19.59        17.82        20.35        12.76        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F4 TCGA-P5-A72U 
        2.37         2.30         4.11         5.88         0.76         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        14.53        13.61         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       30.67        87.12        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       98.24        95.93         5.85       106.39        69.50        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       18.61        15.16        14.07        36.13         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       23.51         7.13        20.02         8.19         2.04        17.03 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
       15.06        13.12        28.37        13.02       169.84        10.39 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       30.05        98.63        31.59        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       59.05        28.08        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       43.04        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       23.47        37.05        16.01         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                         1.28                          0.03 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                        99.06                        211.17 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                        24.26                         18.44 
[1] "1.3 - 99.1 (24.3)"  "0.0 - 211.2 (18.4)"
[1] "hr=" "1.7"
D35V2, continuous
D35V3, binary
                               cls
clus                              0   1
  DEL PEAK 14(7P22.3) MUTATED     8  11
  DEL PEAK 14(7P22.3) WILD-TYPE 198 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7P22.3) MUTATED      8   11
  DEL PEAK 14(7P22.3) WILD-TYPE  198  255
        clus
vv       DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE
  FEMALE                           8                           198
  MALE                            11                           255
[1] 2 2
[1] FALSE
D35V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 14(7P22.3) MUTATED             8                4                 7
  DEL PEAK 14(7P22.3) WILD-TYPE         168              114               171
D35V5, multiclass
                   clus
vv                  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE
  ASTROCYTOMA                                 8                           168
  OLIGOASTROCYTOMA                            4                           114
  OLIGODENDROGLIOMA                           7                           171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(7P22.3) MUTATED     4  15
  DEL PEAK 14(7P22.3) WILD-TYPE  88 365
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7P22.3) MUTATED      4   15
  DEL PEAK 14(7P22.3) WILD-TYPE   88  365
     clus
vv    DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE
  NO                            4                            88
  YES                          15                           365
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(7P22.3) MUTATED                                  0     1
  DEL PEAK 14(7P22.3) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(7P22.3) MUTATED                           0    18
  DEL PEAK 14(7P22.3) WILD-TYPE                        15   419
D35V7, multiclass
                                  clus
vv                                 DEL PEAK 14(7P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     18
                                  clus
vv                                 DEL PEAK 14(7P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   15
  WHITE                                                      419
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(7P22.3) MUTATED     0  17
  DEL PEAK 14(7P22.3) WILD-TYPE  18 402
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7P22.3) MUTATED      0   17
  DEL PEAK 14(7P22.3) WILD-TYPE   18  402
                        clus
vv                       DEL PEAK 14(7P22.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          17
                        clus
vv                       DEL PEAK 14(7P22.3) WILD-TYPE
  HISPANIC OR LATINO                                18
  NOT HISPANIC OR LATINO                           402
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 15(8Q24.3) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(8Q24.3) MUTATED    22   4
  DEL PEAK 15(8Q24.3) WILD-TYPE 354  90
  DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE 
                           26                           444 
  DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE 
                            4                            90 
$`DEL PEAK 15(8Q24.3) MUTATED`
TCGA-DB-5281 TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-A7UU TCGA-DU-7006 TCGA-DU-7301 
       78.28        18.51        19.96         3.45        11.47        25.91 
TCGA-DU-8165 TCGA-DU-A7TJ TCGA-FG-5965 TCGA-FG-8185 TCGA-FG-A4MY TCGA-FG-A70Y 
       19.13         0.56        36.82        14.24        23.70        28.54 
TCGA-HT-7473 TCGA-HT-7610 TCGA-HT-7688 TCGA-HT-7879 TCGA-HT-8111 TCGA-HT-8564 
       16.54        56.09        31.69         3.68         0.23        15.72 
TCGA-HT-A4DS TCGA-HW-8321 TCGA-P5-A5F6 TCGA-QH-A6CV TCGA-S9-A6WM TCGA-VM-A8C8 
        0.23        19.59         1.28        14.53        19.86        43.04 
TCGA-WY-A859 TCGA-WY-A85E 
       39.88        20.81 

$`DEL PEAK 15(8Q24.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 
       72.92        50.86        50.17        44.52        36.56        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       18.84        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        31.63        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K 
       31.40        27.45        27.81        29.23        14.40        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5142 
       11.24        17.88        30.74        16.18        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5847 
       17.19        54.25        13.12        13.38        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 
       94.52       114.08         7.96         7.73        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      138.28        14.99       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       18.94        44.02        62.01        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74        14.60        20.68        21.40 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC 
       21.30        17.98       124.50        77.88        42.31        23.51 
TCGA-DU-A7TD TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
        7.50        44.42        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       57.93       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       32.45        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       47.77        25.48        34.36        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        18.44        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       20.09        12.95        13.68        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        22.26 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
       27.52         0.10         6.67        11.54        40.11         0.13 
TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
        0.03         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
        3.16        22.06        45.99        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
        0.10        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 
       13.78        29.59        34.19        28.27        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
       16.93         1.81        16.14        16.83        21.40        17.52 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
        4.31        21.70        21.60        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        5.88         7.63         0.76         0.16        10.42        13.25 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S 
       11.64         0.20         9.01        13.61        15.16         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW 
       12.62        15.85        14.04        19.33        14.83        13.61 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         9.17        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.73         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS 
        9.90        28.08         2.07        19.59        30.67        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       87.12        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       32.45        84.99        31.10        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
       20.02         8.19         2.04        17.03        15.06        13.12 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       169.84        10.39        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       98.63        31.59        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        24.92        16.18        59.05 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       40.64        30.44        28.08        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       26.99        30.08        13.51         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       13.32        43.96        43.40        45.80        46.88        37.71 

  DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE 
                         0.23                          0.03 
  DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE 
                        78.28                        211.17 
  DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE 
                        19.36                         18.61 
[1] "0.2 - 78.3 (19.4)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "1.1"
D36V2, continuous
D36V3, binary
                               cls
clus                              0   1
  DEL PEAK 15(8Q24.3) MUTATED    13  13
  DEL PEAK 15(8Q24.3) WILD-TYPE 193 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8Q24.3) MUTATED     13   13
  DEL PEAK 15(8Q24.3) WILD-TYPE  193  253
        clus
vv       DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE
  FEMALE                          13                           193
  MALE                            13                           253
[1] 2 2
[1] FALSE
D36V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 15(8Q24.3) MUTATED            10               10                 6
  DEL PEAK 15(8Q24.3) WILD-TYPE         166              108               172
D36V5, multiclass
                   clus
vv                  DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE
  ASTROCYTOMA                                10                           166
  OLIGOASTROCYTOMA                           10                           108
  OLIGODENDROGLIOMA                           6                           172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(8Q24.3) MUTATED     7  19
  DEL PEAK 15(8Q24.3) WILD-TYPE  85 361
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8Q24.3) MUTATED      7   19
  DEL PEAK 15(8Q24.3) WILD-TYPE   85  361
     clus
vv    DEL PEAK 15(8Q24.3) MUTATED DEL PEAK 15(8Q24.3) WILD-TYPE
  NO                            7                            85
  YES                          19                           361
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(8Q24.3) MUTATED                                  0     1
  DEL PEAK 15(8Q24.3) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(8Q24.3) MUTATED                           1    24
  DEL PEAK 15(8Q24.3) WILD-TYPE                        14   413
D36V7, multiclass
                                  clus
vv                                 DEL PEAK 15(8Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     24
                                  clus
vv                                 DEL PEAK 15(8Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                      413
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(8Q24.3) MUTATED     3  20
  DEL PEAK 15(8Q24.3) WILD-TYPE  15 399
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8Q24.3) MUTATED      3   20
  DEL PEAK 15(8Q24.3) WILD-TYPE   15  399
                        clus
vv                       DEL PEAK 15(8Q24.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          20
                        clus
vv                       DEL PEAK 15(8Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           399
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 16(9P23) MUTATION ANALYSIS
D37V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 16(9P23) MUTATED    95  38
  DEL PEAK 16(9P23) WILD-TYPE 281  56
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                        133                         337 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                         38                          56 
$`DEL PEAK 16(9P23) MUTATED`
TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6188 
       18.15        40.18        21.01         9.96         6.38        23.84 
TCGA-CS-6666 TCGA-CS-6670 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4XB 
        8.48         6.61        50.86        44.52        78.28        30.21 
TCGA-DB-A4XC TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64Q TCGA-DB-A64V 
       46.72        33.57        31.63        24.20         5.98        29.23 
TCGA-DB-A75L TCGA-DB-A75P TCGA-DH-A7UR TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 
       11.24        16.18        54.25        18.02        17.46         6.74 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6402 
        8.45         6.81        49.02        46.06        65.75         7.04 
TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7014 
       11.64        19.89         7.73        11.47        62.96       117.40 
TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-7304 
       90.77        26.30         7.96        18.94        25.91        23.31 
TCGA-DU-7306 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8168 TCGA-DU-A5TY TCGA-DU-A6S7 
       41.98        23.74        14.60        14.17        12.20         7.23 
TCGA-DU-A6S8 TCGA-DU-A7T6 TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5304 
        5.98        17.98        77.88         7.50         0.56        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-A7YV TCGA-EZ-7264 TCGA-F6-A8O4 TCGA-FG-5963 
       79.99        57.93        32.45        14.33         0.20        25.48 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-8185 
       34.36        36.82        24.99        18.44        17.88        14.24 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A6J3 TCGA-FG-A711 TCGA-FG-A87Q 
       18.38        18.71        23.70        22.26        48.69         5.72 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7606 
       40.11         0.13        17.42         6.54        24.26        17.29 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-7902 
        0.10        31.69        14.96         2.96        19.23        31.43 
TCGA-HT-8104 TCGA-HT-8108 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A618 
       12.23         2.50        27.35         0.10         2.70        16.83 
TCGA-HT-A74J TCGA-HW-7490 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KM 
       10.52        19.23        21.70        21.60        17.82        20.71 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
       14.40         0.23         2.30         7.63         0.76         1.28 
TCGA-P5-A72Z TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CZ TCGA-QH-A6X9 TCGA-RY-A83Z 
       11.64        14.53        12.23         9.17         1.91         9.90 
TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A6WH TCGA-S9-A6WP TCGA-S9-A7IS TCGA-S9-A7IX 
       62.17        37.84        32.45        15.16         7.92        22.32 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A7CF 
        7.13        20.02       169.84        99.06        31.59        48.39 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84Q TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       30.44        24.16        25.38        15.98        26.99        43.04 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VV-A829 TCGA-VV-A86M TCGA-W9-A837 TCGA-WH-A86K 
        0.10         7.89        37.05        16.01        51.06        13.32 
TCGA-WY-A859 
       39.88 

$`DEL PEAK 16(9P23) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 
        4.70         7.69        43.89        10.62        64.64         0.10 
TCGA-CS-6186 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.69        17.95        12.43         7.56         8.02         7.40 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        50.17 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG 
       36.56        46.42        18.84        39.78        37.45        72.95 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64W 
       25.48        30.12        31.40        27.45        27.81        14.40 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-5140 TCGA-DH-5141 
       18.51        12.10        17.88        30.74        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        17.19        13.12        13.38         3.45        18.61 
TCGA-DU-5849 TCGA-DU-5853 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
       14.56        13.38       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6400 TCGA-DU-6401 
      211.17        52.11        22.42        75.16         1.22        87.45 
TCGA-DU-6404 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7008 
      133.74        16.83        94.52       114.08         7.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7018 
      138.28        14.99       105.21         6.54         8.84        30.67 
TCGA-DU-7290 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7309 
       10.36        94.32        44.02        62.01        60.30         2.76 
TCGA-DU-8158 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
        5.10        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
        8.65         2.70        77.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5302 
       21.30       124.50        42.31        23.51        44.42        50.14 
TCGA-E1-5303 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       67.46       134.27        78.21        95.57       130.78        75.02 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-6688 TCGA-FG-6689 
       36.82        32.35         0.23        47.77        18.77        14.93 
TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       23.97        15.35        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       13.68        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       38.27        10.72        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FG-A87N 
       16.44        28.54        10.78        36.66        20.45        13.58 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7472 TCGA-HT-7473 
       27.52         0.10         6.67        11.54         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
        3.75         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      172.77         4.01         5.03        29.85        23.18       122.47 
TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
        4.57         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 
        6.05        42.74         0.10         0.10        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       14.53        39.48        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
       35.47         3.72        11.28         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 
       63.55         0.10        37.87        33.01         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        0.46         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A619 
        0.07         5.33        16.93         1.81        16.14        21.40 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.52        17.65         2.43        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       29.92        19.89         8.32        40.18        35.90         4.31 
TCGA-HW-8321 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-7675 TCGA-IK-8125 
       19.59        20.35        12.76        20.81        19.00        42.77 
TCGA-KT-A74X TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
       14.40         6.71         1.64         2.37         4.11         5.88 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
        0.16        10.42        13.25         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       14.83        13.61         2.20        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
       16.73        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 
       94.03        32.65        59.38        30.87         5.46        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX 
        2.07        19.59        30.67        87.12        18.77        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        28.70        22.95        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
       16.08        98.24        95.93         5.85       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        80.12        84.99        31.10        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 
       18.61        14.07        36.13        23.51         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 
       17.03        15.06        13.12        28.37        13.02        10.39 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       30.05        98.63        18.71        11.97        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       49.32        34.78        24.92        16.18        59.05        40.64 
TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S 
       28.08        40.83        24.79        33.24        18.61        14.93 
TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VW-A7QS 
       23.80        30.08        13.51        35.93        23.47        23.21 
TCGA-VW-A8FI TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
        8.05        43.96        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                       0.10                        0.03 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                     169.84                      211.17 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                      18.44                       18.71 
[1] "0.1 - 169.8 (18.4)" "0.0 - 211.2 (18.7)"
[1] "hr=" "2.2"
D37V2, continuous
D37V3, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED    61  73
  DEL PEAK 16(9P23) WILD-TYPE 145 193
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED     61   73
  DEL PEAK 16(9P23) WILD-TYPE  145  193
        clus
vv       DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  FEMALE                        61                         145
  MALE                          73                         193
[1] 2 2
[1] FALSE
D37V4, continuous
                             vv
clus                          ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 16(9P23) MUTATED            62               32                40
  DEL PEAK 16(9P23) WILD-TYPE         114               86               138
D37V5, multiclass
                   clus
vv                  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  ASTROCYTOMA                              62                         114
  OLIGOASTROCYTOMA                         32                          86
  OLIGODENDROGLIOMA                        40                         138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED    35  99
  DEL PEAK 16(9P23) WILD-TYPE  57 281
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED     35   99
  DEL PEAK 16(9P23) WILD-TYPE   57  281
     clus
vv    DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  NO                         35                          57
  YES                        99                         281
[1] 2 2
[1] FALSE
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(9P23) MUTATED                                  0     2
  DEL PEAK 16(9P23) WILD-TYPE                                1     6
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(9P23) MUTATED                           3   123
  DEL PEAK 16(9P23) WILD-TYPE                        12   314
D37V7, multiclass
                                  clus
vv                                 DEL PEAK 16(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                                3
  WHITE                                                  123
                                  clus
vv                                 DEL PEAK 16(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                    314
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED     6 117
  DEL PEAK 16(9P23) WILD-TYPE  12 302
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED      6  117
  DEL PEAK 16(9P23) WILD-TYPE   12  302
                        clus
vv                       DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  HISPANIC OR LATINO                             6                          12
  NOT HISPANIC OR LATINO                       117                         302
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 17(9P21.3) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(9P21.3) MUTATED   108  52
  DEL PEAK 17(9P21.3) WILD-TYPE 268  42
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                          160                           310 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                           52                            42 
$`DEL PEAK 17(9P21.3) MUTATED`
TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       18.15        40.18        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6666 TCGA-CS-6670 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 
       23.84         8.48         6.61        47.93        50.86        44.52 
TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64L 
       78.28        30.21        46.72        33.57        31.63        24.20 
TCGA-DB-A64V TCGA-DB-A75L TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-A7UR TCGA-DU-5847 
       29.23        11.24        16.18        19.96        54.25        18.02 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-6395 TCGA-DU-6397 
       17.46         6.74         8.45         6.81        49.02        46.06 
TCGA-DU-6399 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
       65.75         7.04        11.64        19.89        16.83        94.52 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7015 
        7.73        11.47        62.96         6.54       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-7302 
       30.67        26.30         7.96        18.94        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8168 
       23.31        41.98         5.10        23.74        14.60        14.17 
TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7T6 
       12.20         7.23         5.98        11.41        26.76        17.98 
TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5304 TCGA-E1-5307 TCGA-E1-A7YV 
       77.88         7.50         0.56        41.13        57.93        32.45 
TCGA-EZ-7264 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6690 
       14.33         0.20        25.48        34.36        36.82        24.99 
TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       18.44        17.88        14.24        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A87N 
       23.70        22.26        28.54        10.78        48.69        13.58 
TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7475 TCGA-HT-7476 
        5.72        11.54        40.11         0.13        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7606 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7692 
       24.26        17.29         0.10        31.69        14.96         2.96 
TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8104 
       19.23         0.23         0.49        31.43        16.24        12.23 
TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        2.50        13.78         0.23        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A61C TCGA-HT-A74J TCGA-HW-7490 TCGA-HW-8319 TCGA-HW-8320 
        2.70        17.65        10.52        19.23        21.70        21.60 
TCGA-HW-8322 TCGA-HW-A5KK TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EV 
       17.82        12.76        20.71        19.00        14.40         0.23 
TCGA-P5-A5EZ TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72Z 
        2.30         7.63         0.76         1.28         0.16        11.64 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CZ TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-RY-A83Z 
       14.53        12.23         9.17         1.91         5.03         9.90 
TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WH TCGA-S9-A6WM 
       62.17        37.84        22.95         5.85        32.45        19.86 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7R1 TCGA-S9-A7R3 
        7.92        22.32         7.13        20.02       169.84        99.06 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7CF TCGA-TM-A84H TCGA-TM-A84J TCGA-TQ-A7RH 
       31.59        11.97        48.39        30.44        24.16        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VV-A86M TCGA-W9-A837 
       26.99        43.04         0.10         7.89        16.01        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85B 
       13.32        43.96        39.88        45.80 

$`DEL PEAK 17(9P21.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 
        4.70         7.69        43.89        10.62        64.64         0.10 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 
       17.95        12.43         7.56         8.02         7.40       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-A4X9 
       81.96        75.25        72.92        50.17        36.56        46.42 
TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64O TCGA-DB-A64P 
       18.84        39.78        37.45        72.95        25.48        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A64X 
        5.98        31.40        27.45        27.81        14.40        18.51 
TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       12.10        17.88        30.74        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
        8.02        30.21        42.05        27.81        17.19        17.19 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5853 
       13.12        13.38         3.45        18.61        14.56        13.38 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6404 TCGA-DU-6408 
       22.42        75.16         1.22        87.45       133.74       114.08 
TCGA-DU-6410 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 
        7.96       156.23       138.28        14.99       105.21         8.84 
TCGA-DU-7290 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7309 TCGA-DU-8163 
       10.36        94.32        44.02        62.01         2.76        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR 
       21.40        19.13        16.96        15.48        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 
       15.12         4.96         3.65         5.65         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC 
       77.98         7.13        21.30       124.50        42.31        23.51 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 
       44.42        50.14        67.46        79.99       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O3 
       95.57       130.78        75.02        36.82        32.35         0.23 
TCGA-FG-5962 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7638 
       47.77        18.77        14.93        23.97        15.35        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 
       20.61        20.09        12.95        13.68        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A60J TCGA-FG-A60K 
       14.96        22.52        32.61        38.27        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
       16.41        15.02        16.44        36.66        20.45        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7478 
        0.10         6.67         0.03        16.54         3.75         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 
        5.03        29.85        23.18       122.47         4.57         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         0.10        17.52         6.90        14.53        39.48 
TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       39.09        50.63        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 
        3.68         5.33        35.47         3.72        11.28         1.64 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 
        9.40        63.55         0.10        37.87        33.01         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        0.10         0.46         5.56         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       28.27        15.72        26.04         0.13        20.22         0.07 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B 
       16.93         1.81        16.14        16.83        21.40        17.52 
TCGA-HT-A74H TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
        2.43        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8321 TCGA-HW-A5KJ 
        8.32        40.18        35.90         4.31        19.59        20.35 
TCGA-HW-A5KL TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
       20.81        42.77        14.40         6.71         1.64         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A730 TCGA-P5-A731 
        4.11         5.88        10.42        13.25         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
       13.61        15.16         2.53        12.62        15.85        14.04 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 
       19.33        14.83        13.61         2.20        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
       16.34        16.73        16.50        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 
       94.03        32.65        59.38        30.87         5.46        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX 
        2.07        19.59        30.67        87.12        18.77        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       31.33        28.70        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       98.24        95.93       106.39        69.50        72.59        80.12 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        31.10        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       36.13        23.51         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.12        28.37        13.02        10.39        30.05        98.63 
TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B 
       18.71        49.45        48.33        49.32        34.78        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M 
       16.18        59.05        40.64        28.08        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 
       33.24        25.38        18.61        14.93        23.80        30.08 
TCGA-VM-A8CA TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VW-A7QS TCGA-VW-A8FI 
       13.51        35.93        23.47        37.05        23.21         8.05 
TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.40        46.88        37.71        20.81 

  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                       169.84                        211.17 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                       17.930                        19.035 
[1] "0.1 - 169.8 (17.9)" "0.0 - 211.2 (19.0)"
[1] "hr=" "3.4"
D38V2, continuous
D38V3, binary
                               cls
clus                              0   1
  DEL PEAK 17(9P21.3) MUTATED    76  85
  DEL PEAK 17(9P21.3) WILD-TYPE 130 181
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9P21.3) MUTATED     76   85
  DEL PEAK 17(9P21.3) WILD-TYPE  130  181
        clus
vv       DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  FEMALE                          76                           130
  MALE                            85                           181
[1] 2 2
[1] FALSE
D38V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 17(9P21.3) MUTATED            76               35                50
  DEL PEAK 17(9P21.3) WILD-TYPE         100               83               128
D38V5, multiclass
                   clus
vv                  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  ASTROCYTOMA                                76                           100
  OLIGOASTROCYTOMA                           35                            83
  OLIGODENDROGLIOMA                          50                           128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                               cls
clus                              0   1
  DEL PEAK 17(9P21.3) MUTATED    41 120
  DEL PEAK 17(9P21.3) WILD-TYPE  51 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9P21.3) MUTATED     41  120
  DEL PEAK 17(9P21.3) WILD-TYPE   51  260
     clus
vv    DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  NO                           41                            51
  YES                         120                           260
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(9P21.3) MUTATED                                  0     3
  DEL PEAK 17(9P21.3) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(9P21.3) MUTATED                           5   148
  DEL PEAK 17(9P21.3) WILD-TYPE                        10   289
D38V7, multiclass
                                  clus
vv                                 DEL PEAK 17(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                    148
                                  clus
vv                                 DEL PEAK 17(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                      289
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK 17(9P21.3) MUTATED     7 141
  DEL PEAK 17(9P21.3) WILD-TYPE  11 278
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9P21.3) MUTATED      7  141
  DEL PEAK 17(9P21.3) WILD-TYPE   11  278
                        clus
vv                       DEL PEAK 17(9P21.3) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         141
                        clus
vv                       DEL PEAK 17(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           278
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 18(10Q26.3) MUTATION ANALYSIS
D39V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(10Q26.3) MUTATED    81  53
  DEL PEAK 18(10Q26.3) WILD-TYPE 295  41
  DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE 
                           134                            336 
  DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE 
                            53                             41 
$`DEL PEAK 18(10Q26.3) MUTATED`
TCGA-CS-4941 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6665 
        7.69        21.01         6.38        17.69        23.84        12.43 
TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XF TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A75L 
       50.86        44.52        33.57        24.20        25.48        11.24 
TCGA-DH-5140 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A7UU TCGA-DU-5847 
       19.96        30.21        42.05        27.81         3.45        18.02 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5872 TCGA-DU-6396 TCGA-DU-6399 
        6.74        13.38         8.45        17.49        75.16        65.75 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
       87.45         7.04        11.64        19.89        16.83        94.52 
TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7012 
      114.08        11.47        62.96       156.23        14.99         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 
        8.84       117.40        90.77        10.36         7.96        18.94 
TCGA-DU-7301 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-8167 
       25.91         5.10        23.74        14.60        19.13        15.48 
TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7TD TCGA-DU-A7TJ 
       12.20        11.41        26.76        21.30         7.50         0.56 
TCGA-E1-5311 TCGA-E1-A7YV TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-8188 
      134.27        32.45        18.77        18.44        20.09        14.96 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A87N 
       10.72        18.38        22.26        10.78        48.69        13.58 
TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7483 
        5.72        11.54         0.13        16.54         6.54       172.77 
TCGA-HT-7485 TCGA-HT-7606 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7693 TCGA-HT-7857 
        4.01        17.29        31.69         0.10        17.52         0.23 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8011 
        0.49        23.61         3.68         3.72        31.43        16.24 
TCGA-HT-8104 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
       12.23         2.50        13.78        28.27        15.72         0.23 
TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74H 
       20.22        27.35         5.33        16.14        17.65         2.43 
TCGA-HW-8321 TCGA-HW-A5KK TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EZ TCGA-P5-A5F2 
       19.59        12.76        19.00        14.40         2.30         7.63 
TCGA-P5-A72U TCGA-P5-A72W TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6X3 
        0.16        10.42        19.33        14.53        12.23        10.29 
TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-RY-A83X TCGA-RY-A83Z TCGA-S9-A6TS TCGA-S9-A6U0 
        1.91         5.03        30.87         9.90        62.17        22.95 
TCGA-S9-A6UB TCGA-S9-A6WM TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7J0 
      106.39        19.86        14.07         7.92        22.32        20.02 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A89Z TCGA-TM-A7C3 
       15.06        13.12        10.39        99.06        11.97        49.45 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84I TCGA-TM-A84J TCGA-VM-A8CD TCGA-VW-A8FI 
       48.39        24.92        28.08        24.16         7.89         8.05 
TCGA-WH-A86K TCGA-WY-A85D 
       13.32        37.71 

$`DEL PEAK 18(10Q26.3) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
        0.10         9.96        17.95         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       72.92        50.17        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A4XH 
       30.21        46.72        39.78        37.45        72.95        31.63 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       30.12         5.98        31.40        27.45        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       14.40        18.51        12.10        17.88        30.74        16.18 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66F TCGA-DH-A66G 
       31.82        30.31        14.40         8.02        17.19        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 
       54.25        13.12        13.38        18.61        14.56        17.46 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        6.81       182.33        18.94        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6404 TCGA-DU-6410 
       22.42        49.02        46.06         1.22       133.74         7.96 
TCGA-DU-6542 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 
        7.73       138.28       105.21        30.67        26.30        94.32 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       44.02        62.01        60.30        23.31        41.98         2.76 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       20.68        21.40        16.96        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 
       15.12         4.96         3.65         5.65         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 
       77.98         7.23         5.98         7.13        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 
       77.88        42.31        23.51        44.42        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       41.13        79.99        57.93        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       75.02        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 
       47.77        25.48        34.36        36.82        14.93        24.99 
TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 
       23.97        15.35        17.88        22.55        20.61        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 
       13.68        14.24        16.01        20.09        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       38.27        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
       15.02        16.44        28.54        36.66        20.45        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 
        0.10         6.67        40.11         0.03         3.75        17.42 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38        40.34        75.19        95.93       106.95 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 
        5.03        29.85        23.18       122.47         4.57         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 
        0.10        14.96         0.10         2.96         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7874 TCGA-HT-7875 
       39.48        19.23        39.09        50.63        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8012 
        0.13         5.33        35.47        11.28         1.64         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 
       63.55         0.10        37.87        33.01         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-A4DV 
        0.46         5.56         0.23        29.59        34.19        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
        0.13         0.07         0.10         2.70        16.93         1.81 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       16.83        21.40        17.52        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.90         4.31        21.70        21.60        17.82        20.35 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW 
       20.81        20.71        42.77        14.40         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F4 TCGA-P5-A5F6 
        1.64         2.37         4.11         5.88         0.76         1.28 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       13.25        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CW 
        2.53        12.62        15.85        14.04        14.83        13.61 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA 
        2.20         9.17        14.53        16.34        16.73        16.50 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU 
        5.46        28.08         2.07        19.59        30.67        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 
       18.77        37.84        34.49        31.33        28.70        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       69.50        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7IZ 
       15.91        18.61        15.16        36.13        23.51         7.13 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.19         2.04        17.03        28.37        13.02       169.84 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C4 TCGA-TM-A7C5 
       30.05        98.63        31.59        18.71        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L 
       34.78        16.18        59.05        40.64        30.44        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       35.93        23.47        37.05        16.01        23.21        51.06 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85E 
       43.96        39.88        43.40        45.80        46.88        20.81 

  DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE 
                        172.77                         211.17 
  DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE 
                         16.39                          20.22 
[1] "0.1 - 172.8 (16.4)" "0.0 - 211.2 (20.2)"
[1] "hr=" "3.9"
D39V2, continuous
D39V3, binary
                                cls
clus                               0   1
  DEL PEAK 18(10Q26.3) MUTATED    68  67
  DEL PEAK 18(10Q26.3) WILD-TYPE 138 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q26.3) MUTATED     68   67
  DEL PEAK 18(10Q26.3) WILD-TYPE  138  199
        clus
vv       DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE
  FEMALE                           68                            138
  MALE                             67                            199
[1] 2 2
[1] FALSE
D39V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 18(10Q26.3) MUTATED            72               29                34
  DEL PEAK 18(10Q26.3) WILD-TYPE         104               89               144
D39V5, multiclass
                   clus
vv                  DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE
  ASTROCYTOMA                                 72                            104
  OLIGOASTROCYTOMA                            29                             89
  OLIGODENDROGLIOMA                           34                            144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                                cls
clus                               0   1
  DEL PEAK 18(10Q26.3) MUTATED    28 107
  DEL PEAK 18(10Q26.3) WILD-TYPE  64 273
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q26.3) MUTATED     28  107
  DEL PEAK 18(10Q26.3) WILD-TYPE   64  273
     clus
vv    DEL PEAK 18(10Q26.3) MUTATED DEL PEAK 18(10Q26.3) WILD-TYPE
  NO                            28                             64
  YES                          107                            273
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(10Q26.3) MUTATED                                  1     2
  DEL PEAK 18(10Q26.3) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(10Q26.3) MUTATED                           7   124
  DEL PEAK 18(10Q26.3) WILD-TYPE                         8   313
D39V7, multiclass
                                  clus
vv                                 DEL PEAK 18(10Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                     124
                                  clus
vv                                 DEL PEAK 18(10Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                     8
  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"
D39V8, binary
                                cls
clus                               0   1
  DEL PEAK 18(10Q26.3) MUTATED     5 124
  DEL PEAK 18(10Q26.3) WILD-TYPE  13 295
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q26.3) MUTATED      5  124
  DEL PEAK 18(10Q26.3) WILD-TYPE   13  295
                        clus
vv                       DEL PEAK 18(10Q26.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          124
                        clus
vv                       DEL PEAK 18(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            295
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 19(11P15.5) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(11P15.5) MUTATED    72  21
  DEL PEAK 19(11P15.5) WILD-TYPE 304  73
  DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE 
                            93                            377 
  DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE 
                            21                             73 
$`DEL PEAK 19(11P15.5) MUTATED`
TCGA-CS-4943 TCGA-CS-6290 TCGA-CS-6665 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-A64X 
       18.15        17.95        12.43        47.93        50.86        18.51 
TCGA-DB-A75L TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT 
       11.24        19.96        30.31        27.81        17.19        13.38 
TCGA-DH-A7UU TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-6396 TCGA-DU-6408 TCGA-DU-7006 
        3.45        17.46        13.38        75.16       114.08        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7298 
       62.96       156.23        14.99       117.40        90.77        18.94 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TR 
        2.76         5.10        19.13        16.96        15.48        12.59 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A6S7 TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5304 
       15.12         3.65         7.23        77.88        50.14        41.13 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-8188 TCGA-FG-A4MW 
       32.45        36.82        36.82        14.93        14.96        18.38 
TCGA-FG-A4MY TCGA-FG-A60L TCGA-HT-7470 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7601 
       23.70        16.41        40.11        24.26         6.38         5.03 
TCGA-HT-7603 TCGA-HT-7607 TCGA-HT-7676 TCGA-HT-7686 TCGA-HT-7690 TCGA-HT-7693 
       23.18         3.16         0.16        42.74         0.10        17.52 
TCGA-HT-7873 TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8111 TCGA-HT-8114 
       23.61        31.43        63.55        37.87         0.23        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A5R7 TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 
       28.27        15.72        20.22         2.70         1.81        16.83 
TCGA-HT-A61B TCGA-HT-A74O TCGA-HW-7493 TCGA-HW-8319 TCGA-IK-7675 TCGA-P5-A5F6 
       17.52         0.10        35.90        21.70        19.00         1.28 
TCGA-QH-A65S TCGA-QH-A6XA TCGA-RY-A83Z TCGA-S9-A6TV TCGA-S9-A6WM TCGA-S9-A7IZ 
        2.53        16.50         9.90        18.77        19.86         7.13 
TCGA-S9-A7J0 TCGA-S9-A7QX TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z 
       20.02        13.12        30.05        98.63        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A84I TCGA-TM-A84J TCGA-TQ-A7RH TCGA-WH-A86K 
       49.45        48.33        28.08        24.16        15.98        13.32 
TCGA-WY-A859 TCGA-WY-A85C TCGA-WY-A85E 
       39.88        46.88        20.81 

$`DEL PEAK 19(11P15.5) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
        8.48         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       81.96        75.25        72.92        50.17        44.52        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       78.28        46.42        18.84        30.21        46.72        39.78 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O 
       37.45        33.57        72.95        31.63        24.20        25.48 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       30.12         5.98        31.40        27.45        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 
       14.40        12.10        17.88        30.74        16.18        31.82 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66F TCGA-DH-A7UR 
       14.40         8.02        30.21        42.05        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5852 TCGA-DU-5854 
       13.12        18.61        18.02        14.56         6.74         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       52.11        22.42        49.02        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
       94.52         7.96         7.73       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
        8.84        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A5TP 
       23.74        14.60        20.68        21.40        14.17        14.24 
TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        4.96         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
      124.50        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
      130.78        75.02        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 
       47.77        25.48        34.36        18.77        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 
       12.95        13.68        14.24        16.01        20.09        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K 
       32.61        38.27        10.72        18.71        14.76        17.82 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        6.67        11.54         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       17.42         6.54        40.34        75.19        95.93       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
      172.77         4.01        29.85       122.47         4.57        17.29 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7688 
       16.24         0.76        44.68         6.05         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
       14.96         0.10         2.96         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 
       19.23        39.09         0.23        50.63         0.49        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8019 
       11.28         1.64        16.24         9.40         0.10        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
       13.78        29.59         0.23        26.04         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A619 
       27.35         0.10         5.33        16.93        16.14        21.40 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 
       17.65         2.43        10.52        15.35        11.05        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8320 
       19.89         8.32        19.23        40.18         4.31        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35        12.76        20.81        20.71 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77        14.40        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        0.16        10.42        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       13.61        15.16        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XC 
       10.29        14.53        16.34        16.73         1.91         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 
       30.87         5.46        28.08         2.07        19.59        30.67 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       62.17        87.12        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       32.45        84.99        31.10        15.91        18.61        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J1 
       14.07        36.13         7.92        22.32        23.51         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        2.04        17.03        15.06        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       10.39        99.06        31.59        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L 
       24.92        16.18        59.05        40.64        30.44        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       26.99        43.04        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI 
       35.93        23.47        37.05        16.01        23.21         8.05 
TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85D 
       51.06        43.96        43.40        45.80        37.71 

  DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE 
                        156.23                         211.17 
  DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE 
                         18.71                          18.61 
[1] "0.1 - 156.2 (18.7)" "0.0 - 211.2 (18.6)"
[1] "hr=" "1.3"
D40V2, continuous
D40V3, binary
                                cls
clus                               0   1
  DEL PEAK 19(11P15.5) MUTATED    49  45
  DEL PEAK 19(11P15.5) WILD-TYPE 157 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11P15.5) MUTATED     49   45
  DEL PEAK 19(11P15.5) WILD-TYPE  157  221
        clus
vv       DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE
  FEMALE                           49                            157
  MALE                             45                            221
[1] 2 2
[1] FALSE
D40V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 19(11P15.5) MUTATED            50               27                17
  DEL PEAK 19(11P15.5) WILD-TYPE         126               91               161
D40V5, multiclass
                   clus
vv                  DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE
  ASTROCYTOMA                                 50                            126
  OLIGOASTROCYTOMA                            27                             91
  OLIGODENDROGLIOMA                           17                            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                                cls
clus                               0   1
  DEL PEAK 19(11P15.5) MUTATED    21  73
  DEL PEAK 19(11P15.5) WILD-TYPE  71 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11P15.5) MUTATED     21   73
  DEL PEAK 19(11P15.5) WILD-TYPE   71  307
     clus
vv    DEL PEAK 19(11P15.5) MUTATED DEL PEAK 19(11P15.5) WILD-TYPE
  NO                            21                             71
  YES                           73                            307
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(11P15.5) MUTATED                                  0     0
  DEL PEAK 19(11P15.5) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(11P15.5) MUTATED                           2    90
  DEL PEAK 19(11P15.5) WILD-TYPE                        13   347
D40V7, multiclass
                                  clus
vv                                 DEL PEAK 19(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      90
                                  clus
vv                                 DEL PEAK 19(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    13
  WHITE                                                       347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, binary
                                cls
clus                               0   1
  DEL PEAK 19(11P15.5) MUTATED     4  85
  DEL PEAK 19(11P15.5) WILD-TYPE  14 334
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11P15.5) MUTATED      4   85
  DEL PEAK 19(11P15.5) WILD-TYPE   14  334
                        clus
vv                       DEL PEAK 19(11P15.5) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           85
                        clus
vv                       DEL PEAK 19(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            334
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 20(11P15.1) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(11P15.1) MUTATED    45  20
  DEL PEAK 20(11P15.1) WILD-TYPE 331  74
  DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE 
                            65                            405 
  DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE 
                            20                             74 
$`DEL PEAK 20(11P15.1) MUTATED`
TCGA-CS-6665 TCGA-DB-5277 TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A66D TCGA-DH-A66G 
       12.43        50.86        19.96        30.31        27.81        17.19 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DU-6396 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7007 
       13.38         3.45        75.16       114.08        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-8158 TCGA-DU-8165 
      156.23        14.99       117.40        90.77         5.10        19.13 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-A7YV 
       12.59        15.12         3.65        50.14        41.13        32.45 
TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-A4MW TCGA-FG-A60L TCGA-HT-7470 
       25.48        36.82        14.93        18.38        16.41        40.11 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7601 TCGA-HT-7607 TCGA-HT-7686 TCGA-HT-7693 
       24.26         6.38         5.03         3.16        42.74        17.52 
TCGA-HT-7873 TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8111 TCGA-HT-8563 
       23.61        31.43        63.55        37.87         0.23        28.27 
TCGA-HT-8564 TCGA-HT-A5R7 TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B 
       15.72        20.22         2.70         1.81        16.83        17.52 
TCGA-HW-8319 TCGA-IK-7675 TCGA-P5-A5F6 TCGA-P5-A72Z TCGA-QH-A65S TCGA-RY-A83Z 
       21.70        19.00         1.28        11.64         2.53         9.90 
TCGA-S9-A6WM TCGA-S9-A7J0 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       19.86        20.02        98.63        18.71        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A84I TCGA-TM-A84J TCGA-TQ-A7RH TCGA-WY-A859 
       48.33        28.08        24.16        15.98        39.88 

$`DEL PEAK 20(11P15.1) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5143 
       11.24        17.88        30.74        16.18        31.82        14.40 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US 
        8.02        30.21        42.05        17.19        54.25        13.12 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       18.61        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 
      211.17        52.11        22.42        49.02        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7009 TCGA-DU-7011 
       16.83        94.52         7.96         7.73       138.28       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        6.54         8.84        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       23.31        41.98         2.76        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TT 
       21.40        16.96        15.48        14.17        14.24         4.96 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        5.98        11.41        26.76         7.13        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
      124.50        77.88        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
        0.56        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
       95.57       130.78        75.02        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6690 
        0.23         0.20        47.77        34.36        18.77        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        18.44        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX 
       14.96        22.52        32.61        38.27        10.72        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       23.70        14.76        17.82        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        36.66        48.69        20.45        13.58 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 
        5.72        27.52         0.10         6.67        11.54         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7479 
        0.03        16.54         3.75        17.42         6.54        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7602 
       75.19        95.93       106.95       172.77         4.01        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 
       23.18       122.47         4.57        17.29        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
        0.76        44.68         6.05         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         0.10         2.96         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 
       19.23        39.09         0.23        50.63         0.49        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8019 
       11.28         1.64        16.24         9.40         0.10        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       13.78        29.59        34.19         0.23        26.04         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A617 
        0.07        27.35         0.10         5.33        16.93        16.14 
TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
       21.40        17.65         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        19.89         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.90         4.31        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       12.76        20.81        20.71        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        5.88         7.63         0.76         0.16        10.42        13.25 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X 
        0.20         9.01        13.61        15.16        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       14.04        19.33        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 
       94.03        32.65        59.38        30.87         5.46        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       31.10        15.91        18.61        15.16        14.07        36.13 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 
        7.92        22.32        23.51         7.13         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
       17.03        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A7C5 TCGA-TM-A7CA 
       10.39        99.06        30.05        31.59        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       23.80        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B 
        8.05        51.06        13.32        43.96        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE 
                          0.23                           0.03 
  DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE 
                        156.23                         211.17 
  DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE 
                         19.86                          18.51 
[1] "0.2 - 156.2 (19.9)" "0.0 - 211.2 (18.5)"
[1] "hr=" "1.6"
D41V2, continuous
D41V3, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.1) MUTATED    36  30
  DEL PEAK 20(11P15.1) WILD-TYPE 170 236
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.1) MUTATED     36   30
  DEL PEAK 20(11P15.1) WILD-TYPE  170  236
        clus
vv       DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE
  FEMALE                           36                            170
  MALE                             30                            236
[1] 2 2
[1] FALSE
D41V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 20(11P15.1) MUTATED            38               14                14
  DEL PEAK 20(11P15.1) WILD-TYPE         138              104               164
D41V5, multiclass
                   clus
vv                  DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE
  ASTROCYTOMA                                 38                            138
  OLIGOASTROCYTOMA                            14                            104
  OLIGODENDROGLIOMA                           14                            164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.1) MUTATED    16  50
  DEL PEAK 20(11P15.1) WILD-TYPE  76 330
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.1) MUTATED     16   50
  DEL PEAK 20(11P15.1) WILD-TYPE   76  330
     clus
vv    DEL PEAK 20(11P15.1) MUTATED DEL PEAK 20(11P15.1) WILD-TYPE
  NO                            16                             76
  YES                           50                            330
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(11P15.1) MUTATED                                  0     0
  DEL PEAK 20(11P15.1) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(11P15.1) MUTATED                           1    64
  DEL PEAK 20(11P15.1) WILD-TYPE                        14   373
D41V7, multiclass
                                  clus
vv                                 DEL PEAK 20(11P15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      64
                                  clus
vv                                 DEL PEAK 20(11P15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.1) MUTATED     3  62
  DEL PEAK 20(11P15.1) WILD-TYPE  15 357
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.1) MUTATED      3   62
  DEL PEAK 20(11P15.1) WILD-TYPE   15  357
                        clus
vv                       DEL PEAK 20(11P15.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           62
                        clus
vv                       DEL PEAK 20(11P15.1) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            357
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 21(12P13.1) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(12P13.1) MUTATED    22  12
  DEL PEAK 21(12P13.1) WILD-TYPE 354  82
  DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE 
                            34                            436 
  DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE 
                            12                             82 
$`DEL PEAK 21(12P13.1) MUTATED`
TCGA-CS-4943 TCGA-CS-6665 TCGA-DB-5279 TCGA-DB-A4XH TCGA-DU-5855 TCGA-DU-6403 
       18.15        12.43        44.52        31.63         6.81        11.64 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7299 TCGA-DU-7304 TCGA-DU-A6S6 TCGA-DU-A76R 
        7.73        62.96        44.02        23.31        77.98        21.30 
TCGA-E1-5302 TCGA-E1-A7YV TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-A6J3 TCGA-FG-A711 
       50.14        32.45        36.82        24.99        22.26        48.69 
TCGA-HT-7470 TCGA-HT-7879 TCGA-HT-8106 TCGA-HT-8108 TCGA-HT-A5R7 TCGA-HW-A5KM 
       40.11         3.68         0.10         2.50        20.22        20.71 
TCGA-P5-A5EW TCGA-P5-A72X TCGA-S9-A6U1 TCGA-S9-A6UA TCGA-S9-A7J0 TCGA-S9-A7QX 
        6.71        13.25        17.62         5.85        20.02        13.12 
TCGA-S9-A7R2 TCGA-S9-A7R4 TCGA-S9-A89V TCGA-TM-A84I 
       10.39        30.05        18.71        28.08 

$`DEL PEAK 21(12P13.1) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       50.17        36.56        78.28        46.42        18.84        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L 
       46.72        39.78        37.45        33.57        72.95        24.20 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       29.23        14.40        18.51        12.10        11.24        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       30.74        16.18        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
        8.02        30.21        42.05        27.81        17.19        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       54.25        13.12        13.38         3.45        18.61        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5870 
       14.56        17.46         6.74        13.38         8.45       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
       18.94        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 
       49.02        75.16        46.06        65.75         1.22        87.45 
TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
        7.04       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
        7.96        11.47       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7301 
       10.36         7.96        94.32        18.94        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       60.30        41.98         2.76         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
       12.20         8.65         2.70         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       26.76         7.13        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 
       23.51         7.50        44.42         0.56        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       75.02        36.82        32.35        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6691 
       47.77        25.48        34.36        18.77        14.93        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       28.54        10.78        36.66        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 
       27.52         0.10         6.67        11.54         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.33         0.13         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8109 
       37.87        33.01        12.23         6.25         0.46         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
       13.78         0.23        29.59        34.19        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        26.04         0.13         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        16.93         1.81        16.14        16.83 
TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       21.40        17.52        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       11.05         0.10        29.92        19.89         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-7675 TCGA-IK-8125 
       17.82        20.35        12.76        20.81        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
       14.40        14.40         0.23         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        4.11         5.88         7.63         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       10.42        11.64         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.53        13.61        12.23         2.20         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       11.08        12.99        88.83        94.03        32.65        59.38 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       30.87         5.46         9.90        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       30.67        62.17        87.12        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       31.33        28.70        22.95        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       98.24        95.93       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY 
        7.13         8.19         2.04        17.03        15.06        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       13.02       169.84        99.06        98.63        31.59        11.97 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        24.92 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L 
       16.18        59.05        40.64        30.44        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       15.98        26.99        43.04        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        35.93        23.47        37.05        16.01        23.21 
TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
        8.05        51.06        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

  DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE 
                         77.98                         211.17 
  DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE 
                        20.465                         18.560 
[1] "0.1 - 78.0 (20.5)"  "0.0 - 211.2 (18.6)"
[1] "hr=" "2.4"
D42V2, continuous
D42V3, binary
                                cls
clus                               0   1
  DEL PEAK 21(12P13.1) MUTATED    15  20
  DEL PEAK 21(12P13.1) WILD-TYPE 191 246
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(12P13.1) MUTATED     15   20
  DEL PEAK 21(12P13.1) WILD-TYPE  191  246
        clus
vv       DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE
  FEMALE                           15                            191
  MALE                             20                            246
[1] 2 2
[1] FALSE
D42V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 21(12P13.1) MUTATED            19                9                 7
  DEL PEAK 21(12P13.1) WILD-TYPE         157              109               171
D42V5, multiclass
                   clus
vv                  DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE
  ASTROCYTOMA                                 19                            157
  OLIGOASTROCYTOMA                             9                            109
  OLIGODENDROGLIOMA                            7                            171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                                cls
clus                               0   1
  DEL PEAK 21(12P13.1) MUTATED     9  26
  DEL PEAK 21(12P13.1) WILD-TYPE  83 354
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(12P13.1) MUTATED      9   26
  DEL PEAK 21(12P13.1) WILD-TYPE   83  354
     clus
vv    DEL PEAK 21(12P13.1) MUTATED DEL PEAK 21(12P13.1) WILD-TYPE
  NO                             9                             83
  YES                           26                            354
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(12P13.1) MUTATED                                  0     0
  DEL PEAK 21(12P13.1) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(12P13.1) MUTATED                           0    34
  DEL PEAK 21(12P13.1) WILD-TYPE                        15   403
D42V7, multiclass
                                  clus
vv                                 DEL PEAK 21(12P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      34
                                  clus
vv                                 DEL PEAK 21(12P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       403
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, binary
                                cls
clus                               0   1
  DEL PEAK 21(12P13.1) MUTATED     0  32
  DEL PEAK 21(12P13.1) WILD-TYPE  18 387
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(12P13.1) MUTATED      0   32
  DEL PEAK 21(12P13.1) WILD-TYPE   18  387
                        clus
vv                       DEL PEAK 21(12P13.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           32
                        clus
vv                       DEL PEAK 21(12P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 18
  NOT HISPANIC OR LATINO                            387
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 22(12Q12) MUTATION ANALYSIS
D43V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 22(12Q12) MUTATED    54  11
  DEL PEAK 22(12Q12) WILD-TYPE 322  83
  DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE 
                          65                          405 
  DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE 
                          11                           83 
$`DEL PEAK 22(12Q12) MUTATED`
TCGA-CS-4941 TCGA-CS-6665 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XF 
        7.69        12.43        47.93        50.86        44.52        33.57 
TCGA-DB-A4XH TCGA-DB-A75K TCGA-DH-A66B TCGA-DU-5871 TCGA-DU-6401 TCGA-DU-6542 
       31.63        12.10        42.05        18.94        87.45         7.73 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TU 
       62.96       156.23        14.99        16.96        15.48         3.65 
TCGA-DU-A5TY TCGA-DU-A6S6 TCGA-DU-A76O TCGA-DU-A76R TCGA-E1-5302 TCGA-E1-5304 
       12.20        77.98         7.13        21.30        50.14        41.13 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-A4MX TCGA-FG-A6J3 TCGA-HT-7470 TCGA-HT-7474 
       14.93        24.99        18.71        22.26        40.11         3.75 
TCGA-HT-7478 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7884 TCGA-HT-7902 
        6.38        42.74        31.69         0.10        11.28        31.43 
TCGA-HT-8018 TCGA-HT-8106 TCGA-HT-8108 TCGA-HT-8563 TCGA-HT-A5R7 TCGA-HT-A618 
       37.87         0.10         2.50        28.27        20.22        16.83 
TCGA-HT-A61B TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F4 TCGA-P5-A72W TCGA-P5-A72X 
       17.52         6.71         2.30         0.76        10.42        13.25 
TCGA-P5-A731 TCGA-S9-A6TV TCGA-S9-A6U1 TCGA-S9-A6UA TCGA-S9-A6WQ TCGA-S9-A7QX 
        9.01        18.77        17.62         5.85        14.07        13.12 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-TM-A84G TCGA-TM-A84I 
       99.06        30.05        98.63        18.71        40.64        28.08 
TCGA-VM-A8C8 TCGA-VM-A8CB TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85B 
       43.04         0.10        13.32        39.88        45.80 

$`DEL PEAK 22(12Q12) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5280 
      122.73        81.96        75.25        72.92        50.17        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       78.28        46.42        18.84        30.21        46.72        39.78 
TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       37.45        72.95        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       31.40        27.45        27.81        29.23        14.40        18.51 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
       11.24        17.88        30.74        16.18        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F 
       30.31        14.40         8.02        30.21        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        6.81       182.33        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
      114.08         7.96        11.47       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8168 TCGA-DU-A5TP 
       14.60        20.68        21.40        19.13        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 
       12.59        15.12         4.96         5.65         8.65         2.70 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7T6 TCGA-DU-A7T8 
        7.23         5.98        11.41        26.76        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       18.77        23.97        18.44        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.38        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       16.44        28.54        10.78        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       13.58         5.72        27.52         0.10         6.67        11.54 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.13         0.03        16.54        17.42         6.54        24.26 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       40.34        75.19        95.93       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       122.47         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
        0.10        14.96         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        5.33        35.47         3.72         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 
       63.55         0.10        33.01        12.23         6.25         0.46 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8564 
        5.56        13.78         0.23        29.59        34.19        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        26.04         0.13         0.07        27.35         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A619 
        5.33         2.70        16.93         1.81        16.14        21.40 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       12.76        20.81        20.71        19.00        42.77        14.40 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
       14.40         0.23         1.64         2.37         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A733 
        7.63         1.28         0.16        11.64         0.20        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
       15.16         2.53        12.62        15.85        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
       14.83        14.53        13.61        12.23         2.20         9.17 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
       10.29        14.53        16.34        16.73         1.91        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A843 
       59.38        30.87         5.46         9.90        28.08         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX 
       19.59        30.67        62.17        87.12        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       31.33        28.70        22.95        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       98.24        95.93       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       15.16        36.13         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY 
       20.02         8.19         2.04        17.03        15.06        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
       13.02       169.84        10.39        31.59        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       59.05        30.44        24.16        40.83        24.79        33.24 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW 
       25.38        18.61        14.93        23.80        15.98        26.99 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       30.08        13.51         7.89        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A85A 
       16.01        23.21         8.05        51.06        43.96        43.40 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE 
                        0.10                         0.03 
  DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE 
                      156.23                       211.17 
  DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE 
                       18.71                        18.61 
[1] "0.1 - 156.2 (18.7)" "0.0 - 211.2 (18.6)"
[1] "hr=" "1.2"
D43V2, continuous
D43V3, binary
                              cls
clus                             0   1
  DEL PEAK 22(12Q12) MUTATED    32  34
  DEL PEAK 22(12Q12) WILD-TYPE 174 232
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(12Q12) MUTATED     32   34
  DEL PEAK 22(12Q12) WILD-TYPE  174  232
        clus
vv       DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE
  FEMALE                         32                          174
  MALE                           34                          232
[1] 2 2
[1] FALSE
D43V4, continuous
                              vv
clus                           ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 22(12Q12) MUTATED            39               15                12
  DEL PEAK 22(12Q12) WILD-TYPE         137              103               166
D43V5, multiclass
                   clus
vv                  DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE
  ASTROCYTOMA                               39                          137
  OLIGOASTROCYTOMA                          15                          103
  OLIGODENDROGLIOMA                         12                          166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                              cls
clus                             0   1
  DEL PEAK 22(12Q12) MUTATED    12  54
  DEL PEAK 22(12Q12) WILD-TYPE  80 326
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(12Q12) MUTATED     12   54
  DEL PEAK 22(12Q12) WILD-TYPE   80  326
     clus
vv    DEL PEAK 22(12Q12) MUTATED DEL PEAK 22(12Q12) WILD-TYPE
  NO                          12                           80
  YES                         54                          326
[1] 2 2
[1] FALSE
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(12Q12) MUTATED                                  0     0
  DEL PEAK 22(12Q12) WILD-TYPE                                1     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(12Q12) MUTATED                           0    64
  DEL PEAK 22(12Q12) WILD-TYPE                        15   373
D43V7, multiclass
                                  clus
vv                                 DEL PEAK 22(12Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 0
  WHITE                                                    64
                                  clus
vv                                 DEL PEAK 22(12Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                     373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, binary
                              cls
clus                             0   1
  DEL PEAK 22(12Q12) MUTATED     0  61
  DEL PEAK 22(12Q12) WILD-TYPE  18 358
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(12Q12) MUTATED      0   61
  DEL PEAK 22(12Q12) WILD-TYPE   18  358
                        clus
vv                       DEL PEAK 22(12Q12) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         61
                        clus
vv                       DEL PEAK 22(12Q12) WILD-TYPE
  HISPANIC OR LATINO                               18
  NOT HISPANIC OR LATINO                          358
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 23(13Q14.2) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(13Q14.2) MUTATED    95  33
  DEL PEAK 23(13Q14.2) WILD-TYPE 281  61
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                           128                            342 
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                            33                             61 
$`DEL PEAK 23(13Q14.2) MUTATED`
TCGA-CS-4943 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6670 TCGA-DB-5275 TCGA-DB-5277 
       18.15        17.95         8.48         6.61        47.93        50.86 
TCGA-DB-A4XA TCGA-DB-A4XE TCGA-DB-A64X TCGA-DB-A75O TCGA-DH-5140 TCGA-DH-5142 
       18.84        37.45        18.51        30.74        19.96        30.31 
TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5852 
       30.21        27.81        17.19         3.45        18.02         6.74 
TCGA-DU-5853 TCGA-DU-6392 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6407 TCGA-DU-6408 
       13.38       211.17        65.75         1.22        94.52       114.08 
TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 
       11.47       156.23        14.99        10.36         7.96        18.94 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-8158 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-8168 
       44.02        25.91         5.10        19.13        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A76R 
       14.24        15.12         3.65         2.70         7.23        21.30 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5307 
      124.50        77.88        50.14        67.46        41.13        57.93 
TCGA-E1-5322 TCGA-E1-A7YW TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6688 
      130.78        36.82        47.77        25.48        34.36        18.77 
TCGA-FG-6689 TCGA-FG-6692 TCGA-FG-7641 TCGA-FG-8188 TCGA-FG-A4MY TCGA-FG-A60J 
       14.93        18.44        20.61        14.96        23.70        14.76 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A87Q 
       16.41        15.02        22.26        28.54        10.78         5.72 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
       11.54        40.11         0.13        17.42         6.54        24.26 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7616 
      106.95       172.77       122.47         4.57        17.29         0.23 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7856 TCGA-HT-7857 
       31.69        14.96         0.10         2.96        39.09         0.23 
TCGA-HT-7873 TCGA-HT-7902 TCGA-HT-8106 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A5R7 
       23.61        31.43         0.10        28.27        15.72        20.22 
TCGA-HT-A614 TCGA-HT-A617 TCGA-HT-A61B TCGA-HT-A74O TCGA-HW-7489 TCGA-HW-7491 
        2.70        16.14        17.52         0.10         8.32        40.18 
TCGA-KT-A74X TCGA-P5-A5EZ TCGA-P5-A5F4 TCGA-P5-A72W TCGA-QH-A65S TCGA-QH-A65Z 
       14.40         2.30         0.76        10.42         2.53        14.04 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6X8 TCGA-RY-A83Z TCGA-RY-A847 
       14.53        13.61         2.20        16.73         9.90        30.67 
TCGA-S9-A6TV TCGA-S9-A6UA TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       18.77         5.85         7.92        22.32        23.51         7.13 
TCGA-S9-A7J0 TCGA-S9-A7J3 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84F 
       20.02        17.03        18.71        11.97        49.45        59.05 
TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RH TCGA-TQ-A7RW 
       28.08        40.83        18.61        14.93        15.98        26.99 
TCGA-VM-A8CD TCGA-WY-A85E 
        7.89        20.81 

$`DEL PEAK 23(13Q14.2) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 
       12.43         7.56         8.02         7.40       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       75.25        72.92        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       46.42        30.21        46.72        39.78        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L 
       27.45        27.81        29.23        14.40        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B 
       17.88        16.18        31.82        14.40         8.02        42.05 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5849 
       17.19        54.25        13.12        13.38        18.61        14.56 
TCGA-DU-5851 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       17.46         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
        7.96         7.73        62.96       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 
        8.84       117.40        90.77        30.67        26.30        94.32 
TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 
       62.01        60.30        23.31        41.98         2.76        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT 
       14.60        20.68        21.40        16.96        12.59         4.96 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K 
        5.65        12.20         8.65        77.98         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       26.76         7.13        17.98        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       44.42         0.56        79.99       134.27        78.21        95.57 
TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       75.02        32.45        32.35        14.33         0.23         0.20 
TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       36.82        24.99        23.97        15.35        17.88        22.55 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A60K TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       17.82        16.44        36.66        48.69        20.45        13.58 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
       27.52         0.10         6.67         0.03        16.54         3.75 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7485 TCGA-HT-7601 
        6.38        40.34        75.19        95.93         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
       29.85        23.18         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
       57.60        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 
        6.05        42.74         0.10         0.10        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 
       14.53        39.48        19.23        50.63         0.49        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33        35.47         3.72 
TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       11.28         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 
       37.87        33.01        12.23         6.25         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-A4DS 
        5.56        13.78         0.23        29.59        34.19         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       26.04         0.13         0.07        27.35         0.10         5.33 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H 
       16.93         1.81        16.83        21.40        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 
       10.52        15.35        11.05        29.92        19.89        19.23 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35        12.76        20.81        20.71        19.00        42.77 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 
       14.40         0.23         6.71         1.64         2.37         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z 
        5.88         7.63         1.28         0.16        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X 
        0.20         9.01        13.61        15.16        12.62        15.85 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       19.33        14.83        12.23         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
       16.34         1.91        16.50         5.03        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y 
       88.83        94.03        32.65        59.38        30.87         5.46 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW 
       28.08         2.07        19.59        62.17        87.12        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD 
       32.61        16.08        98.24        95.93       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7J1 
       15.91        18.61        15.16        14.07        36.13         8.19 
TCGA-S9-A7J2 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        2.04        15.06        13.12        28.37        13.02       169.84 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C4 
       10.39        99.06        30.05        98.63        31.59        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84G 
       49.32        34.78        48.39        24.92        16.18        40.64 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84T 
       30.44        24.16        24.79        33.24        25.38        23.80 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
       43.04        30.08        13.51         0.10        35.93        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K 
       37.05        16.01        23.21         8.05        51.06        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 

  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                        211.17                         182.33 
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                        17.985                         19.280 
[1] "0.1 - 211.2 (18.0)" "0.0 - 182.3 (19.3)"
[1] "hr=" "1.5"
D44V2, continuous
D44V3, binary
                                cls
clus                               0   1
  DEL PEAK 23(13Q14.2) MUTATED    49  80
  DEL PEAK 23(13Q14.2) WILD-TYPE 157 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED     49   80
  DEL PEAK 23(13Q14.2) WILD-TYPE  157  186
        clus
vv       DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  FEMALE                           49                            157
  MALE                             80                            186
[1] 2 2
[1] FALSE
D44V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 23(13Q14.2) MUTATED            56               33                40
  DEL PEAK 23(13Q14.2) WILD-TYPE         120               85               138
D44V5, multiclass
                   clus
vv                  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  ASTROCYTOMA                                 56                            120
  OLIGOASTROCYTOMA                            33                             85
  OLIGODENDROGLIOMA                           40                            138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                                cls
clus                               0   1
  DEL PEAK 23(13Q14.2) MUTATED    32  97
  DEL PEAK 23(13Q14.2) WILD-TYPE  60 283
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED     32   97
  DEL PEAK 23(13Q14.2) WILD-TYPE   60  283
     clus
vv    DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  NO                            32                             60
  YES                           97                            283
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(13Q14.2) MUTATED                                  1     1
  DEL PEAK 23(13Q14.2) WILD-TYPE                                0     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(13Q14.2) MUTATED                           5   120
  DEL PEAK 23(13Q14.2) WILD-TYPE                        10   317
D44V7, multiclass
                                  clus
vv                                 DEL PEAK 23(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                     120
                                  clus
vv                                 DEL PEAK 23(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    10
  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"
D44V8, binary
                                cls
clus                               0   1
  DEL PEAK 23(13Q14.2) MUTATED     5 118
  DEL PEAK 23(13Q14.2) WILD-TYPE  13 301
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED      5  118
  DEL PEAK 23(13Q14.2) WILD-TYPE   13  301
                        clus
vv                       DEL PEAK 23(13Q14.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          118
                        clus
vv                       DEL PEAK 23(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            301
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 24(13Q14.2) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(13Q14.2) MUTATED    97  33
  DEL PEAK 24(13Q14.2) WILD-TYPE 279  61
  DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE 
                           130                            340 
  DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE 
                            33                             61 
$`DEL PEAK 24(13Q14.2) MUTATED`
TCGA-CS-4943 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6670 TCGA-DB-5275 TCGA-DB-5277 
       18.15        17.95         8.48         6.61        47.93        50.86 
TCGA-DB-A4XA TCGA-DB-A4XE TCGA-DB-A64X TCGA-DB-A75O TCGA-DH-5140 TCGA-DH-5142 
       18.84        37.45        18.51        30.74        19.96        30.31 
TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5852 
       30.21        27.81        17.19         3.45        18.02         6.74 
TCGA-DU-5853 TCGA-DU-6392 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6407 TCGA-DU-6408 
       13.38       211.17        65.75         1.22        94.52       114.08 
TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 
       11.47       156.23        14.99        10.36         7.96        18.94 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-8158 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-8168 
       44.02        25.91         5.10        19.13        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S3 TCGA-DU-A6S7 
       14.24        15.12         3.65        12.20         2.70         7.23 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
       21.30       124.50        77.88        50.14        67.46        41.13 
TCGA-E1-5307 TCGA-E1-5322 TCGA-E1-A7YW TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       57.93       130.78        36.82        47.77        25.48        34.36 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6692 TCGA-FG-7641 TCGA-FG-8188 TCGA-FG-A4MY 
       18.77        14.93        18.44        20.61        14.96        23.70 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       14.76        16.41        15.02        22.26        28.54        10.78 
TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7475 TCGA-HT-7476 
        5.72        11.54        40.11         0.13        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
       24.26       106.95       172.77       122.47         4.57        17.29 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7692 
       57.60         0.23        31.69        14.96         0.10         2.96 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7873 TCGA-HT-7902 TCGA-HT-8106 TCGA-HT-8563 
       39.09         0.23        23.61        31.43         0.10        28.27 
TCGA-HT-8564 TCGA-HT-A5R7 TCGA-HT-A614 TCGA-HT-A617 TCGA-HT-A61B TCGA-HT-A74O 
       15.72        20.22         2.70        16.14        17.52         0.10 
TCGA-HW-7489 TCGA-HW-7491 TCGA-KT-A74X TCGA-P5-A5EZ TCGA-P5-A5F4 TCGA-P5-A72W 
        8.32        40.18        14.40         2.30         0.76        10.42 
TCGA-QH-A65S TCGA-QH-A65Z TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6X8 
        2.53        14.04        14.53        13.61         2.20        16.73 
TCGA-RY-A83Z TCGA-RY-A847 TCGA-S9-A6TV TCGA-S9-A6UA TCGA-S9-A7IS TCGA-S9-A7IX 
        9.90        30.67        18.77         5.85         7.92        22.32 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J3 TCGA-S9-A89V TCGA-S9-A89Z 
       23.51         7.13        20.02        17.03        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A84F TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84R TCGA-TM-A84S 
       49.45        59.05        28.08        40.83        18.61        14.93 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8CD TCGA-WY-A85E 
       15.98        26.99         7.89        20.81 

$`DEL PEAK 24(13Q14.2) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 
       12.43         7.56         8.02         7.40       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       75.25        72.92        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       46.42        30.21        46.72        39.78        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       31.63        24.20        25.48        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L 
       27.45        27.81        29.23        14.40        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B 
       17.88        16.18        31.82        14.40         8.02        42.05 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5849 
       17.19        54.25        13.12        13.38        18.61        14.56 
TCGA-DU-5851 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       17.46         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
        7.96         7.73        62.96       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 
        8.84       117.40        90.77        30.67        26.30        94.32 
TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 
       62.01        60.30        23.31        41.98         2.76        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT 
       14.60        20.68        21.40        16.96        12.59         4.96 
TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        5.65         8.65        77.98         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG 
        7.13        17.98        42.31        23.51         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO 
        0.56        79.99       134.27        78.21        95.57        75.02 
TCGA-E1-A7YV TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5965 
       32.45        32.35        14.33         0.23         0.20        36.82 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7643 
       24.99        23.97        15.35        17.88        22.55        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 
       12.95        13.68        14.24        16.01        20.09        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60K 
       32.61        38.27        10.72        18.38        18.71        17.82 
TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 
       16.44        36.66        48.69        20.45        13.58        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7478 
        0.10         6.67         0.03        16.54         3.75         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       40.34        75.19        95.93         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7620 
       23.18         3.16        22.06        45.99        56.09        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         0.10        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       19.23        50.63         0.49        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 
        3.68         5.33        35.47         3.72        11.28         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
       12.23         6.25         0.46         2.50         5.56        13.78 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        0.23        29.59        34.19         0.23        26.04         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 
        0.07        27.35         0.10         5.33        16.93         1.81 
TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K 
       16.83        21.40        17.65         2.43        10.52        15.35 
TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 
       11.05        29.92        19.89        19.23        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35        12.76 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.81        20.71        19.00        42.77        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        6.71         1.64         2.37         4.11         5.88         7.63 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        1.28         0.16        13.25        11.64         0.20         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU 
       13.61        15.16        12.62        15.85        19.33        14.83 
TCGA-QH-A6CX TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X9 
       12.23         9.17        10.29        14.53        16.34         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 
       32.65        59.38        30.87         5.46        28.08         2.07 
TCGA-RY-A845 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       19.59        62.17        87.12        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       28.70        22.95        17.62        23.64        32.61        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       98.24        95.93       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QW 
       15.16        14.07        36.13         8.19         2.04        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       30.05        98.63        31.59        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J 
       48.39        24.92        16.18        40.64        30.44        24.16 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 
       24.79        33.24        25.38        23.80        43.04        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
       13.51         0.10        35.93        23.47        37.05        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 
       23.21         8.05        51.06        13.32        43.96        39.88 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.40        45.80        46.88        37.71 

  DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE 
                        211.17                         182.33 
  DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE 
                        17.985                         19.280 
[1] "0.1 - 211.2 (18.0)" "0.0 - 182.3 (19.3)"
[1] "hr=" "1.4"
D45V2, continuous
D45V3, binary
                                cls
clus                               0   1
  DEL PEAK 24(13Q14.2) MUTATED    50  81
  DEL PEAK 24(13Q14.2) WILD-TYPE 156 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(13Q14.2) MUTATED     50   81
  DEL PEAK 24(13Q14.2) WILD-TYPE  156  185
        clus
vv       DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE
  FEMALE                           50                            156
  MALE                             81                            185
[1] 2 2
[1] FALSE
D45V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 24(13Q14.2) MUTATED            57               34                40
  DEL PEAK 24(13Q14.2) WILD-TYPE         119               84               138
D45V5, multiclass
                   clus
vv                  DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE
  ASTROCYTOMA                                 57                            119
  OLIGOASTROCYTOMA                            34                             84
  OLIGODENDROGLIOMA                           40                            138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                                cls
clus                               0   1
  DEL PEAK 24(13Q14.2) MUTATED    32  99
  DEL PEAK 24(13Q14.2) WILD-TYPE  60 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(13Q14.2) MUTATED     32   99
  DEL PEAK 24(13Q14.2) WILD-TYPE   60  281
     clus
vv    DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE
  NO                            32                             60
  YES                           99                            281
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(13Q14.2) MUTATED                                  1     1
  DEL PEAK 24(13Q14.2) WILD-TYPE                                0     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(13Q14.2) MUTATED                           5   122
  DEL PEAK 24(13Q14.2) WILD-TYPE                        10   315
D45V7, multiclass
                                  clus
vv                                 DEL PEAK 24(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                     122
                                  clus
vv                                 DEL PEAK 24(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       315
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                                cls
clus                               0   1
  DEL PEAK 24(13Q14.2) MUTATED     5 120
  DEL PEAK 24(13Q14.2) WILD-TYPE  13 299
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(13Q14.2) MUTATED      5  120
  DEL PEAK 24(13Q14.2) WILD-TYPE   13  299
                        clus
vv                       DEL PEAK 24(13Q14.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          120
                        clus
vv                       DEL PEAK 24(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            299
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 25(13Q34) MUTATION ANALYSIS
D46V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 25(13Q34) MUTATED    73  26
  DEL PEAK 25(13Q34) WILD-TYPE 303  68
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                          99                          371 
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                          26                           68 
$`DEL PEAK 25(13Q34) MUTATED`
TCGA-CS-6290 TCGA-CS-6666 TCGA-DB-A4XA TCGA-DB-A4XE TCGA-DH-5140 TCGA-DH-A669 
       17.95         8.48        18.84        37.45        19.96        30.21 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5871 TCGA-DU-6392 
       27.81        17.19         3.45        18.02        18.94       211.17 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7008 
       65.75         1.22        94.52       114.08        11.47       156.23 
TCGA-DU-7010 TCGA-DU-7290 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-8158 TCGA-DU-8165 
       14.99        10.36        18.94        44.02         5.10        19.13 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TS TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A76R 
       15.48        14.17        15.12         2.70         7.23        21.30 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5322 TCGA-E1-A7YW 
      124.50        77.88        67.46        41.13       130.78        36.82 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6689 TCGA-FG-6692 TCGA-FG-7641 
       47.77        25.48        34.36        14.93        18.44        20.61 
TCGA-FG-8188 TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J3 TCGA-FG-A70Z 
       14.96        14.76        16.41        15.02        22.26        10.78 
TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7477 TCGA-HT-7482 
        5.72        11.54        40.11         0.13        24.26       106.95 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7611 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7692 
        4.57        17.29        57.60        14.96         0.10         2.96 
TCGA-HT-7694 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8106 
        6.90        39.09         0.23         3.72        31.43         0.10 
TCGA-HT-8564 TCGA-HT-A617 TCGA-HT-A61B TCGA-HW-7489 TCGA-HW-7491 TCGA-IK-7675 
       15.72        16.14        17.52         8.32        40.18        19.00 
TCGA-KT-A74X TCGA-P5-A5EZ TCGA-P5-A5F4 TCGA-P5-A72W TCGA-QH-A65Z TCGA-QH-A6CV 
       14.40         2.30         0.76        10.42        14.04        14.53 
TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6X8 TCGA-RY-A83Z TCGA-RY-A847 TCGA-S9-A6UA 
       13.61         2.20        16.73         9.90        30.67         5.85 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J3 TCGA-S9-A89V TCGA-S9-A89Z 
       22.32        23.51        20.02        17.03        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A84F TCGA-TM-A84I TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RH 
       49.45        59.05        28.08        18.61        14.93        15.98 
TCGA-TQ-A7RW TCGA-VM-A8CD TCGA-WY-A85E 
       26.99         7.89        20.81 

$`DEL PEAK 25(13Q34) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       23.84        12.43         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB 
       50.17        44.52        36.56        78.28        46.42        30.21 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       46.72        39.78        33.57        72.95        31.63        24.20 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       29.23        14.40        18.51        12.10        11.24        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       30.74        16.18        31.82        30.31        14.40         8.02 
TCGA-DH-A66B TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV 
       42.05        17.19        54.25        13.12        13.38        18.61 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
      182.33        17.49        15.16        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       75.16        46.06        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7009 
       19.89        16.83         7.96         7.73        62.96       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       26.30         7.96        94.32        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       23.31        41.98         2.76        23.74        14.60        20.68 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU 
       21.40        16.96        14.24        12.59         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K 
        5.65        12.20         8.65        77.98         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       26.76         7.13        17.98        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       44.42         0.56        50.14        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7Z6 TCGA-EZ-7264 
       78.21        95.57        75.02        32.45        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 
        0.23         0.20        36.82        18.77        24.99        23.97 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       15.35        17.88        22.55        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       14.24        16.01        20.09        22.52        32.61        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60K TCGA-FG-A6J1 
       10.72        18.38        18.71        23.70        17.82        16.44 
TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 
       28.54        36.66        48.69        20.45        13.58        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        0.10         6.67         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 
        6.54         6.38        40.34        75.19        95.93       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7607 
        4.01         5.03        29.85        23.18       122.47         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       22.06        45.99        56.09         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
       31.69         0.10        17.52        14.53        39.48        19.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 
        3.68         5.33        35.47        11.28         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        6.25         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59        34.19        28.27         0.23        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74H 
       16.93         1.81        16.83        21.40        17.65         2.43 
TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       10.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 
       17.82        20.35        12.76        20.81        20.71        42.77 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 
       14.40         0.23         6.71         1.64         2.37         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72X TCGA-P5-A72Z 
        5.88         7.63         1.28         0.16        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CZ TCGA-QH-A6X3 
       15.85        19.33        14.83        12.23         9.17        10.29 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
       14.53        16.34         1.91        16.50         5.03        11.08 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       12.99        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS TCGA-S9-A6TU 
        5.46        28.08         2.07        19.59        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61        16.08        98.24        95.93 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        69.50        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       31.10        19.86        15.91        18.61        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QW 
       36.13         7.92         7.13         8.19         2.04        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
       13.12        28.37        13.02       169.84        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       30.05        98.63        31.59        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J 
       48.39        24.92        16.18        40.64        30.44        24.16 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84T TCGA-VM-A8C8 
       40.83        24.79        33.24        25.38        23.80        43.04 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       30.08        13.51         0.10        35.93        23.47        37.05 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A858 
       16.01        23.21         8.05        51.06        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       39.88        43.40        45.80        46.88        37.71 

  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                        0.10                         0.03 
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                      211.17                       182.33 
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                       17.29                        19.33 
[1] "0.1 - 211.2 (17.3)" "0.0 - 182.3 (19.3)"
[1] "hr=" "1.5"
D46V2, continuous
D46V3, binary
                              cls
clus                             0   1
  DEL PEAK 25(13Q34) MUTATED    38  61
  DEL PEAK 25(13Q34) WILD-TYPE 168 205
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(13Q34) MUTATED     38   61
  DEL PEAK 25(13Q34) WILD-TYPE  168  205
        clus
vv       DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE
  FEMALE                         38                          168
  MALE                           61                          205
[1] 2 2
[1] FALSE
D46V4, continuous
                              vv
clus                           ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 25(13Q34) MUTATED            37               24                38
  DEL PEAK 25(13Q34) WILD-TYPE         139               94               140
D46V5, multiclass
                   clus
vv                  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE
  ASTROCYTOMA                               37                          139
  OLIGOASTROCYTOMA                          24                           94
  OLIGODENDROGLIOMA                         38                          140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                              cls
clus                             0   1
  DEL PEAK 25(13Q34) MUTATED    23  76
  DEL PEAK 25(13Q34) WILD-TYPE  69 304
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(13Q34) MUTATED     23   76
  DEL PEAK 25(13Q34) WILD-TYPE   69  304
     clus
vv    DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE
  NO                          23                           69
  YES                         76                          304
[1] 2 2
[1] FALSE
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(13Q34) MUTATED                                  1     1
  DEL PEAK 25(13Q34) WILD-TYPE                                0     7
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(13Q34) MUTATED                           3    92
  DEL PEAK 25(13Q34) WILD-TYPE                        12   345
D46V7, multiclass
                                  clus
vv                                 DEL PEAK 25(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 3
  WHITE                                                    92
                                  clus
vv                                 DEL PEAK 25(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                     345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                              cls
clus                             0   1
  DEL PEAK 25(13Q34) MUTATED     5  89
  DEL PEAK 25(13Q34) WILD-TYPE  13 330
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(13Q34) MUTATED      5   89
  DEL PEAK 25(13Q34) WILD-TYPE   13  330
                        clus
vv                       DEL PEAK 25(13Q34) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                         89
                        clus
vv                       DEL PEAK 25(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               13
  NOT HISPANIC OR LATINO                          330
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 26(14Q24.3) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(14Q24.3) MUTATED    72  35
  DEL PEAK 26(14Q24.3) WILD-TYPE 304  59
  DEL PEAK 26(14Q24.3) MUTATED DEL PEAK 26(14Q24.3) WILD-TYPE 
                           107                            363 
  DEL PEAK 26(14Q24.3) MUTATED DEL PEAK 26(14Q24.3) WILD-TYPE 
                            35                             59 
$`DEL PEAK 26(14Q24.3) MUTATED`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-6668 TCGA-DB-5279 
        4.70         7.69        43.89        10.62         8.02        44.52 
TCGA-DB-A4XA TCGA-DB-A64L TCGA-DB-A64O TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 
       18.84        24.20        25.48        19.96        30.31        14.40 
TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5855 TCGA-DU-5872 TCGA-DU-6396 TCGA-DU-6397 
       18.02         6.74         6.81        17.49        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6403 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       65.75        11.64       114.08         7.73        11.47        62.96 
TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7298 TCGA-DU-7302 
       14.99         6.54        26.30        10.36        18.94        60.30 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A6S8 TCGA-DU-A76L TCGA-DU-A76R 
        5.10        23.74        19.13         5.98        26.76        21.30 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YV 
       41.13        79.99        57.93        95.57       130.78        32.45 
TCGA-EZ-7264 TCGA-FG-5963 TCGA-FG-7643 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MY 
       14.33        25.48        20.09        32.61        38.27        23.70 
TCGA-FG-A6J3 TCGA-HT-7477 TCGA-HT-7603 TCGA-HT-7606 TCGA-HT-7616 TCGA-HT-7688 
       22.26        24.26        23.18        17.29         0.23        31.69 
TCGA-HT-7689 TCGA-HT-7858 TCGA-HT-7902 TCGA-HT-8110 TCGA-HT-8563 TCGA-HT-8564 
       14.96        50.63        31.43        13.78        28.27        15.72 
TCGA-HT-A4DS TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61C 
        0.23        16.93        16.14        16.83        21.40        17.65 
TCGA-HW-7489 TCGA-HW-A5KK TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EX TCGA-P5-A5EZ 
        8.32        12.76        42.77         0.23         1.64         2.30 
TCGA-P5-A5F2 TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CZ TCGA-QH-A6X4 
        7.63        19.33        14.53        13.61         9.17        14.53 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A73M TCGA-RY-A83Z TCGA-RY-A840 TCGA-S9-A6TS 
       12.99        88.83        59.38         9.90        28.08        62.17 
TCGA-S9-A6WD TCGA-S9-A6WM TCGA-S9-A6WP TCGA-S9-A7IX TCGA-S9-A7J0 TCGA-S9-A7J1 
       69.50        19.86        15.16        22.32        20.02         8.19 
TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-S9-A89V 
       13.12        13.02        10.39        99.06        31.59        18.71 
TCGA-TM-A7C3 TCGA-TM-A84I TCGA-TM-A84Q TCGA-TQ-A7RW TCGA-VM-A8CB TCGA-VM-A8CD 
       49.45        28.08        25.38        26.99         0.10         7.89 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-WY-A858 TCGA-WY-A85B 
       37.05        16.01        23.21        43.96        45.80 

$`DEL PEAK 26(14Q24.3) WILD-TYPE`
TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 
       18.15        64.64        40.18         0.10        21.01         9.96 
TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 
        6.38        17.69        23.84        17.95        12.43         8.48 
TCGA-CS-6667 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 
        7.56         7.40         6.61       122.73        81.96        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 
       47.93        72.92        50.86        50.17        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       46.42        30.21        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       72.95        31.63        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A669 
       17.88        30.74        16.18        31.82         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
       13.38         3.45        18.61        14.56        17.46        13.38 
TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        8.45       182.33        18.94        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6404 
       22.42        49.02         1.22        87.45         7.04       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-7008 TCGA-DU-7009 
       19.89        16.83        94.52         7.96       156.23       138.28 
TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7292 
      105.21         8.84       117.40        90.77        30.67         7.96 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 
       94.32        44.02        62.01        25.91        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
        2.76        14.60        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A76K TCGA-DU-A76O TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB 
       11.41         7.13        17.98       124.50        77.88        42.31 
TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 
       23.51         7.50        44.42         0.56        50.14        67.46 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O3 
      134.27        78.21        75.02        36.82        32.35         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
        0.20        47.77        34.36        36.82        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        18.44        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.61        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J 
       14.96        22.52        10.72        18.38        18.71        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z 
       17.82        16.41        15.02        16.44        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       36.66        48.69        20.45        13.58         5.72        27.52 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67        11.54        40.11         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42         6.54         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
       29.85       122.47         4.57         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       56.09        57.60        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 
       44.68         6.05        42.74         0.10         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
       39.09         0.23         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        37.87 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-A4DV TCGA-HT-A5R5 
        5.56         0.23        29.59        34.19        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       20.22         0.07        27.35         0.10         5.33         2.70 
TCGA-HT-A616 TCGA-HT-A61B TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
        1.81        17.52         2.43        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
        0.10        29.92        19.89        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW 
       20.81        20.71        19.00        14.40        14.40         6.71 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U 
        2.37         4.11         5.88         0.76         1.28         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64         0.20         9.01        13.61 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU 
       15.16         2.53        12.62        15.85        14.04        14.83 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
       12.23         2.20        10.29        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X 
       16.50         5.03        11.08        94.03        32.65        30.87 
TCGA-RY-A83Y TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV 
        5.46         2.07        19.59        30.67        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        28.70        22.95        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61        16.08        98.24        95.93         5.85 
TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
      106.39        72.59        80.12        32.45        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY 
       15.91        18.61        14.07        36.13         7.92        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7R1 
        7.13         2.04        17.03        15.06        28.37       169.84 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       30.05        98.63        11.97        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        24.92        16.18        59.05        40.64        30.44 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S 
       24.16        40.83        24.79        33.24        18.61        14.93 
TCGA-TM-A84T TCGA-TQ-A7RH TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CE 
       23.80        15.98        43.04        30.08        13.51        35.93 
TCGA-VM-A8CH TCGA-VW-A8FI TCGA-W9-A837 TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85A 
       23.47         8.05        51.06        13.32        39.88        43.40 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  DEL PEAK 26(14Q24.3) MUTATED DEL PEAK 26(14Q24.3) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 26(14Q24.3) MUTATED DEL PEAK 26(14Q24.3) WILD-TYPE 
                        130.78                         211.17 
  DEL PEAK 26(14Q24.3) MUTATED DEL PEAK 26(14Q24.3) WILD-TYPE 
                         19.86                          18.38 
[1] "0.1 - 130.8 (19.9)" "0.0 - 211.2 (18.4)"
[1] "hr=" "2.2"
D47V2, continuous
D47V3, binary
                                cls
clus                               0   1
  DEL PEAK 26(14Q24.3) MUTATED    54  54
  DEL PEAK 26(14Q24.3) WILD-TYPE 152 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(14Q24.3) MUTATED     54   54
  DEL PEAK 26(14Q24.3) WILD-TYPE  152  212
        clus
vv       DEL PEAK 26(14Q24.3) MUTATED DEL PEAK 26(14Q24.3) WILD-TYPE
  FEMALE                           54                            152
  MALE                             54                            212
[1] 2 2
[1] FALSE
D47V4, continuous
                                vv
clus                             ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 26(14Q24.3) MUTATED            48               26                34
  DEL PEAK 26(14Q24.3) WILD-TYPE         128               92               144
D47V5, multiclass
                   clus
vv                  DEL PEAK 26(14Q24.3) MUTATED DEL PEAK 26(14Q24.3) WILD-TYPE
  ASTROCYTOMA                                 48                            128
  OLIGOASTROCYTOMA                            26                             92
  OLIGODENDROGLIOMA                           34                            144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(14Q24.3) MUTATED    22  86
  DEL PEAK 26(14Q24.3) WILD-TYPE  70 294
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(14Q24.3) MUTATED     22   86
  DEL PEAK 26(14Q24.3) WILD-TYPE   70  294
     clus
vv    DEL PEAK 26(14Q24.3) MUTATED DEL PEAK 26(14Q24.3) WILD-TYPE
  NO                            22                             70
  YES                           86                            294
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(14Q24.3) MUTATED                                  1     3
  DEL PEAK 26(14Q24.3) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(14Q24.3) MUTATED                           4    96
  DEL PEAK 26(14Q24.3) WILD-TYPE                        11   341
D47V7, multiclass
                                  clus
vv                                 DEL PEAK 26(14Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      96
                                  clus
vv                                 DEL PEAK 26(14Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    11
  WHITE                                                       341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(14Q24.3) MUTATED     4  93
  DEL PEAK 26(14Q24.3) WILD-TYPE  14 326
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(14Q24.3) MUTATED      4   93
  DEL PEAK 26(14Q24.3) WILD-TYPE   14  326
                        clus
vv                       DEL PEAK 26(14Q24.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           93
                        clus
vv                       DEL PEAK 26(14Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            326
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 27(18Q23) MUTATION ANALYSIS
D48V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 27(18Q23) MUTATED    60  14
  DEL PEAK 27(18Q23) WILD-TYPE 316  80
  DEL PEAK 27(18Q23) MUTATED DEL PEAK 27(18Q23) WILD-TYPE 
                          74                          396 
  DEL PEAK 27(18Q23) MUTATED DEL PEAK 27(18Q23) WILD-TYPE 
                          14                           80 
$`DEL PEAK 27(18Q23) MUTATED`
TCGA-CS-5396 TCGA-CS-6665 TCGA-CS-6667 TCGA-DB-5275 TCGA-DB-5279 TCGA-DB-5280 
        9.96        12.43         7.56        47.93        44.52        36.56 
TCGA-DB-A4XD TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DH-5140 TCGA-DH-5142 
       39.78        72.95        31.63        24.20        19.96        30.31 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 
       30.21        42.05        13.38        18.61        14.56        17.46 
TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-6393 TCGA-DU-6407 TCGA-DU-7009 TCGA-DU-7012 
        8.45       182.33        52.11        94.52       138.28         6.54 
TCGA-DU-7014 TCGA-DU-7300 TCGA-DU-8158 TCGA-DU-A5TT TCGA-DU-A7T6 TCGA-E1-5307 
      117.40        62.01         5.10         4.96        17.98        57.93 
TCGA-FG-8185 TCGA-FG-8188 TCGA-HT-7476 TCGA-HT-7480 TCGA-HT-7606 TCGA-HT-7616 
       14.24        14.96         6.54        75.19        17.29         0.23 
TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-7857 TCGA-HT-7873 TCGA-HT-8114 TCGA-HT-8564 
       31.69         2.96         0.23        23.61        34.19        15.72 
TCGA-HT-A5RB TCGA-HT-A617 TCGA-HT-A74L TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-8320 
        0.10        16.14        11.05         8.32        40.18        21.60 
TCGA-HW-A5KJ TCGA-HW-A5KM TCGA-P5-A5EX TCGA-P5-A72Z TCGA-QH-A65R TCGA-QH-A65Z 
       20.35        20.71         1.64        11.64        15.16        14.04 
TCGA-RY-A840 TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6WD TCGA-S9-A6WH 
       28.08        62.17        37.84        34.49        69.50        32.45 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7QY TCGA-S9-A7R2 
       31.10        19.86        15.91        15.16        28.37        10.39 
TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8CA 
       40.64        28.08        24.16        15.98        26.99        13.51 
TCGA-WH-A86K TCGA-WY-A85B 
       13.32        45.80 

$`DEL PEAK 27(18Q23) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       17.95         8.48         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5281 
       81.96        75.25        72.92        50.86        50.17        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A4XF 
       46.42        18.84        30.21        46.72        37.45        33.57 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       25.48        30.12         5.98        31.40        27.45        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       29.23        14.40        18.51        12.10        11.24        17.88 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D 
       30.74        16.18        31.82        14.40         8.02        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DU-5847 
       17.19        17.19        54.25        13.12         3.45        18.02 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        6.74        13.38         6.81        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
      211.17        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       16.83       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 
      156.23        14.99       105.21         8.84        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 
       25.91        60.30        23.31        41.98         2.76        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       14.60        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW 
       14.17        14.24        12.59        15.12         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA 
       11.41        26.76         7.13        21.30       124.50        77.88 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 
       42.31        23.51         7.50        44.42         0.56        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        41.13        79.99       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 
      130.78        75.02        32.45        36.82        32.35        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        25.48        34.36        36.82 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        18.44        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       16.01        20.09        22.52        32.61        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       18.38        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 
        3.75        17.42        24.26         6.38        40.34        95.93 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
      106.95       172.77         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
      122.47         4.57         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
       57.60        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74         0.10        14.96         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
       50.63         0.49        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33        35.47         3.72        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        37.87        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         5.56 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV 
       13.78         0.23        29.59        28.27         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 
        0.13        20.22         0.07        27.35         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A61C 
       16.93         1.81        16.83        21.40        17.52        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
        2.43        10.52        15.35         0.10        29.92        19.89 
TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-8322 
       19.23        35.90         4.31        21.70        19.59        17.82 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       12.76        20.81        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        0.23         6.71         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        7.63         0.76         1.28         0.16        10.42        13.25 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        0.20         9.01        13.61         2.53        12.62        15.85 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
       19.33        14.83        14.53        13.61        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        9.17        10.29        14.53        16.34        16.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.50         5.03        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A843 
       32.65        59.38        30.87         5.46         9.90         2.07 
TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TY TCGA-S9-A6TZ 
       19.59        30.67        87.12        18.77        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI 
       95.93         5.85       106.39        72.59        80.12        84.99 
TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       18.61        14.07        36.13         7.92        22.32        23.51 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.13        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.12        13.02       169.84        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71        11.97        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H 
       34.78        48.39        24.92        16.18        59.05        30.44 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        24.79        33.24        25.38        18.61        14.93 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       23.80        43.04        30.08         0.10         7.89        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.96        39.88        43.40        46.88        37.71        20.81 

  DEL PEAK 27(18Q23) MUTATED DEL PEAK 27(18Q23) WILD-TYPE 
                        0.10                         0.03 
  DEL PEAK 27(18Q23) MUTATED DEL PEAK 27(18Q23) WILD-TYPE 
                      182.33                       211.17 
  DEL PEAK 27(18Q23) MUTATED DEL PEAK 27(18Q23) WILD-TYPE 
                      20.530                       18.475 
[1] "0.1 - 182.3 (20.5)" "0.0 - 211.2 (18.5)"
[1] "hr=" "1.2"
D48V2, continuous
D48V3, binary
                              cls
clus                             0   1
  DEL PEAK 27(18Q23) MUTATED    28  46
  DEL PEAK 27(18Q23) WILD-TYPE 178 220
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 27(18Q23) MUTATED     28   46
  DEL PEAK 27(18Q23) WILD-TYPE  178  220
        clus
vv       DEL PEAK 27(18Q23) MUTATED DEL PEAK 27(18Q23) WILD-TYPE
  FEMALE                         28                          178
  MALE                           46                          220
[1] 2 2
[1] FALSE
D48V4, continuous
                              vv
clus                           ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 27(18Q23) MUTATED            27               15                32
  DEL PEAK 27(18Q23) WILD-TYPE         149              103               146
D48V5, multiclass
                   clus
vv                  DEL PEAK 27(18Q23) MUTATED DEL PEAK 27(18Q23) WILD-TYPE
  ASTROCYTOMA                               27                          149
  OLIGOASTROCYTOMA                          15                          103
  OLIGODENDROGLIOMA                         32                          146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                              cls
clus                             0   1
  DEL PEAK 27(18Q23) MUTATED    15  59
  DEL PEAK 27(18Q23) WILD-TYPE  77 321
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 27(18Q23) MUTATED     15   59
  DEL PEAK 27(18Q23) WILD-TYPE   77  321
     clus
vv    DEL PEAK 27(18Q23) MUTATED DEL PEAK 27(18Q23) WILD-TYPE
  NO                          15                           77
  YES                         59                          321
[1] 2 2
[1] FALSE
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(18Q23) MUTATED                                  1     0
  DEL PEAK 27(18Q23) WILD-TYPE                                0     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(18Q23) MUTATED                           1    68
  DEL PEAK 27(18Q23) WILD-TYPE                        14   369
D48V7, multiclass
                                  clus
vv                                 DEL PEAK 27(18Q23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 1
  WHITE                                                    68
                                  clus
vv                                 DEL PEAK 27(18Q23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, binary
                              cls
clus                             0   1
  DEL PEAK 27(18Q23) MUTATED     5  61
  DEL PEAK 27(18Q23) WILD-TYPE  13 358
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 27(18Q23) MUTATED      5   61
  DEL PEAK 27(18Q23) WILD-TYPE   13  358
                        clus
vv                       DEL PEAK 27(18Q23) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                         61
                        clus
vv                       DEL PEAK 27(18Q23) WILD-TYPE
  HISPANIC OR LATINO                               13
  NOT HISPANIC OR LATINO                          358
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 28(19Q13.41) MUTATION ANALYSIS
D49V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(19Q13.41) MUTATED   204  41
  DEL PEAK 28(19Q13.41) WILD-TYPE 172  53
  DEL PEAK 28(19Q13.41) MUTATED DEL PEAK 28(19Q13.41) WILD-TYPE 
                            245                             225 
  DEL PEAK 28(19Q13.41) MUTATED DEL PEAK 28(19Q13.41) WILD-TYPE 
                             41                              53 
$`DEL PEAK 28(19Q13.41) MUTATED`
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 
       43.89        18.15        10.62        64.64         0.10         9.96 
TCGA-CS-6668 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5277 
        8.02         6.61       122.73        75.25        47.93        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XG TCGA-DB-A4XH 
       50.17        44.52        18.84        30.21        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V 
       24.20        30.12         5.98        31.40        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75O TCGA-DH-5140 TCGA-DH-5141 
       14.40        12.10        11.24        30.74        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5855 
       17.19        54.25        13.12        14.56        17.46         6.81 
TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 
      182.33        17.49        15.16        52.11        22.42        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       46.06        65.75         1.22       114.08         7.96         7.73 
TCGA-DU-7007 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7292 
       62.96       138.28        14.99       117.40        30.67         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 
       94.32        18.94        62.01        60.30        41.98         2.76 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A6S2 
       21.40        16.96        14.17        14.24        15.12         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 
        2.70        77.98         5.98        21.30        17.98       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5304 
       77.88        42.31        23.51        44.42        50.14        41.13 
TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YO 
       79.99       134.27        78.21        95.57       130.78        75.02 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6690 
       14.33         0.23        47.77        34.36        36.82        24.99 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8186 TCGA-FG-8187 
       15.35        17.88        22.55        20.61        16.01        20.09 
TCGA-FG-8188 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 
       14.96        38.27        18.71        17.82        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-7467 
       22.26        36.66        48.69        20.45        13.58         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7475 TCGA-HT-7480 
        6.67        11.54         0.13         0.03        17.42        75.19 
TCGA-HT-7481 TCGA-HT-7601 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       95.93         5.03         4.57        17.29         3.16        22.06 
TCGA-HT-7610 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 
       56.09         0.23        14.27        16.24        44.68         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 
       31.69        14.96         2.96         6.90        14.53        39.09 
TCGA-HT-7857 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7881 TCGA-HT-8010 
        0.23        37.15         0.33         0.13        35.47         1.64 
TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8563 TCGA-HT-8564 
        9.40         6.25         5.56         0.23        28.27        15.72 
TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HT-A618 TCGA-HT-A619 
       26.04        20.22         0.07        16.93        16.83        21.40 
TCGA-HT-A61B TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       17.52        15.35        11.05         0.10        29.92        19.89 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-IK-8125 TCGA-KT-A74X 
       40.18         4.31        17.82        20.35        42.77        14.40 
TCGA-P5-A5EV TCGA-P5-A5EX TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F2 TCGA-P5-A5F6 
        0.23         1.64         2.30         4.11         7.63         1.28 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X 
       11.64         0.20         9.01        15.16        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 
       14.04        14.83         2.20         9.17        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
       16.73         1.91        11.08        12.99        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 
       32.65        59.38        30.87         5.46         9.90        28.08 
TCGA-RY-A847 TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       30.67        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH 
       23.64        32.61       106.39        69.50        72.59        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IS 
       84.99        31.10        15.91        15.16        36.13         7.92 
TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY 
       23.51         8.19         2.04        17.03        15.06        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C5 TCGA-TM-A84B 
       13.02       169.84        31.59        18.71        49.32        24.92 
TCGA-TM-A84G TCGA-TM-A84J TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       40.64        24.16        24.79        33.24        25.38        18.61 
TCGA-TM-A84S TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8CA TCGA-VM-A8CB 
       14.93        15.98        26.99        43.04        13.51         0.10 
TCGA-VM-A8CE TCGA-VV-A829 TCGA-VW-A7QS TCGA-W9-A837 TCGA-WY-A858 
       35.93        37.05        23.21        51.06        43.96 

$`DEL PEAK 28(19Q13.41) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 
        4.70         7.69        40.18        21.01         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 
       23.84        17.95        12.43         8.48         7.56         7.40 
TCGA-DB-5273 TCGA-DB-5276 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XC 
       81.96        72.92        36.56        78.28        46.42        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64O TCGA-DB-A64S TCGA-DB-A64X 
       39.78        37.45        33.57        25.48        27.45        18.51 
TCGA-DB-A75M TCGA-DB-A75P TCGA-DH-5143 TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.88        16.18        14.40        13.38         3.45        18.61 
TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5871 TCGA-DU-6392 
       18.02         6.74        13.38         8.45        18.94       211.17 
TCGA-DU-6395 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       49.02        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7011 TCGA-DU-7012 
       16.83        94.52        11.47       156.23       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7299 TCGA-DU-7301 
        8.84        90.77        26.30        10.36        44.02        25.91 
TCGA-DU-7304 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 
       23.31         5.10        23.74        14.60        20.68        19.13 
TCGA-DU-8167 TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       15.48        12.59         4.96         3.65         5.65        12.20 
TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7TD TCGA-DU-A7TJ 
        7.23        11.41        26.76         7.13         7.50         0.56 
TCGA-E1-5303 TCGA-E1-5307 TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O4 
       67.46        57.93        32.45        36.82        32.35         0.20 
TCGA-FG-5963 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7643 
       25.48        18.77        14.93        23.97        18.44        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MU 
       12.95        13.68        14.24        22.52        32.61        10.72 
TCGA-FG-A4MW TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A70Y TCGA-FG-A70Z 
       18.38        23.70        14.76        16.41        28.54        10.78 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7470 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 
        5.72        27.52        40.11        16.54         3.75         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       24.26         6.38        40.34       106.95       172.77         4.01 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7676 
       29.85        23.18       122.47        45.99        57.60         0.16 
TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 
        0.76         6.05        42.74         0.10         0.10        17.52 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7879 
       39.48        19.23        50.63         0.49        23.61         3.68 
TCGA-HT-7880 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8013 
        5.33         3.72        11.28        31.43        16.24        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 
        0.10        37.87        33.01        12.23         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-A4DS TCGA-HT-A5R5 
        2.50        13.78        29.59        34.19         0.23         0.13 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 
       27.35         0.10         5.33         2.70         1.81        16.14 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 
       17.65         2.43        10.52         8.32        19.23        35.90 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       21.70        21.60        19.59        12.76        20.81        20.71 
TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5F1 TCGA-P5-A5F4 
       19.00        14.40         6.71         2.37         5.88         0.76 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A733 TCGA-QH-A65S TCGA-QH-A6CS 
        0.16        10.42        13.25        13.61         2.53        19.33 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6X3 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        13.61        12.23        10.29        16.50         5.03 
TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6U0 TCGA-S9-A6U1 
        2.07        19.59        62.17        87.12        22.95        17.62 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WM 
       16.08        98.24        95.93         5.85        80.12        19.86 
TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QX 
       18.61        14.07        22.32         7.13        20.02        13.12 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A7C3 
       10.39        99.06        30.05        98.63        11.97        49.45 
TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H 
       48.33        34.78        48.39        16.18        59.05        30.44 
TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CH 
       28.08        40.83        23.80        30.08         7.89        23.47 
TCGA-VV-A86M TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       16.01         8.05        13.32        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  DEL PEAK 28(19Q13.41) MUTATED DEL PEAK 28(19Q13.41) WILD-TYPE 
                           0.03                            0.10 
  DEL PEAK 28(19Q13.41) MUTATED DEL PEAK 28(19Q13.41) WILD-TYPE 
                         182.33                          211.17 
  DEL PEAK 28(19Q13.41) MUTATED DEL PEAK 28(19Q13.41) WILD-TYPE 
                          19.89                           18.02 
[1] "0.0 - 182.3 (19.9)" "0.1 - 211.2 (18.0)"
[1] "hr=" "1.6"
D49V2, continuous
D49V3, binary
                                 cls
clus                                0   1
  DEL PEAK 28(19Q13.41) MUTATED   111 136
  DEL PEAK 28(19Q13.41) WILD-TYPE  95 130
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(19Q13.41) MUTATED    111  136
  DEL PEAK 28(19Q13.41) WILD-TYPE   95  130
        clus
vv       DEL PEAK 28(19Q13.41) MUTATED DEL PEAK 28(19Q13.41) WILD-TYPE
  FEMALE                           111                              95
  MALE                             136                             130
[1] 2 2
[1] FALSE
D49V4, continuous
                                 vv
clus                              ASTROCYTOMA OLIGOASTROCYTOMA
  DEL PEAK 28(19Q13.41) MUTATED            50               53
  DEL PEAK 28(19Q13.41) WILD-TYPE         126               65
                                 vv
clus                              OLIGODENDROGLIOMA
  DEL PEAK 28(19Q13.41) MUTATED                 144
  DEL PEAK 28(19Q13.41) WILD-TYPE                34
D49V5, multiclass
                   clus
vv                  DEL PEAK 28(19Q13.41) MUTATED
  ASTROCYTOMA                                  50
  OLIGOASTROCYTOMA                             53
  OLIGODENDROGLIOMA                           144
                   clus
vv                  DEL PEAK 28(19Q13.41) WILD-TYPE
  ASTROCYTOMA                                   126
  OLIGOASTROCYTOMA                               65
  OLIGODENDROGLIOMA                              34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                                 cls
clus                                0   1
  DEL PEAK 28(19Q13.41) MUTATED    45 202
  DEL PEAK 28(19Q13.41) WILD-TYPE  47 178
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(19Q13.41) MUTATED     45  202
  DEL PEAK 28(19Q13.41) WILD-TYPE   47  178
     clus
vv    DEL PEAK 28(19Q13.41) MUTATED DEL PEAK 28(19Q13.41) WILD-TYPE
  NO                             45                              47
  YES                           202                             178
[1] 2 2
[1] FALSE
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(19Q13.41) MUTATED                                  0     6
  DEL PEAK 28(19Q13.41) WILD-TYPE                                1     2
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(19Q13.41) MUTATED                           7   227
  DEL PEAK 28(19Q13.41) WILD-TYPE                         8   210
D49V7, multiclass
                                  clus
vv                                 DEL PEAK 28(19Q13.41) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                      227
                                  clus
vv                                 DEL PEAK 28(19Q13.41) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          2
  BLACK OR AFRICAN AMERICAN                                      8
  WHITE                                                        210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, binary
                                 cls
clus                                0   1
  DEL PEAK 28(19Q13.41) MUTATED     9 221
  DEL PEAK 28(19Q13.41) WILD-TYPE   9 198
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(19Q13.41) MUTATED      9  221
  DEL PEAK 28(19Q13.41) WILD-TYPE    9  198
                        clus
vv                       DEL PEAK 28(19Q13.41) MUTATED
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           221
                        clus
vv                       DEL PEAK 28(19Q13.41) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             198
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 29(19Q13.42) MUTATION ANALYSIS
D50V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 29(19Q13.42) MUTATED   213  40
  DEL PEAK 29(19Q13.42) WILD-TYPE 163  54
  DEL PEAK 29(19Q13.42) MUTATED DEL PEAK 29(19Q13.42) WILD-TYPE 
                            253                             217 
  DEL PEAK 29(19Q13.42) MUTATED DEL PEAK 29(19Q13.42) WILD-TYPE 
                             40                              54 
$`DEL PEAK 29(19Q13.42) MUTATED`
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 
       43.89        18.15        10.62        64.64         0.10         9.96 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 
       17.95         8.48         8.02         6.61       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA 
       75.25        47.93        50.86        50.17        44.52        18.84 
TCGA-DB-A4XB TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q 
       30.21        72.95        31.63        24.20        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L 
       31.40        27.81        29.23        14.40        12.10        11.24 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       19.96        31.82        30.31         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 
       27.81        17.19        17.19        54.25        13.12        14.56 
TCGA-DU-5851 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
       17.46         6.81       182.33        17.49        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6408 
       22.42        75.16        46.06        65.75         1.22       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7014 
        7.96         7.73        62.96       138.28        14.99       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 
       90.77        30.67        94.32        18.94        62.01        60.30 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP 
       41.98         2.76        21.40        16.96        14.17        14.24 
TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R 
       15.12         8.65         2.70        77.98         5.98        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG 
       17.98       124.50        77.88        42.31        23.51        44.42 
TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       50.14        41.13        79.99       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 
      130.78        75.02        14.33         0.23        47.77        34.36 
TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       36.82        24.99        15.35        17.88        22.55        20.61 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A60K 
       16.01        20.09        14.96        38.27        18.71        17.82 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       15.02        16.44        22.26        36.66        48.69        20.45 
TCGA-FG-A87N TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 
       13.58         0.10         6.67        11.54         0.13         0.03 
TCGA-HT-7475 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7601 TCGA-HT-7605 
       17.42        75.19        95.93       172.77         5.03         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7616 
       17.29         3.16        22.06        45.99        56.09         0.23 
TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       14.27        16.24        44.68         0.10        31.69        14.96 
TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7874 
        2.96         6.90        14.53        39.09         0.23        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8105 
        0.33         0.13        35.47         1.64         9.40         6.25 
TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R7 
        5.56         0.23        28.27        15.72        26.04        20.22 
TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HT-A618 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A74K 
        0.07        16.93        16.83        21.40        17.52        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7495 
       11.05         0.10        29.92        19.89        40.18         4.31 
TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV 
       21.60        17.82        20.35        42.77        14.40         0.23 
TCGA-P5-A5EX TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72Z 
        1.64         2.30         4.11         7.63         1.28        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        0.20         9.01        15.16        12.62        15.85        14.04 
TCGA-QH-A6CU TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
       14.83         2.20         9.17        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        1.91        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A83Z TCGA-RY-A840 TCGA-RY-A845 
       59.38        30.87         5.46         9.90        28.08        19.59 
TCGA-RY-A847 TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       30.67        18.77        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       22.95        23.64        32.61       106.39        69.50        72.59 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7IQ 
       32.45        84.99        31.10        15.91        15.16        36.13 
TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        7.92        23.51         8.19         2.04        17.03        15.06 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C5 
       28.37        13.02       169.84        31.59        18.71        49.32 
TCGA-TM-A84B TCGA-TM-A84G TCGA-TM-A84J TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       24.92        40.64        24.16        24.79        33.24        25.38 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       18.61        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VV-A829 TCGA-VW-A7QS TCGA-W9-A837 
       13.51         0.10        35.93        37.05        23.21        51.06 
TCGA-WY-A858 
       43.96 

$`DEL PEAK 29(19Q13.42) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 
        4.70         7.69        40.18        21.01         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5276 TCGA-DB-5280 
       23.84        12.43         7.56         7.40        72.92        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       78.28        46.42        46.72        39.78        37.45        33.57 
TCGA-DB-A64O TCGA-DB-A64S TCGA-DB-A64X TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       25.48        27.45        18.51        17.88        30.74        16.18 
TCGA-DH-5143 TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5852 
       14.40        13.38         3.45        18.61        18.02         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5871 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6401 
       13.38         8.45        18.94       211.17        49.02        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7019 
       11.47       156.23       105.21         6.54         8.84        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-8158 
       10.36         7.96        44.02        25.91        23.31         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TR 
       23.74        14.60        20.68        19.13        15.48        12.59 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A76K 
        4.96         3.65         5.65        12.20         7.23        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5307 
       26.76         7.13         7.50         0.56        67.46        57.93 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-6688 
       32.45        36.82        32.35         0.20        25.48        18.77 
TCGA-FG-6689 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       14.93        23.97        18.44        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MY 
       14.24        22.52        32.61        10.72        18.38        23.70 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A87Q TCGA-FN-7833 
       14.76        16.41        28.54        10.78         5.72        27.52 
TCGA-HT-7470 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       40.11        16.54         3.75         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
       40.34       106.95         4.01        29.85        23.18       122.47 
TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7690 
       57.60         0.16         0.76         6.05        42.74         0.10 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 
        0.10        17.52        39.48        19.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
       23.61         3.68         5.33         3.72        11.28        31.43 
TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24        63.55         0.10        37.87        33.01        12.23 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 
        0.10         0.46         2.50        13.78        29.59        34.19 
TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
        0.23         0.13        27.35         0.10         5.33         2.70 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HW-7489 
        1.81        16.14        17.65         2.43        10.52         8.32 
TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL 
       19.23        35.90        21.70        19.59        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5F1 
       20.71        19.00        14.40         6.71         2.37         5.88 
TCGA-P5-A5F4 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A733 TCGA-QH-A65S 
        0.76         0.16        10.42        13.25        13.61         2.53 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6X3 TCGA-QH-A6XA 
       19.33        14.53        13.61        12.23        10.29        16.50 
TCGA-QH-A6XC TCGA-RY-A843 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6U1 TCGA-S9-A6U6 
        5.03         2.07        62.17        87.12        17.62        16.08 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WM TCGA-S9-A6WO 
       98.24        95.93         5.85        80.12        19.86        18.61 
TCGA-S9-A6WQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QX TCGA-S9-A7R2 
       14.07        22.32         7.13        20.02        13.12        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       99.06        30.05        98.63        11.97        49.45        48.33 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I 
       34.78        48.39        16.18        59.05        30.44        28.08 
TCGA-TM-A84L TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A8FI 
       40.83        30.08         7.89        23.47        16.01         8.05 
TCGA-WH-A86K TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       13.32        39.88        43.40        45.80        46.88        37.71 
TCGA-WY-A85E 
       20.81 

  DEL PEAK 29(19Q13.42) MUTATED DEL PEAK 29(19Q13.42) WILD-TYPE 
                           0.03                            0.10 
  DEL PEAK 29(19Q13.42) MUTATED DEL PEAK 29(19Q13.42) WILD-TYPE 
                         182.33                          211.17 
  DEL PEAK 29(19Q13.42) MUTATED DEL PEAK 29(19Q13.42) WILD-TYPE 
                          20.09                           17.65 
[1] "0.0 - 182.3 (20.1)" "0.1 - 211.2 (17.6)"
[1] "hr=" "2"  
D50V2, continuous
D50V3, binary
                                 cls
clus                                0   1
  DEL PEAK 29(19Q13.42) MUTATED   113 142
  DEL PEAK 29(19Q13.42) WILD-TYPE  93 124
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.42) MUTATED    113  142
  DEL PEAK 29(19Q13.42) WILD-TYPE   93  124
        clus
vv       DEL PEAK 29(19Q13.42) MUTATED DEL PEAK 29(19Q13.42) WILD-TYPE
  FEMALE                           113                              93
  MALE                             142                             124
[1] 2 2
[1] FALSE
D50V4, continuous
                                 vv
clus                              ASTROCYTOMA OLIGOASTROCYTOMA
  DEL PEAK 29(19Q13.42) MUTATED            53               57
  DEL PEAK 29(19Q13.42) WILD-TYPE         123               61
                                 vv
clus                              OLIGODENDROGLIOMA
  DEL PEAK 29(19Q13.42) MUTATED                 145
  DEL PEAK 29(19Q13.42) WILD-TYPE                33
D50V5, multiclass
                   clus
vv                  DEL PEAK 29(19Q13.42) MUTATED
  ASTROCYTOMA                                  53
  OLIGOASTROCYTOMA                             57
  OLIGODENDROGLIOMA                           145
                   clus
vv                  DEL PEAK 29(19Q13.42) WILD-TYPE
  ASTROCYTOMA                                   123
  OLIGOASTROCYTOMA                               61
  OLIGODENDROGLIOMA                              33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                                 cls
clus                                0   1
  DEL PEAK 29(19Q13.42) MUTATED    48 207
  DEL PEAK 29(19Q13.42) WILD-TYPE  44 173
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.42) MUTATED     48  207
  DEL PEAK 29(19Q13.42) WILD-TYPE   44  173
     clus
vv    DEL PEAK 29(19Q13.42) MUTATED DEL PEAK 29(19Q13.42) WILD-TYPE
  NO                             48                              44
  YES                           207                             173
[1] 2 2
[1] FALSE
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(19Q13.42) MUTATED                                  0     6
  DEL PEAK 29(19Q13.42) WILD-TYPE                                1     2
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(19Q13.42) MUTATED                           7   234
  DEL PEAK 29(19Q13.42) WILD-TYPE                         8   203
D50V7, multiclass
                                  clus
vv                                 DEL PEAK 29(19Q13.42) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                      234
                                  clus
vv                                 DEL PEAK 29(19Q13.42) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          2
  BLACK OR AFRICAN AMERICAN                                      8
  WHITE                                                        203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, binary
                                 cls
clus                                0   1
  DEL PEAK 29(19Q13.42) MUTATED     9 228
  DEL PEAK 29(19Q13.42) WILD-TYPE   9 191
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.42) MUTATED      9  228
  DEL PEAK 29(19Q13.42) WILD-TYPE    9  191
                        clus
vv                       DEL PEAK 29(19Q13.42) MUTATED
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           228
                        clus
vv                       DEL PEAK 29(19Q13.42) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             191
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 30(22Q13.31) MUTATION ANALYSIS
D51V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 30(22Q13.31) MUTATED    42  26
  DEL PEAK 30(22Q13.31) WILD-TYPE 334  68
  DEL PEAK 30(22Q13.31) MUTATED DEL PEAK 30(22Q13.31) WILD-TYPE 
                             68                             402 
  DEL PEAK 30(22Q13.31) MUTATED DEL PEAK 30(22Q13.31) WILD-TYPE 
                             26                              68 
$`DEL PEAK 30(22Q13.31) MUTATED`
TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-5397 TCGA-CS-6186 TCGA-DB-5273 TCGA-DB-5277 
       18.15        40.18         6.38        17.69        81.96        50.86 
TCGA-DB-A4XB TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A75O TCGA-DH-A669 TCGA-DU-5847 
       30.21        24.20        25.48        30.74        30.21        18.02 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-6399 TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-7007 
        6.74        13.38        65.75         7.04       133.74        62.96 
TCGA-DU-7008 TCGA-DU-7290 TCGA-DU-7298 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 
      156.23        10.36        18.94        41.98         5.10        23.74 
TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY 
       19.13        15.48        14.24         4.96         3.65        12.20 
TCGA-DU-A76K TCGA-DU-A76L TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5322 TCGA-FG-7643 
       11.41        26.76        67.46        41.13       130.78        20.09 
TCGA-FG-A4MY TCGA-FG-A60L TCGA-HT-7477 TCGA-HT-7611 TCGA-HT-7686 TCGA-HT-7688 
       23.70        16.41        24.26        57.60        42.74        31.69 
TCGA-HT-7690 TCGA-HT-7860 TCGA-HT-A614 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B 
        0.10         0.49         2.70        16.14        16.83        17.52 
TCGA-HT-A74H TCGA-HW-A5KK TCGA-P5-A5F6 TCGA-P5-A72U TCGA-QH-A6CS TCGA-RY-A83Z 
        2.43        12.76         1.28         0.16        19.33         9.90 
TCGA-S9-A6TS TCGA-S9-A6UA TCGA-S9-A7IX TCGA-S9-A7J0 TCGA-S9-A7R2 TCGA-S9-A7R7 
       62.17         5.85        22.32        20.02        10.39        98.63 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A84B TCGA-TM-A84G TCGA-TQ-A7RW TCGA-VM-A8CD 
       18.71        11.97        24.92        40.64        26.99         7.89 
TCGA-WH-A86K TCGA-WY-A859 
       13.32        39.88 

$`DEL PEAK 30(22Q13.31) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 
        4.70         7.69        43.89        10.62        64.64         0.10 
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 
       21.01         9.96        23.84        17.95        12.43         8.48 
TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5274 
        7.56         8.02         7.40         6.61       122.73        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       47.93        72.92        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       46.42        18.84        46.72        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       72.95        31.63        30.12         5.98        31.40        27.45 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        29.23        14.40        18.51        12.10        11.24 
TCGA-DB-A75M TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       17.88        16.18        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
        8.02        42.05        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 
       13.12        13.38         3.45        18.61        14.56        17.46 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        1.22        87.45        11.64        19.89        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7009 TCGA-DU-7010 
      114.08         7.96         7.73        11.47       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
       26.30         7.96        94.32        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       60.30        23.31         2.76        14.60        20.68        21.40 
TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S2 
       16.96        14.17        12.59        15.12         5.65         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R 
        2.70        77.98         7.23         5.98         7.13        21.30 
TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD 
       17.98       124.50        77.88        42.31        23.51         7.50 
TCGA-DU-A7TG TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       44.42         0.56        50.14        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 
       78.21        95.57        75.02        32.45        36.82        32.35 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        25.48        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       36.82        18.77        14.93        24.99        23.97        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 
       15.35        17.88        22.55        20.61        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        32.61 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K 
       38.27        10.72        18.38        18.71        14.76        17.82 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        22.26        28.54        10.78        36.66 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       48.69        20.45        13.58         5.72        27.52         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67        11.54        40.11         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54         6.38        40.34        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       95.93       106.95       172.77         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       122.47         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       45.99        56.09         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7691 
        0.76        44.68         6.05         0.10        14.96         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
       39.09         0.23        50.63        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33        35.47         3.72        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       37.87        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         5.56        13.78         0.23        29.59        34.19 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       28.27        15.72         0.23        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 
        0.07        27.35         0.10         5.33        16.93         1.81 
TCGA-HT-A619 TCGA-HT-A61C TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       21.40        17.65        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        19.89         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77        14.40        14.40 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z 
        5.88         7.63         0.76        10.42        13.25        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        0.20         9.01        13.61        15.16         2.53        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX 
       15.85        14.04        14.83        14.53        13.61        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         9.17        10.29        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91        16.50         5.03        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 
       94.03        32.65        59.38        30.87         5.46        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
        2.07        19.59        30.67        87.12        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        28.70        22.95        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD 
       32.61        16.08        98.24        95.93       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        31.10        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91        18.61        15.16        14.07        36.13         7.92 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       23.51         7.13         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 
       13.12        28.37        13.02       169.84        99.06        30.05 
TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       31.59        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       16.18        59.05        30.44        28.08        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RH TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       15.98        43.04        30.08        13.51         0.10        35.93 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 
       23.47        37.05        16.01        23.21         8.05        51.06 
TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       43.96        43.40        45.80        46.88        37.71        20.81 

  DEL PEAK 30(22Q13.31) MUTATED DEL PEAK 30(22Q13.31) WILD-TYPE 
                           0.10                            0.03 
  DEL PEAK 30(22Q13.31) MUTATED DEL PEAK 30(22Q13.31) WILD-TYPE 
                         156.23                          211.17 
  DEL PEAK 30(22Q13.31) MUTATED DEL PEAK 30(22Q13.31) WILD-TYPE 
                         19.035                          18.610 
[1] "0.1 - 156.2 (19.0)" "0.0 - 211.2 (18.6)"
[1] "hr=" "2.2"
D51V2, continuous
D51V3, binary
                                 cls
clus                                0   1
  DEL PEAK 30(22Q13.31) MUTATED    27  41
  DEL PEAK 30(22Q13.31) WILD-TYPE 179 225
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(22Q13.31) MUTATED     27   41
  DEL PEAK 30(22Q13.31) WILD-TYPE  179  225
        clus
vv       DEL PEAK 30(22Q13.31) MUTATED DEL PEAK 30(22Q13.31) WILD-TYPE
  FEMALE                            27                             179
  MALE                              41                             225
[1] 2 2
[1] FALSE
D51V4, continuous
                                 vv
clus                              ASTROCYTOMA OLIGOASTROCYTOMA
  DEL PEAK 30(22Q13.31) MUTATED            39               13
  DEL PEAK 30(22Q13.31) WILD-TYPE         137              105
                                 vv
clus                              OLIGODENDROGLIOMA
  DEL PEAK 30(22Q13.31) MUTATED                  16
  DEL PEAK 30(22Q13.31) WILD-TYPE               162
D51V5, multiclass
                   clus
vv                  DEL PEAK 30(22Q13.31) MUTATED
  ASTROCYTOMA                                  39
  OLIGOASTROCYTOMA                             13
  OLIGODENDROGLIOMA                            16
                   clus
vv                  DEL PEAK 30(22Q13.31) WILD-TYPE
  ASTROCYTOMA                                   137
  OLIGOASTROCYTOMA                              105
  OLIGODENDROGLIOMA                             162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                                 cls
clus                                0   1
  DEL PEAK 30(22Q13.31) MUTATED    15  53
  DEL PEAK 30(22Q13.31) WILD-TYPE  77 327
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(22Q13.31) MUTATED     15   53
  DEL PEAK 30(22Q13.31) WILD-TYPE   77  327
     clus
vv    DEL PEAK 30(22Q13.31) MUTATED DEL PEAK 30(22Q13.31) WILD-TYPE
  NO                             15                              77
  YES                            53                             327
[1] 2 2
[1] FALSE
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(22Q13.31) MUTATED                                  1     0
  DEL PEAK 30(22Q13.31) WILD-TYPE                                0     8
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(22Q13.31) MUTATED                           1    66
  DEL PEAK 30(22Q13.31) WILD-TYPE                        14   371
D51V7, multiclass
                                  clus
vv                                 DEL PEAK 30(22Q13.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    1
  WHITE                                                       66
                                  clus
vv                                 DEL PEAK 30(22Q13.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     14
  WHITE                                                        371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, binary
                                 cls
clus                                0   1
  DEL PEAK 30(22Q13.31) MUTATED     2  60
  DEL PEAK 30(22Q13.31) WILD-TYPE  16 359
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(22Q13.31) MUTATED      2   60
  DEL PEAK 30(22Q13.31) WILD-TYPE   16  359
                        clus
vv                       DEL PEAK 30(22Q13.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            60
                        clus
vv                       DEL PEAK 30(22Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                  16
  NOT HISPANIC OR LATINO                             359
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 31(XQ21.1) MUTATION ANALYSIS
D52V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 31(XQ21.1) MUTATED    45  20
  DEL PEAK 31(XQ21.1) WILD-TYPE 331  74
  DEL PEAK 31(XQ21.1) MUTATED DEL PEAK 31(XQ21.1) WILD-TYPE 
                           65                           405 
  DEL PEAK 31(XQ21.1) MUTATED DEL PEAK 31(XQ21.1) WILD-TYPE 
                           20                            74 
$`DEL PEAK 31(XQ21.1) MUTATED`
TCGA-CS-6665 TCGA-CS-6667 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XF 
       12.43         7.56        47.93        50.86        44.52        33.57 
TCGA-DB-A4XH TCGA-DB-A64W TCGA-DH-5140 TCGA-DU-5847 TCGA-DU-6404 TCGA-DU-6410 
       31.63        14.40        19.96        18.02       133.74         7.96 
TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-8158 
       11.47       156.23        14.99        30.67        94.32         5.10 
TCGA-DU-8168 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T6 TCGA-E1-5302 TCGA-E1-5311 
       14.17         5.98        21.30        17.98        50.14       134.27 
TCGA-E1-A7YV TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5964 TCGA-FG-A6IZ TCGA-FG-A6J3 
       32.45        14.33         0.23        34.36        15.02        22.26 
TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7616 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7692 
       11.54         0.13         0.23        31.69         0.10         2.96 
TCGA-HT-A61B TCGA-HW-7491 TCGA-HW-8321 TCGA-IK-7675 TCGA-KT-A74X TCGA-P5-A5F2 
       17.52        40.18        19.59        19.00        14.40         7.63 
TCGA-P5-A5F6 TCGA-P5-A72Z TCGA-QH-A65Z TCGA-QH-A6CX TCGA-QH-A6X4 TCGA-QH-A6X8 
        1.28        11.64        14.04        12.23        14.53        16.73 
TCGA-QH-A6X9 TCGA-RY-A83Z TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6WP TCGA-S9-A7IS 
        1.91         9.90        87.12        18.77        15.16         7.92 
TCGA-S9-A7QW TCGA-S9-A89Z TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84I TCGA-TQ-A7RW 
       15.06        11.97        49.32        48.39        28.08        26.99 
TCGA-VM-A8C8 TCGA-VM-A8CD TCGA-VV-A829 TCGA-WH-A86K TCGA-WY-A859 
       43.04         7.89        37.05        13.32        39.88 

$`DEL PEAK 31(XQ21.1) WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       23.84        17.95         8.48         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5280 
      122.73        81.96        75.25        72.92        50.17        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       78.28        46.42        18.84        30.21        46.72        39.78 
TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       37.45        72.95        24.20        25.48        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64X TCGA-DB-A75K 
       31.40        27.45        27.81        29.23        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5142 
       11.24        17.88        30.74        16.18        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        13.12        13.38         3.45        18.61 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
       87.45         7.04        11.64        19.89        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
      114.08         7.73        62.96       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84       117.40        90.77        26.30        10.36         7.96 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       41.98         2.76        23.74        14.60        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       19.13        16.96        15.48        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 
       77.98         7.23        11.41        26.76         7.13       124.50 
TCGA-DU-A7TA TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TD TCGA-DU-A7TG TCGA-DU-A7TJ 
       77.88        42.31        23.51         7.50        44.42         0.56 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 TCGA-E1-5319 
       67.46        41.13        79.99        57.93        78.21        95.57 
TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O4 TCGA-FG-5962 
      130.78        75.02        36.82        32.35         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       25.48        36.82        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       18.44        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        32.61        38.27        10.72        18.38        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6J1 TCGA-FG-A70Y 
       23.70        14.76        17.82        16.41        16.44        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        36.66        48.69        20.45        13.58         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 
       27.52         0.10         6.67        40.11         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38        40.34 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        95.93       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       122.47         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 
       22.06        45.99        56.09        57.60        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
       14.96         0.10        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33        35.47 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        3.72        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        37.87        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         5.56        13.78         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59        34.19        28.27        15.72         0.23        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        20.22         0.07        27.35         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A619 
        2.70        16.93         1.81        16.14        16.83        21.40 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       17.65         2.43        10.52        15.35        11.05         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 
       29.92        19.89         8.32        19.23        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.70        21.60        17.82        20.35        12.76        20.81 
TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       20.71        42.77        14.40         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F4 TCGA-P5-A72U 
        2.37         2.30         4.11         5.88         0.76         0.16 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65R 
       10.42        13.25         0.20         9.01        13.61        15.16 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
        2.53        12.62        15.85        19.33        14.83        14.53 
TCGA-QH-A6CW TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X5 TCGA-QH-A6XA 
       13.61         2.20         9.17        10.29        16.34        16.50 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03        11.08        12.99        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 
       59.38        30.87         5.46        28.08         2.07        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       30.67        62.17        37.84        34.49        31.33        28.70 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       22.95        17.62        23.64        32.61        16.08        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       95.93         5.85       106.39        69.50        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        31.10        19.86        15.91        18.61 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.07        36.13        22.32        23.51         7.13        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        8.19         2.04        17.03        13.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      169.84        10.39        99.06        30.05        98.63        31.59 
TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C 
       18.71        49.45        48.33        34.78        24.92        16.18 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       59.05        40.64        30.44        24.16        40.83        24.79 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH 
       33.24        25.38        18.61        14.93        23.80        15.98 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A86M 
       30.08        13.51         0.10        35.93        23.47        16.01 
TCGA-VW-A7QS TCGA-VW-A8FI TCGA-W9-A837 TCGA-WY-A858 TCGA-WY-A85A TCGA-WY-A85B 
       23.21         8.05        51.06        43.96        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

  DEL PEAK 31(XQ21.1) MUTATED DEL PEAK 31(XQ21.1) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK 31(XQ21.1) MUTATED DEL PEAK 31(XQ21.1) WILD-TYPE 
                       156.23                        211.17 
  DEL PEAK 31(XQ21.1) MUTATED DEL PEAK 31(XQ21.1) WILD-TYPE 
                        16.73                         18.84 
[1] "0.1 - 156.2 (16.7)" "0.0 - 211.2 (18.8)"
[1] "hr=" "1.7"
D52V2, continuous
D52V3, binary
                               cls
clus                              0   1
  DEL PEAK 31(XQ21.1) MUTATED    31  35
  DEL PEAK 31(XQ21.1) WILD-TYPE 175 231
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 31(XQ21.1) MUTATED     31   35
  DEL PEAK 31(XQ21.1) WILD-TYPE  175  231
        clus
vv       DEL PEAK 31(XQ21.1) MUTATED DEL PEAK 31(XQ21.1) WILD-TYPE
  FEMALE                          31                           175
  MALE                            35                           231
[1] 2 2
[1] FALSE
D52V4, continuous
                               vv
clus                            ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  DEL PEAK 31(XQ21.1) MUTATED            25               13                28
  DEL PEAK 31(XQ21.1) WILD-TYPE         151              105               150
D52V5, multiclass
                   clus
vv                  DEL PEAK 31(XQ21.1) MUTATED DEL PEAK 31(XQ21.1) WILD-TYPE
  ASTROCYTOMA                                25                           151
  OLIGOASTROCYTOMA                           13                           105
  OLIGODENDROGLIOMA                          28                           150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                               cls
clus                              0   1
  DEL PEAK 31(XQ21.1) MUTATED    13  53
  DEL PEAK 31(XQ21.1) WILD-TYPE  79 327
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 31(XQ21.1) MUTATED     13   53
  DEL PEAK 31(XQ21.1) WILD-TYPE   79  327
     clus
vv    DEL PEAK 31(XQ21.1) MUTATED DEL PEAK 31(XQ21.1) WILD-TYPE
  NO                           13                            79
  YES                          53                           327
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(XQ21.1) MUTATED                                  0     1
  DEL PEAK 31(XQ21.1) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(XQ21.1) MUTATED                           0    64
  DEL PEAK 31(XQ21.1) WILD-TYPE                        15   373
D52V7, multiclass
                                  clus
vv                                 DEL PEAK 31(XQ21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     64
                                  clus
vv                                 DEL PEAK 31(XQ21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   15
  WHITE                                                      373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V8, binary
                               cls
clus                              0   1
  DEL PEAK 31(XQ21.1) MUTATED     2  59
  DEL PEAK 31(XQ21.1) WILD-TYPE  16 360
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 31(XQ21.1) MUTATED      2   59
  DEL PEAK 31(XQ21.1) WILD-TYPE   16  360
                        clus
vv                       DEL PEAK 31(XQ21.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          59
                        clus
vv                       DEL PEAK 31(XQ21.1) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           360
[1] 2 2
[1] FALSE
