[1] "ofn"        "-oTKIRC-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/KIRC-TP/19775258/KIRC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRC-TP/19781826/transformed.cor.cli.txt"

nPatients in clinical file=537, in cluster file=528, common to both=528
[1]  30 528
[1] "AMP PEAK  1(1Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE 
                           62                           466 
  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE 
                           62                           466 
[1] "AMP PEAK  2(1Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           62                           466 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           62                           466 
[1] "AMP PEAK  3(3Q26.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                            87                            441 
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                            87                            441 
[1] "AMP PEAK  4(4Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE 
                           16                           512 
  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE 
                           16                           512 
[1] "AMP PEAK  5(5Q35.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE 
                          332                           196 
  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE 
                          332                           196 
[1] "AMP PEAK  6(7Q36.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE 
                          176                           352 
  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE 
                          176                           352 
[1] "AMP PEAK  7(8Q24.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE 
                            79                            449 
  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE 
                            79                            449 
[1] "AMP PEAK  8(10P14) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE 
                          20                          508 
  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE 
                          20                          508 
[1] "AMP PEAK  9(XP22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE 
                           31                           497 
  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE 
                           31                           497 
[1] "AMP PEAK 10(XP11.4) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE 
                           33                           495 
  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE 
                           33                           495 
[1] "AMP PEAK 11(XQ11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE 
                           29                           499 
  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE 
                           29                           499 
[1] "AMP PEAK 12(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                         37                         491 
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                         37                         491 
[1] "DEL PEAK  1(1P36.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                           103                            425 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                           103                            425 
[1] "DEL PEAK  2(1P31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                           77                           451 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                           77                           451 
[1] "DEL PEAK  3(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         42                         486 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         42                         486 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           50                           478 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           50                           478 
[1] "DEL PEAK  5(3P26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                          455                            73 
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                          455                            73 
[1] "DEL PEAK  6(3P22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P22.2) MUTATED DEL PEAK  6(3P22.2) WILD-TYPE 
                          465                            63 
  DEL PEAK  6(3P22.2) MUTATED DEL PEAK  6(3P22.2) WILD-TYPE 
                          465                            63 
[1] "DEL PEAK  7(3P14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE 
                          373                           155 
  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE 
                          373                           155 
[1] "DEL PEAK  8(3P12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE 
                          305                           223 
  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE 
                          305                           223 
[1] "DEL PEAK  9(3Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3Q11.2) MUTATED DEL PEAK  9(3Q11.2) WILD-TYPE 
                          161                           367 
  DEL PEAK  9(3Q11.2) MUTATED DEL PEAK  9(3Q11.2) WILD-TYPE 
                          161                           367 
[1] "DEL PEAK 10(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                           78                           450 
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                           78                           450 
[1] "DEL PEAK 11(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                        151                         377 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                        151                         377 
[1] "DEL PEAK 12(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        151                         377 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        151                         377 
[1] "DEL PEAK 13(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                          154                           374 
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                          154                           374 
[1] "DEL PEAK 14(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                        152                         376 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                        152                         376 
[1] "DEL PEAK 15(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                          159                           369 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                          159                           369 
[1] "DEL PEAK 16(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             96                             432 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             96                             432 
[1] "DEL PEAK 17(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                            82                            446 
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                            82                            446 
[1] "DEL PEAK 18(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                           228                            300 
  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                           228                            300 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 528 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=165,	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=357,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=38,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "134"   "2"    
freq.contrast "2"     "134"  
both >= 3     "FALSE" "FALSE"
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 528 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "KARNOFSKY_PERFORMANCE_SCORE"   "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RACE"                         
[11] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=59, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
268  69 180  11 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
268  69 180  11 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
268  69 180  11 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
268  69 180  11 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=6, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=13, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=10, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q24.1) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1Q24.1) MUTATED    33  29
  AMP PEAK  1(1Q24.1) WILD-TYPE 318 146
  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE 
                           62                           464 
  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE 
                           29                           146 
$`AMP PEAK  1(1Q24.1) MUTATED`
TCGA-A3-3316 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3430 
       49.08        34.29        31.07        24.16        18.87        15.78 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4713 TCGA-B0-4815 TCGA-B0-4819 
       49.28        28.73        22.45         6.64        52.21         6.02 
TCGA-B0-4838 TCGA-B0-4848 TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5096 TCGA-B0-5109 
       27.42        29.03         7.30        15.09         2.24        19.30 
TCGA-B0-5115 TCGA-B0-5706 TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-5551 TCGA-BP-4161 
       52.73       105.37         0.36        23.31         0.53        90.28 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4329 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4352 
       61.78        64.27        27.78        80.68        74.17        11.31 
TCGA-BP-4756 TCGA-BP-4765 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4781 TCGA-BP-4974 
       12.30        71.80        13.15         5.33        68.38         6.90 
TCGA-BP-4986 TCGA-BP-5173 TCGA-BP-5175 TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4640 
       25.81         1.74        30.64        46.55        14.17       114.41 
TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4916 TCGA-CJ-4923 TCGA-CJ-5675 
       74.27        64.27        66.21        45.14        18.81       129.40 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-6027 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6090 
       18.87        22.32       118.85        73.18        78.18        83.90 
TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-5452 TCGA-CZ-5454 
       18.77        46.16        69.21        58.75        58.82        23.74 
TCGA-G6-A5PC TCGA-MM-A564 
        7.96        19.96 

$`AMP PEAK  1(1Q24.1) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 
       38.99        38.47        37.38        48.82        62.01         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 
       53.29        43.20        55.76        20.71        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
       73.08       109.41        73.68       112.08        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
       94.19        46.78        48.36        78.64        40.01        94.29 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       83.21        37.58        38.40        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       40.70         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        3.48        28.47        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        7.82         5.98         2.14        19.73        57.70        43.96 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       45.30        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       65.29        39.45        26.07         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.24        11.90        25.32        18.51 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       90.87        90.48        52.54        30.48        58.59        66.05 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       38.63        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5709 
      126.28        80.91        71.41        73.84       149.16       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       24.82        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5844 
        5.10         0.85         0.53         4.64         5.46         0.23 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        50.14        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
       48.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 
       14.17       111.02        85.51        94.72       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4330 
       62.24        54.90        97.45        53.42         3.58        62.07 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 
       31.89        12.33        33.99        31.33        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4769 
       77.62         5.98        44.15        41.75        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
       10.82        61.97        60.59        13.51        56.91        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        31.30        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       74.20        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4642 
      115.00        63.25        73.22       106.16        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
       10.72        75.06       116.84        71.87        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4918 
       49.18        49.28        50.33        54.48        38.56         3.06 
TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5680 
        4.57       131.08        72.00       133.71        25.71        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5591 
       92.02        81.83         5.39        85.78        66.31        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 
        1.35       105.93       103.43        25.45         0.59        47.08 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
        6.77        14.66       107.54        63.39        93.04         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       61.41        63.42        79.53        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       69.96        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX 
       11.67        37.15        66.28        56.84        23.90        53.46 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       12.00        81.21        18.12         3.91         6.77         4.18 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A84U 
       10.29        70.13        35.87         2.01        19.43        23.01 
TCGA-MW-A4EC TCGA-T7-A92I 
       16.37        11.70 

  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE 
                         0.36                          0.07 
  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE 
                       129.40                        149.16 
  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE 
                       28.880                        38.845 
[1] "0.4 - 129.4 (28.9)" "0.1 - 149.2 (38.8)"
[1] "hr=" "1.6"
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  1(1Q24.1) MUTATED        23       10        16       13
  AMP PEAK  1(1Q24.1) WILD-TYPE     240       47       109       70
D1V3, multiclass
           clus
vv          AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE
  STAGE I                            23                           240
  STAGE II                           10                            47
  STAGE III                          16                           109
  STAGE IV                           13                            70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  1(1Q24.1) MUTATED    25  13  24   0
  AMP PEAK  1(1Q24.1) WILD-TYPE 243  56 156  11
D1V4, multiclass
    clus
vv   AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE
  T1                          25                           243
  T2                          13                            56
  T3                          24                           156
  T4                           0                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q24.1) MUTATED    29   5
  AMP PEAK  1(1Q24.1) WILD-TYPE 205  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.1) MUTATED     29    5
  AMP PEAK  1(1Q24.1) WILD-TYPE  205   12
   clus
vv  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE
  0                          29                           205
  1                           5                            12
[1] 2 2
[1] FALSE
D1V6, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q24.1) MUTATED    48  13
  AMP PEAK  1(1Q24.1) WILD-TYPE 370  65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.1) MUTATED     48   13
  AMP PEAK  1(1Q24.1) WILD-TYPE  370   65
   clus
vv  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE
  0                          48                           370
  1                          13                            65
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q24.1) MUTATED    20  42
  AMP PEAK  1(1Q24.1) WILD-TYPE 169 297
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.1) MUTATED     20   42
  AMP PEAK  1(1Q24.1) WILD-TYPE  169  297
        clus
vv       AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE
  FEMALE                          20                           169
  MALE                            42                           297
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
[1] "Remove cluster labels:"      "AMP PEAK  1(1Q24.1) MUTATED"
clus
  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE 
                            1                            20 
                   TCGA-A3-A8CQ                    TCGA-A3-A8OV 
"AMP PEAK  1(1Q24.1) WILD-TYPE" "AMP PEAK  1(1Q24.1) WILD-TYPE" 
                   TCGA-A3-A8OW                    TCGA-AK-3445 
"AMP PEAK  1(1Q24.1) WILD-TYPE" "AMP PEAK  1(1Q24.1) WILD-TYPE" 
                   TCGA-AK-3451                    TCGA-B2-A4SR 
"AMP PEAK  1(1Q24.1) WILD-TYPE" "AMP PEAK  1(1Q24.1) WILD-TYPE" 
                   TCGA-B8-4146                    TCGA-B8-4621 
"AMP PEAK  1(1Q24.1) WILD-TYPE" "AMP PEAK  1(1Q24.1) WILD-TYPE" 
                   TCGA-B8-5158                    TCGA-B8-5164 
"AMP PEAK  1(1Q24.1) WILD-TYPE" "AMP PEAK  1(1Q24.1) WILD-TYPE" 
                   TCGA-B8-5550                    TCGA-B8-A54E 
"AMP PEAK  1(1Q24.1) WILD-TYPE" "AMP PEAK  1(1Q24.1) WILD-TYPE" 
                   TCGA-B8-A54F                    TCGA-B8-A54G 
"AMP PEAK  1(1Q24.1) WILD-TYPE" "AMP PEAK  1(1Q24.1) WILD-TYPE" 
                   TCGA-B8-A8YJ                    TCGA-DV-A4VX 
"AMP PEAK  1(1Q24.1) WILD-TYPE" "AMP PEAK  1(1Q24.1) WILD-TYPE" 
                   TCGA-DV-A4W0                    TCGA-G6-A8L7 
"AMP PEAK  1(1Q24.1) WILD-TYPE" "AMP PEAK  1(1Q24.1) WILD-TYPE" 
                   TCGA-MM-A563                    TCGA-T7-A92I 
"AMP PEAK  1(1Q24.1) WILD-TYPE" "AMP PEAK  1(1Q24.1) WILD-TYPE" 
D1V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q24.1) MUTATED       1                         4    57
  AMP PEAK  1(1Q24.1) WILD-TYPE     7                        52   400
D1V11, multiclass
                           clus
vv                          AMP PEAK  1(1Q24.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              57
                           clus
vv                          AMP PEAK  1(1Q24.1) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            52
  WHITE                                               400
[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"
D1V12, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q24.1) MUTATED     4  39
  AMP PEAK  1(1Q24.1) WILD-TYPE  22 311
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.1) MUTATED      4   39
  AMP PEAK  1(1Q24.1) WILD-TYPE   22  311
                        clus
vv                       AMP PEAK  1(1Q24.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          39
                        clus
vv                       AMP PEAK  1(1Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                22
  NOT HISPANIC OR LATINO                           311
[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    34  28
  AMP PEAK  2(1Q32.1) WILD-TYPE 317 147
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           62                           464 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           28                           147 
$`AMP PEAK  2(1Q32.1) MUTATED`
TCGA-A3-3316 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3430 
       49.08        34.29        31.07        24.16        18.87        15.78 
TCGA-AK-3450 TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4815 TCGA-B0-4819 
       49.28        22.45        43.96         6.64        52.21         6.02 
TCGA-B0-4838 TCGA-B0-4848 TCGA-B0-5092 TCGA-B0-5096 TCGA-B0-5109 TCGA-B0-5115 
       27.42        29.03        15.09         2.24        19.30        52.73 
TCGA-B0-5701 TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-5551 TCGA-BP-4161 TCGA-BP-4174 
       80.91         0.36        23.31         0.53        90.28        61.78 
TCGA-BP-4176 TCGA-BP-4329 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4352 TCGA-BP-4756 
       64.27        27.78        80.68        74.17        11.31        12.30 
TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4781 TCGA-BP-4963 TCGA-BP-4971 TCGA-BP-4974 
       13.15         5.33        68.38        60.30        48.89         6.90 
TCGA-BP-4975 TCGA-BP-4986 TCGA-BP-5173 TCGA-BP-5175 TCGA-CJ-4635 TCGA-CJ-4640 
       47.11        25.81         1.74        30.64        46.55       114.41 
TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4895 TCGA-CJ-4916 TCGA-CJ-4923 
       74.27        64.27        66.21        39.45        45.14        18.81 
TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-6027 TCGA-CJ-6032 TCGA-CW-5587 
      129.40        18.87        22.32       118.85       119.64        73.18 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-5452 
       83.90        18.77        46.16        69.21        58.75        58.82 
TCGA-G6-A5PC TCGA-MM-A564 
        7.96        19.96 

$`AMP PEAK  2(1Q32.1) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 
       38.99        38.47        37.38        48.82        62.01         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 
       53.29        43.20        55.76        20.71        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
       73.08       109.41        73.68       112.08        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
       94.19        46.78        48.36        78.64        40.01        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       83.21        28.73        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       12.13        40.70         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
        2.53         3.48        28.47        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73        57.70 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       45.30        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       65.29        39.45        26.07         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       18.51        10.95         8.05        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       66.05        38.63        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       48.82        46.39        56.98        42.41       111.52       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      119.38       126.28        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         0.85         0.53         4.64         5.46 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        16.80        27.16        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        50.14        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
        6.38        48.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 
       16.27        14.17       111.02        85.51        94.72       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       77.03        62.24        54.90        97.45        53.42         3.58 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        37.25        21.21        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       12.23        31.89        12.33        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       48.07        61.68        10.82        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       49.38        45.50        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       46.45        31.30        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
       36.23        28.87        48.10         6.35        79.30        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95       115.00 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4642 
       63.25        73.22        14.17       106.16        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
       10.72        75.06       116.84        71.87        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 
       26.93        50.01        24.66        27.65       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.25       108.56        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4918 TCGA-CJ-4920 
       49.28        50.33        54.48        38.56         3.06         4.57 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 
      131.08        72.00       133.71        25.71        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6028 
      122.83        62.10        73.35        67.00        53.26        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       75.58        62.66         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
        5.39        85.78        66.31        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4860 
      105.93       103.43        25.45         0.59        47.08         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66       107.54        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       63.42        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       69.96        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX 
       11.67        37.15        66.28        56.84        23.90        53.46 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       12.00        81.21        18.12         3.91         6.77         4.18 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A84U 
       10.29        70.13        35.87         2.01        19.43        23.01 
TCGA-MW-A4EC TCGA-T7-A92I 
       16.37        11.70 

  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                         0.36                          0.07 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                       129.40                        149.16 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                        36.87                         38.45 
[1] "0.4 - 129.4 (36.9)" "0.1 - 149.2 (38.5)"
[1] "hr=" "1.5"
D2V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  2(1Q32.1) MUTATED        22       10        18       12
  AMP PEAK  2(1Q32.1) WILD-TYPE     241       47       107       71
D2V3, multiclass
           clus
vv          AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  STAGE I                            22                           241
  STAGE II                           10                            47
  STAGE III                          18                           107
  STAGE IV                           12                            71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  2(1Q32.1) MUTATED    24  12  26   0
  AMP PEAK  2(1Q32.1) WILD-TYPE 244  57 154  11
D2V4, multiclass
    clus
vv   AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  T1                          24                           244
  T2                          12                            57
  T3                          26                           154
  T4                           0                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    29   3
  AMP PEAK  2(1Q32.1) WILD-TYPE 205  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     29    3
  AMP PEAK  2(1Q32.1) WILD-TYPE  205   14
   clus
vv  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  0                          29                           205
  1                           3                            14
[1] 2 2
[1] FALSE
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    49  12
  AMP PEAK  2(1Q32.1) WILD-TYPE 369  66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     49   12
  AMP PEAK  2(1Q32.1) WILD-TYPE  369   66
   clus
vv  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  0                          49                           369
  1                          12                            66
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    20  42
  AMP PEAK  2(1Q32.1) WILD-TYPE 169 297
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     20   42
  AMP PEAK  2(1Q32.1) WILD-TYPE  169  297
        clus
vv       AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  FEMALE                          20                           169
  MALE                            42                           297
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
[1] "Remove cluster labels:"      "AMP PEAK  2(1Q32.1) MUTATED"
clus
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                            1                            20 
                   TCGA-A3-A8CQ                    TCGA-A3-A8OV 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-A3-A8OW                    TCGA-AK-3445 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-AK-3451                    TCGA-B2-A4SR 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-B8-4146                    TCGA-B8-4621 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-B8-5158                    TCGA-B8-5164 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-B8-5550                    TCGA-B8-A54E 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-B8-A54F                    TCGA-B8-A54G 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-B8-A8YJ                    TCGA-DV-A4VX 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-DV-A4W0                    TCGA-G6-A8L7 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-MM-A563                    TCGA-T7-A92I 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
D2V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q32.1) MUTATED       1                         4    57
  AMP PEAK  2(1Q32.1) WILD-TYPE     7                        52   400
D2V11, multiclass
                           clus
vv                          AMP PEAK  2(1Q32.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              57
                           clus
vv                          AMP PEAK  2(1Q32.1) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            52
  WHITE                                               400
[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"
D2V12, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED     5  38
  AMP PEAK  2(1Q32.1) WILD-TYPE  21 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED      5   38
  AMP PEAK  2(1Q32.1) WILD-TYPE   21  312
                        clus
vv                       AMP PEAK  2(1Q32.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          38
                        clus
vv                       AMP PEAK  2(1Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                21
  NOT HISPANIC OR LATINO                           312
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(3Q26.32) MUTATION ANALYSIS
D3V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  3(3Q26.32) MUTATED    50  37
  AMP PEAK  3(3Q26.32) WILD-TYPE 301 138
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                            87                            439 
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                            37                            138 
$`AMP PEAK  3(3Q26.32) MUTATED`
TCGA-A3-3325 TCGA-A3-3374 TCGA-A3-3387 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       38.47        43.20        20.28        68.61       109.51        94.19 
TCGA-AK-3453 TCGA-B0-4690 TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4712 TCGA-B0-4713 
       83.21         1.41        28.47         3.62        43.96         6.64 
TCGA-B0-4833 TCGA-B0-4845 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5094 TCGA-B0-5097 
       78.44        65.29        11.90         7.30        10.95        21.86 
TCGA-B0-5098 TCGA-B0-5102 TCGA-B0-5109 TCGA-B0-5116 TCGA-B0-5690 TCGA-B0-5696 
       52.08        90.87        19.30        41.88       111.52        85.78 
TCGA-B0-5710 TCGA-B0-5712 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4620 
       79.89        89.49         0.53         5.46        23.31        25.55 
TCGA-B8-4621 TCGA-B8-5163 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-A54G TCGA-B8-A54I 
       25.91        27.02         6.38         0.53         1.74         4.93 
TCGA-BP-4163 TCGA-BP-4167 TCGA-BP-4329 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4351 
       93.34        89.36        27.78         0.07        93.99        31.89 
TCGA-BP-4352 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4960 
       11.31         5.98        44.15        13.15        68.38        71.41 
TCGA-BP-4964 TCGA-BP-4969 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5175 
       61.22        58.98        31.30        43.00         6.35        30.64 
TCGA-BP-5178 TCGA-BP-5198 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4644 TCGA-CJ-4868 
       62.86        19.82        14.17       114.41        11.05        21.24 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4897 TCGA-CJ-4900 
       79.66        74.27        71.87        66.21       109.84        56.35 
TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-6028 TCGA-CJ-6033 TCGA-CW-5588 TCGA-CW-5591 
       47.67        49.28        53.42         7.36        66.31        74.66 
TCGA-CW-6087 TCGA-CW-6097 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-5456 
        1.35        18.77        69.21         6.77        14.66        79.63 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 
       94.45        10.85        69.96        84.30         1.94        31.10 
TCGA-CZ-5984 TCGA-DV-A4VX TCGA-EU-5905 
       67.96        53.46         3.91 

$`AMP PEAK  3(3Q26.32) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       36.36        38.99        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        24.16        53.29        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.64        18.87        28.31        65.52        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       22.65         0.10         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
      112.08        46.78        48.36        78.64        40.01        49.28 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       94.29        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 
       72.89        12.13        40.70         1.41         3.32         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 
        2.53         3.48        19.00         1.38        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14        19.73        57.70         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       20.94        43.30        11.24        25.32        18.51        15.09 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 
        8.05         2.24        15.95        62.89        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5117 
       30.48        58.59        66.05        38.63        52.73        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5697 
      112.80       129.67       133.94        15.78        70.68        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
      119.38       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
      105.37       130.65       131.15        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       24.82        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
        5.10         0.85         4.64         0.36         0.23        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 
       27.16        42.71        25.05        45.37        17.19        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       20.91        23.74         1.18         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       16.60        48.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
       17.06         8.42        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4164 
      111.02        85.51        94.72        90.28       101.06        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       99.85         0.43        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4330 
       64.27        54.90        97.45        53.42         3.58        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 
       80.68        37.25        21.21        15.16        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.33        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
       77.62        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
        5.33        61.97        60.59        13.51        56.91        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4967 
       87.45        63.62        58.68        60.30        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 
       48.10        79.30         1.74        74.20        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       13.41        24.62        33.47        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4639 
        0.95       115.00        46.55        63.25        73.22       106.16 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 
       54.61       105.37        58.95        83.97        49.25        10.72 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       75.06       116.84        64.27        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4902 
       50.01        24.66        27.65        39.45        50.24        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.25       108.56        49.18        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 
      118.85        75.58        62.66       119.64        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 
       81.83         5.39        85.78        73.18        78.18       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
       83.90       103.43        25.45        46.16         0.59        47.08 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       58.75       107.54        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
       63.42        58.82        79.53        23.74        18.44        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5467 
       91.69        55.33        10.22        21.76        22.52         2.40 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       12.69        80.19        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        13.28        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-DV-A4W0 
       37.15        66.28        56.84        23.90        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
       18.12         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        23.01        16.37 
TCGA-T7-A92I 
       11.70 

  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                        114.41                         149.16 
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                         41.88                          38.40 
[1] "0.1 - 114.4 (41.9)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1.3"
D3V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  3(3Q26.32) MUTATED        28        6        26       27
  AMP PEAK  3(3Q26.32) WILD-TYPE     235       51        99       56
D3V3, multiclass
           clus
vv          AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE
  STAGE I                             28                            235
  STAGE II                             6                             51
  STAGE III                           26                             99
  STAGE IV                            27                             56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  3(3Q26.32) MUTATED    29   8  46   4
  AMP PEAK  3(3Q26.32) WILD-TYPE 239  61 134   7
D3V4, multiclass
    clus
vv   AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE
  T1                           29                            239
  T2                            8                             61
  T3                           46                            134
  T4                            4                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.32) MUTATED    43   7
  AMP PEAK  3(3Q26.32) WILD-TYPE 191  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.32) MUTATED     43    7
  AMP PEAK  3(3Q26.32) WILD-TYPE  191   10
   clus
vv  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE
  0                           43                            191
  1                            7                             10
[1] 2 2
[1] FALSE
D3V6, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.32) MUTATED    59  25
  AMP PEAK  3(3Q26.32) WILD-TYPE 359  53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.32) MUTATED     59   25
  AMP PEAK  3(3Q26.32) WILD-TYPE  359   53
   clus
vv  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE
  0                           59                            359
  1                           25                             53
[1] 2 2
[1] FALSE
D3V7, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.32) MUTATED    32  55
  AMP PEAK  3(3Q26.32) WILD-TYPE 157 284
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.32) MUTATED     32   55
  AMP PEAK  3(3Q26.32) WILD-TYPE  157  284
        clus
vv       AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE
  FEMALE                           32                            157
  MALE                             55                            284
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
D3V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(3Q26.32) MUTATED       0                         8    78
  AMP PEAK  3(3Q26.32) WILD-TYPE     8                        48   379
D3V11, multiclass
                           clus
vv                          AMP PEAK  3(3Q26.32) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                               78
                           clus
vv                          AMP PEAK  3(3Q26.32) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             48
  WHITE                                                379
[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"
D3V12, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.32) MUTATED     4  57
  AMP PEAK  3(3Q26.32) WILD-TYPE  22 293
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.32) MUTATED      4   57
  AMP PEAK  3(3Q26.32) WILD-TYPE   22  293
                        clus
vv                       AMP PEAK  3(3Q26.32) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           57
                        clus
vv                       AMP PEAK  3(3Q26.32) WILD-TYPE
  HISPANIC OR LATINO                                 22
  NOT HISPANIC OR LATINO                            293
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(4Q32.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(4Q32.1) MUTATED    10   6
  AMP PEAK  4(4Q32.1) WILD-TYPE 341 169
  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE 
                           16                           510 
  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE 
                            6                           169 
$`AMP PEAK  4(4Q32.1) MUTATED`
TCGA-A3-3374 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 TCGA-B0-4688 TCGA-B8-4143 
       43.20        15.78       112.08        94.19         3.32        23.31 
TCGA-BP-4166 TCGA-BP-4342 TCGA-BP-4352 TCGA-BP-4782 TCGA-BP-4977 TCGA-BP-4989 
        0.43        74.17        11.31        11.64        14.93         3.88 
TCGA-BP-4994 TCGA-BP-5177 TCGA-CZ-4856 TCGA-CZ-5469 
       43.00         9.63         0.59        31.10 

$`AMP PEAK  4(4Q32.1) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
       28.70        74.63        74.76        24.16        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       73.68        68.61       109.51        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        49.28        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        1.41         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73        57.70        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       58.45        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.90         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80       129.67       133.94        15.78        70.68        85.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       86.47       119.38       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       91.46       126.05        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        31.66        24.82        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67        12.00         5.75         5.10         0.85         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
        4.64         5.46         0.36         0.23        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       32.61        99.85        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 
        0.07        93.99        18.48        52.24        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       44.15        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       68.38        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         6.90        47.11        53.65 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
       27.22        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 
        1.74        74.20        30.64        52.27        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95       115.00        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
      108.56        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       66.31        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 
      103.43        18.77        25.45        46.16        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40         1.94        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       23.90        53.46        12.00        81.21        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
        2.01        19.43        19.96        23.01        16.37        11.70 

  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE 
                         0.43                          0.07 
  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE 
                       112.08                        149.16 
  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE 
                       15.355                        38.665 
[1] "0.4 - 112.1 (15.4)" "0.1 - 149.2 (38.7)"
[1] "hr=" "1.6"
D4V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  4(4Q32.1) MUTATED         7        3         3        3
  AMP PEAK  4(4Q32.1) WILD-TYPE     256       54       122       80
D4V3, multiclass
           clus
vv          AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE
  STAGE I                             7                           256
  STAGE II                            3                            54
  STAGE III                           3                           122
  STAGE IV                            3                            80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  4(4Q32.1) MUTATED     7   3   5   1
  AMP PEAK  4(4Q32.1) WILD-TYPE 261  66 175  10
D4V4, multiclass
    clus
vv   AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE
  T1                           7                           261
  T2                           3                            66
  T3                           5                           175
  T4                           1                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                               cls
clus                              0   1
  AMP PEAK  4(4Q32.1) MUTATED    10   1
  AMP PEAK  4(4Q32.1) WILD-TYPE 224  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(4Q32.1) MUTATED     10    1
  AMP PEAK  4(4Q32.1) WILD-TYPE  224   16
   clus
vv  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE
  0                          10                           224
  1                           1                            16
[1] 2 2
[1] FALSE
D4V6, binary
                               cls
clus                              0   1
  AMP PEAK  4(4Q32.1) MUTATED    13   3
  AMP PEAK  4(4Q32.1) WILD-TYPE 405  75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(4Q32.1) MUTATED     13    3
  AMP PEAK  4(4Q32.1) WILD-TYPE  405   75
   clus
vv  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE
  0                          13                           405
  1                           3                            75
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(4Q32.1) MUTATED     7   9
  AMP PEAK  4(4Q32.1) WILD-TYPE 182 330
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(4Q32.1) MUTATED      7    9
  AMP PEAK  4(4Q32.1) WILD-TYPE  182  330
        clus
vv       AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE
  FEMALE                           7                           182
  MALE                             9                           330
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
D4V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(4Q32.1) MUTATED       0                         1    15
  AMP PEAK  4(4Q32.1) WILD-TYPE     8                        55   442
D4V11, multiclass
                           clus
vv                          AMP PEAK  4(4Q32.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              15
                           clus
vv                          AMP PEAK  4(4Q32.1) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            55
  WHITE                                               442
[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"
D4V12, binary
                               cls
clus                              0   1
  AMP PEAK  4(4Q32.1) MUTATED     0   9
  AMP PEAK  4(4Q32.1) WILD-TYPE  26 341
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(4Q32.1) MUTATED      0    9
  AMP PEAK  4(4Q32.1) WILD-TYPE   26  341
                        clus
vv                       AMP PEAK  4(4Q32.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       AMP PEAK  4(4Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                26
  NOT HISPANIC OR LATINO                           341
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(5Q35.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(5Q35.1) MUTATED   228 104
  AMP PEAK  5(5Q35.1) WILD-TYPE 123  71
  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE 
                          332                           194 
  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE 
                          104                            71 
$`AMP PEAK  5(5Q35.1) MUTATED`
TCGA-3Z-A93Z TCGA-A3-3307 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 
       12.66        47.21        49.08        49.02        49.58        48.59 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3347 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       52.93        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       51.25        74.76        24.16        43.20        55.76        18.64 
TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8OW TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3440 
        0.10        10.62       109.41        15.78       109.51        94.19 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3458 
       48.36        78.64        94.29        83.21        28.73        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4700 TCGA-B0-4701 
       82.45        72.89         4.57         2.53        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        5.98        19.73        57.70        43.96         6.64         3.25 
TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       46.59         5.52        33.50         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 
       14.93        10.09        78.44        40.70        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4844 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
        6.71        56.68        10.29        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5085 
       36.85        70.52        20.94        43.30        11.90        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5099 TCGA-B0-5102 
       18.51        15.09        10.95         8.05        15.95        90.87 
TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       52.54        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       51.02        38.43        48.82        56.98        42.41       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      129.67       133.94        15.78        85.78        86.47       119.38 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       80.91        71.41       149.16       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 
       89.49        91.46       126.05        35.90        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5832 
       31.30        31.66        24.82        32.98        21.57         5.10 
TCGA-B4-5834 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4620 TCGA-B8-5158 
        0.85         5.46        23.31        16.80        25.55        20.91 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       23.74        27.02        24.23         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       34.39        14.30         1.74         8.42         4.93        17.36 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 
       16.27       111.02        85.51        94.72       101.06        93.34 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
        0.43        89.36        62.24        61.78        64.27        54.90 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4342 
       62.07        80.68        15.16         0.07        93.99        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       62.86        54.77        44.94        31.89        11.31        12.33 
TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4768 
       31.33        72.59        77.98        44.15        41.75        13.15 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 
       60.59        13.51        56.91        68.38        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4959 
       36.53        36.39        37.25        36.95        47.97        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        58.98        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        6.90        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       46.45        31.30        25.81        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5004 TCGA-BP-5006 
       16.47        43.00        45.07        41.62        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        36.23        48.10        79.30         1.74 
TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5185 
       30.64         9.63        62.86        49.15        42.44        37.22 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5198 
       13.35        27.02        33.24        31.79        23.47        19.82 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       34.95        31.27         0.95        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4871 
       14.17       106.16        54.61        11.05        83.97        79.66 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4884 TCGA-CJ-4885 
       74.27        75.06       116.84        64.27        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4897 
       64.18        30.64       115.69        50.01        24.66       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.25       108.56 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 
       49.28        50.33        54.48        45.14         3.06        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 
      131.08        72.00       129.40       133.71        18.87        22.32 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
      122.83        62.10        73.35        67.00       118.85        53.42 
TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 
       62.66         7.36        92.02        81.83        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       66.31        78.18        74.66        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 
       47.08        69.21        58.75         6.77        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04        61.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5461 TCGA-CZ-5462 
       18.44        79.63        90.54        91.69        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        69.96        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5568 
       12.69        67.96        65.65        12.26        62.63        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-A4VX TCGA-DV-A4W0 TCGA-EU-5904 
       11.67        37.15        66.28        53.46        81.21        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-GK-A6C7 
        3.91         6.77         4.18         7.96        10.29         2.01 
TCGA-MM-A564 TCGA-MW-A4EC 
       19.96        16.37 

$`AMP PEAK  5(5Q35.1) WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3319 
       11.90        36.82         0.53        39.16        24.16        37.15 
TCGA-A3-3323 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3363 TCGA-A3-3365 
       36.36        31.07         4.50        45.53        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3373 TCGA-A3-3378 TCGA-A3-3383 TCGA-A3-A8CQ TCGA-A3-A8OV 
       74.63        53.29        20.71        28.31         0.10        11.18 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 
      109.91        29.10       117.80        73.08        73.68       112.08 
TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3455 TCGA-AK-3456 
       68.61        46.78        40.01        49.28        22.45        37.58 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4694 
       12.13        40.70         1.41         3.32         1.41         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4718 
       28.47        19.00         1.38         3.62         2.14        58.45 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4824 
       15.72         0.59        52.21        45.07        16.77        54.48 
TCGA-B0-4827 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 
       29.10        68.71        45.30        10.52        65.29        39.45 
TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 
       11.24         7.30         2.24        21.86        52.08        62.89 
TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5399 TCGA-B0-5690 
       90.48        30.48        41.88        52.87        46.39       111.52 
TCGA-B0-5695 TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5706 TCGA-B2-3923 TCGA-B2-4098 
       70.68       126.28        73.84       105.37        32.61         1.68 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
       16.67        12.00         5.75         0.53         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
        0.23        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5546 
       25.91        50.14         1.18         0.85        50.14        16.60 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54K TCGA-B8-A8YJ TCGA-BP-4161 
       27.29        29.88        17.06        15.42        14.17        90.28 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4325 TCGA-BP-4326 
       32.61        99.85        23.05        77.03        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4340 TCGA-BP-4341 
        3.58        27.78        37.25        21.21        18.48        52.24 
TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4756 TCGA-BP-4760 TCGA-BP-4761 
       49.08        12.23        33.99        12.30        77.62         5.98 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        61.68        10.82         5.33        61.97 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4807 
       11.64        60.95        20.38        10.98         6.71         6.94 
TCGA-BP-4970 TCGA-BP-4987 TCGA-BP-4993 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       14.24        36.95         5.82        30.64        18.51        38.70 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5182 
       28.87         6.35        74.20        52.27        74.40        38.30 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
       37.25        22.78        13.41        24.62        33.47        44.55 
TCGA-CJ-4634 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 
      115.00       114.41       105.37        58.95        21.24        49.25 
TCGA-CJ-4872 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4888 TCGA-CJ-4889 
       10.72        71.87        66.21        61.91        51.52        63.98 
TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4905 TCGA-CJ-4913 TCGA-CJ-4920 
       26.93        27.65        39.45        49.18        38.56         4.57 
TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CJ-6032 
       25.71        25.25        18.15        53.26        75.58       119.64 
TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       64.57         5.39         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5465 
       18.77       107.54         5.46        55.33        94.45        84.30 
TCGA-CZ-5982 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       80.19        14.63        22.78        13.28        45.96        65.88 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-MM-A563 
       56.84        23.90        12.00        70.13        35.87        19.43 
TCGA-MM-A84U TCGA-T7-A92I 
       23.01        11.70 

  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE 
                         0.07                          0.10 
  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE 
                       149.16                        126.28 
  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE 
                        43.63                         31.84 
[1] "0.1 - 149.2 (43.6)" "0.1 - 126.3 (31.8)"
[1] "hr=" "1.4"
D5V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  5(5Q35.1) MUTATED       156       37        81       58
  AMP PEAK  5(5Q35.1) WILD-TYPE     107       20        44       25
D5V3, multiclass
           clus
vv          AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE
  STAGE I                           156                           107
  STAGE II                           37                            20
  STAGE III                          81                            44
  STAGE IV                           58                            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  5(5Q35.1) MUTATED   161  48 118   5
  AMP PEAK  5(5Q35.1) WILD-TYPE 107  21  62   6
D5V4, multiclass
    clus
vv   AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE
  T1                         161                           107
  T2                          48                            21
  T3                         118                            62
  T4                           5                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                               cls
clus                              0   1
  AMP PEAK  5(5Q35.1) MUTATED   151   8
  AMP PEAK  5(5Q35.1) WILD-TYPE  83   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.1) MUTATED    151    8
  AMP PEAK  5(5Q35.1) WILD-TYPE   83    9
   clus
vv  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE
  0                         151                            83
  1                           8                             9
[1] 2 2
[1] FALSE
D5V6, binary
                               cls
clus                              0   1
  AMP PEAK  5(5Q35.1) MUTATED   262  54
  AMP PEAK  5(5Q35.1) WILD-TYPE 156  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.1) MUTATED    262   54
  AMP PEAK  5(5Q35.1) WILD-TYPE  156   24
   clus
vv  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE
  0                         262                           156
  1                          54                            24
[1] 2 2
[1] FALSE
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(5Q35.1) MUTATED   108 224
  AMP PEAK  5(5Q35.1) WILD-TYPE  81 115
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.1) MUTATED    108  224
  AMP PEAK  5(5Q35.1) WILD-TYPE   81  115
        clus
vv       AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE
  FEMALE                         108                            81
  MALE                           224                           115
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
D5V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(5Q35.1) MUTATED       3                        25   299
  AMP PEAK  5(5Q35.1) WILD-TYPE     5                        31   158
D5V11, multiclass
                           clus
vv                          AMP PEAK  5(5Q35.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          25
  WHITE                                             299
                           clus
vv                          AMP PEAK  5(5Q35.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            31
  WHITE                                               158
[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"
D5V12, binary
                               cls
clus                              0   1
  AMP PEAK  5(5Q35.1) MUTATED    17 220
  AMP PEAK  5(5Q35.1) WILD-TYPE   9 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.1) MUTATED     17  220
  AMP PEAK  5(5Q35.1) WILD-TYPE    9  130
                        clus
vv                       AMP PEAK  5(5Q35.1) MUTATED
  HISPANIC OR LATINO                              17
  NOT HISPANIC OR LATINO                         220
                        clus
vv                       AMP PEAK  5(5Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           130
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(7Q36.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(7Q36.3) MUTATED   115  61
  AMP PEAK  6(7Q36.3) WILD-TYPE 236 114
  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE 
                          176                           350 
  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE 
                           61                           114 
$`AMP PEAK  6(7Q36.3) MUTATED`
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 
       24.16        49.08        49.02        48.59        38.99        38.47 
TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3358 TCGA-A3-3363 TCGA-A3-3372 TCGA-A3-3374 
       34.29        52.93        42.97        10.49        24.16        43.20 
TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A8CQ TCGA-A3-A8OV 
       18.87        65.52        20.28        33.47         0.10        11.18 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 
      109.91       117.80       109.41        15.78       112.08       109.51 
TCGA-AK-3440 TCGA-AK-3444 TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       94.19        48.36        83.21         3.32         1.41         4.57 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4811 
        3.48        28.47        57.70        43.96         3.25        46.59 
TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-4828 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       52.21         6.02        10.09        27.42        53.88         6.71 
TCGA-B0-4852 TCGA-B0-5077 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5102 TCGA-B0-5109 
       36.85        43.30        10.95         2.24        90.87        19.30 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5694 TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5703 
       38.63        41.88        15.78       119.38        80.91        73.84 
TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-5639 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 
       91.46        35.90        32.98         5.10         0.53         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
        0.36         0.23        16.80        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5550 TCGA-B8-A54E TCGA-B8-A54I TCGA-BP-4158 TCGA-BP-4159 
       50.14        48.53        29.88         4.93       111.02        85.51 
TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
      101.06         0.43        89.36        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       64.27        97.45        37.25        15.16         0.07        93.99 
TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4759 TCGA-BP-4766 
       62.86        31.89        11.31        33.99        77.98        48.07 
TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4790 
       13.15         5.33        60.59        68.38        15.78        36.53 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4962 
       10.98        37.25         6.71        47.97        71.41        58.68 
TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4983 
       60.30         6.74        48.89        45.50        14.93        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       31.30        36.95         3.88        16.47        43.00        30.64 
TCGA-BP-5009 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5177 TCGA-BP-5178 
       36.23         6.35        79.30         1.74         9.63        62.86 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4638 
       19.82        34.95        31.27        46.55        63.25        14.17 
TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4881 
       11.05        79.66        10.72        74.27       116.84        66.21 
TCGA-CJ-4885 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 
      113.46        30.64        63.98       109.84        47.67        51.25 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5677 TCGA-CJ-5679 
       49.18        49.28         4.57       131.08        25.71        22.32 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-5591 
      122.83        62.10        73.35        53.42        66.31        74.66 
TCGA-CW-6087 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35       103.43        18.77        46.16        47.08        69.21 
TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 
        6.77        61.41        23.74        79.63        90.54        94.45 
TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 
       10.85        69.96        22.52         1.94        31.10        67.96 
TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-A4VX TCGA-EU-5907 
       22.78        13.28        66.28        56.84        53.46         4.18 
TCGA-G6-A8L7 TCGA-MM-A564 
       70.13        19.96 

$`AMP PEAK  6(7Q36.3) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       37.15        49.58        36.36        37.38        48.82        62.01 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
       31.07         4.50        45.53        29.92        18.44        88.37 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       82.32        51.25        28.70        74.63        74.76        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-A6NJ TCGA-A3-A6NL 
       55.76        20.71        18.64        28.31        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3434 
        0.10        10.62        29.10        73.08        73.68        68.61 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
       46.78        78.64        40.01        49.28        94.29        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
       40.70         1.41         2.53        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4713 
       65.10         7.82         5.98         2.14        19.73         6.64 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       58.45        15.72         0.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4842 TCGA-B0-4843 
       78.44        68.71        40.70        45.30        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       70.52        20.94        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       18.51        15.09         8.05        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       62.89        90.48        52.54        30.48        58.59        66.05 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5705 
       70.68        85.78        86.47       126.28        71.41       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5812 
      105.37       130.65        79.89       131.15        89.49       126.05 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       32.61         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       24.82        21.57        16.67        12.00         5.75         0.85 
TCGA-B4-5836 TCGA-B8-4143 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        4.64        23.31        27.16        42.71        25.05        45.37 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       50.14        16.60         6.38         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K 
       27.29        17.06         1.74         8.42        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 
       16.27        14.17        94.72        90.28        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       99.85        23.05        54.90        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4334 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       62.07        80.68        21.21        18.48        52.24        74.17 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4355 
       54.77        49.08        44.94        12.23        12.33        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       12.30        72.59        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       71.80        61.68        10.82        61.97        13.51        56.91 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
       11.64        60.95        48.95        20.38        36.39        36.95 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 
        6.94        87.45        63.62        61.22        61.51        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       58.98        14.24        49.38         6.90        47.11        53.65 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4993 
       36.07        33.34        25.81        27.22        46.45         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       45.07        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5174 TCGA-BP-5175 
       37.48        35.21        28.87        48.10        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5202 
       23.47        13.41        24.62        33.47        44.55         0.95 
TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
      115.00        73.22       106.16       114.41        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 
       58.95        21.24        83.97        49.25        75.06        64.27 
TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4890 
       71.87        61.91        57.83        64.18        51.52       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 
       26.93        50.01        24.66        27.65        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       56.35        49.97       108.56        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
       45.14         3.06        18.81        72.00       129.40       133.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       18.87        25.25        18.15        67.00        53.26       118.85 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 
       81.83         5.39        85.78        73.18        78.18       105.93 
TCGA-CW-6090 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
       83.90        25.45         0.59        58.75        14.66       107.54 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39        93.04         5.46        63.42        58.82        79.53 
TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       18.44        91.69        55.33        10.22        21.76        84.30 
TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
        2.40        12.69        80.19        65.65        12.26        14.63 
TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       62.63        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5576 TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       23.90        12.00        81.21        18.12         3.91         6.77 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A84U 
        7.96        10.29        35.87         2.01        19.43        23.01 
TCGA-MW-A4EC TCGA-T7-A92I 
       16.37        11.70 

  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE 
                         0.07                          0.10 
  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE 
                       131.08                        149.16 
  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE 
                       40.435                        37.940 
[1] "0.1 - 131.1 (40.4)" "0.1 - 149.2 (37.9)"
[1] "hr=" "1.1"
D6V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  6(7Q36.3) MUTATED        74       17        46       39
  AMP PEAK  6(7Q36.3) WILD-TYPE     189       40        79       44
D6V3, multiclass
           clus
vv          AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE
  STAGE I                            74                           189
  STAGE II                           17                            40
  STAGE III                          46                            79
  STAGE IV                           39                            44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  6(7Q36.3) MUTATED    76  22  74   4
  AMP PEAK  6(7Q36.3) WILD-TYPE 192  47 106   7
D6V4, multiclass
    clus
vv   AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE
  T1                          76                           192
  T2                          22                            47
  T3                          74                           106
  T4                           4                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                               cls
clus                              0   1
  AMP PEAK  6(7Q36.3) MUTATED    81   8
  AMP PEAK  6(7Q36.3) WILD-TYPE 153   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7Q36.3) MUTATED     81    8
  AMP PEAK  6(7Q36.3) WILD-TYPE  153    9
   clus
vv  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE
  0                          81                           153
  1                           8                             9
[1] 2 2
[1] FALSE
D6V6, binary
                               cls
clus                              0   1
  AMP PEAK  6(7Q36.3) MUTATED   130  38
  AMP PEAK  6(7Q36.3) WILD-TYPE 288  40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7Q36.3) MUTATED    130   38
  AMP PEAK  6(7Q36.3) WILD-TYPE  288   40
   clus
vv  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE
  0                         130                           288
  1                          38                            40
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(7Q36.3) MUTATED    50 126
  AMP PEAK  6(7Q36.3) WILD-TYPE 139 213
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7Q36.3) MUTATED     50  126
  AMP PEAK  6(7Q36.3) WILD-TYPE  139  213
        clus
vv       AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE
  FEMALE                          50                           139
  MALE                           126                           213
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
D6V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(7Q36.3) MUTATED       4                        12   158
  AMP PEAK  6(7Q36.3) WILD-TYPE     4                        44   299
D6V11, multiclass
                           clus
vv                          AMP PEAK  6(7Q36.3) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             158
                           clus
vv                          AMP PEAK  6(7Q36.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            44
  WHITE                                               299
[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"
D6V12, binary
                               cls
clus                              0   1
  AMP PEAK  6(7Q36.3) MUTATED     5 110
  AMP PEAK  6(7Q36.3) WILD-TYPE  21 240
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7Q36.3) MUTATED      5  110
  AMP PEAK  6(7Q36.3) WILD-TYPE   21  240
                        clus
vv                       AMP PEAK  6(7Q36.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         110
                        clus
vv                       AMP PEAK  6(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                21
  NOT HISPANIC OR LATINO                           240
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(8Q24.22) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  7(8Q24.22) MUTATED    46  33
  AMP PEAK  7(8Q24.22) WILD-TYPE 305 142
  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE 
                            79                            447 
  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE 
                            33                            142 
$`AMP PEAK  7(8Q24.22) MUTATED`
TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3336 
        0.53        24.16        49.08        37.15        38.47        34.29 
TCGA-AK-3425 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3445 TCGA-AK-3454 TCGA-B0-4688 
      109.91       112.08        68.61        78.64        28.73         3.32 
TCGA-B0-4698 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4813 
        1.38         5.98        19.73        43.96         6.64         0.59 
TCGA-B0-4815 TCGA-B0-4821 TCGA-B0-4828 TCGA-B0-4844 TCGA-B0-5081 TCGA-B0-5097 
       52.21        40.44        10.09        10.29        11.90        21.86 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5701 TCGA-B0-5703 TCGA-B4-5832 TCGA-B8-5158 
       58.59        19.30        80.91        73.84         5.10        20.91 
TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4174 TCGA-BP-4338 TCGA-BP-4342 
       27.02         0.53         4.93        61.78        93.99        74.17 
TCGA-BP-4352 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4787 TCGA-BP-4798 
       11.31        77.98         5.98        13.15        15.78        10.98 
TCGA-BP-4799 TCGA-BP-4962 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-5000 TCGA-BP-5169 
       37.25        58.68        46.45        31.30        18.51         6.35 
TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5198 
        1.74        30.64         9.63        37.22        31.79        19.82 
TCGA-CJ-4871 TCGA-CJ-4881 TCGA-CJ-4890 TCGA-CJ-4901 TCGA-CJ-4912 TCGA-CJ-4923 
       79.66        66.21       115.69        47.67        54.48        18.81 
TCGA-CJ-5677 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4854 
       25.71        62.66         7.36        66.31        74.66        46.16 
TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5462 TCGA-CZ-5464 TCGA-CZ-5465 
       69.21        61.41        79.63        10.22        69.96        84.30 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5987 TCGA-DV-A4VX 
       22.52         1.94        31.10        12.69        14.63        53.46 
TCGA-MM-A564 
       19.96 

$`AMP PEAK  7(8Q24.22) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3317 
       12.66        11.90        36.82        47.21        39.16        49.02 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
       49.58        48.59        36.36        38.99        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       62.01        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       11.18        10.62        29.10       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       15.78        73.68       109.51        94.19        46.78        48.36 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3455 TCGA-AK-3456 
       40.01        49.28        94.29        83.21        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        12.13        40.70         1.41 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 
        3.62        65.10         7.82         2.14        57.70         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       58.45        15.72        46.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       78.44        68.71        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
        6.71        56.68        10.52        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.24         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       90.48        52.54        30.48        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       71.41       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       31.96        21.30        31.30        31.66        24.82        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       21.57        16.67        12.00         5.75         0.85         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 
       25.91        50.14        23.74         1.18         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
       50.14        16.60         6.38        48.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         8.42        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 
       89.36        23.05        77.03        62.24        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4341 
       37.25        21.21        15.16         0.07        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        54.77        49.08        44.94        12.23        31.89 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4760 
       12.33        33.99        31.33        12.30        72.59        77.62 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        60.95        48.95        36.53        20.38        36.39 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       63.62        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4986 
       47.11        53.65        14.93        36.07        33.34        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 
       43.00        45.07        30.64        41.62        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       79.30        74.20        52.27        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       38.30        42.44        37.25        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
       33.24        23.47        13.41        24.62        33.47        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95       115.00        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17       106.16       114.41        54.61       105.37 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 
       58.95        11.05        21.24        83.97        49.25        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 
       74.27        75.06       116.84        64.27        71.87        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       50.24        56.35        49.97        51.25       108.56        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       49.28        50.33        38.56        45.14         3.06         4.57 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 
      131.08        72.00       129.40       133.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6032 TCGA-CW-5580 
       53.26       118.85        53.42        75.58       119.64        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        73.18        78.18 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        58.75         6.77        14.66       107.54 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39        93.04         5.46        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5467 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
       10.85        21.76         2.40        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       12.26        22.78        62.63        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       12.00        81.21        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE 
                          0.53                           0.07 
  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE 
                        115.69                         149.16 
  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE 
                         31.10                          39.45 
[1] "0.5 - 115.7 (31.1)" "0.1 - 149.2 (39.5)"
[1] "hr=" "1.5"
D7V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  7(8Q24.22) MUTATED        23       11        26       19
  AMP PEAK  7(8Q24.22) WILD-TYPE     240       46        99       64
D7V3, multiclass
           clus
vv          AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE
  STAGE I                             23                            240
  STAGE II                            11                             46
  STAGE III                           26                             99
  STAGE IV                            19                             64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  7(8Q24.22) MUTATED    24  12  41   2
  AMP PEAK  7(8Q24.22) WILD-TYPE 244  57 139   9
D7V4, multiclass
    clus
vv   AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE
  T1                           24                            244
  T2                           12                             57
  T3                           41                            139
  T4                            2                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                                cls
clus                               0   1
  AMP PEAK  7(8Q24.22) MUTATED    35   3
  AMP PEAK  7(8Q24.22) WILD-TYPE 199  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q24.22) MUTATED     35    3
  AMP PEAK  7(8Q24.22) WILD-TYPE  199   14
   clus
vv  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE
  0                           35                            199
  1                            3                             14
[1] 2 2
[1] FALSE
D7V6, binary
                                cls
clus                               0   1
  AMP PEAK  7(8Q24.22) MUTATED    58  18
  AMP PEAK  7(8Q24.22) WILD-TYPE 360  60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q24.22) MUTATED     58   18
  AMP PEAK  7(8Q24.22) WILD-TYPE  360   60
   clus
vv  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE
  0                           58                            360
  1                           18                             60
[1] 2 2
[1] FALSE
D7V7, binary
                                cls
clus                               0   1
  AMP PEAK  7(8Q24.22) MUTATED    21  58
  AMP PEAK  7(8Q24.22) WILD-TYPE 168 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q24.22) MUTATED     21   58
  AMP PEAK  7(8Q24.22) WILD-TYPE  168  281
        clus
vv       AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE
  FEMALE                           21                            168
  MALE                             58                            281
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
D7V10, continuous
[1] "Remove cluster labels:"       "AMP PEAK  7(8Q24.22) MUTATED"
clus
  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE 
                             2                             10 
                    TCGA-A3-A8OV                     TCGA-A3-A8OW 
"AMP PEAK  7(8Q24.22) WILD-TYPE" "AMP PEAK  7(8Q24.22) WILD-TYPE" 
                    TCGA-AK-3451                     TCGA-B2-A4SR 
"AMP PEAK  7(8Q24.22) WILD-TYPE" "AMP PEAK  7(8Q24.22) WILD-TYPE" 
                    TCGA-B8-5550                     TCGA-DV-A4W0 
"AMP PEAK  7(8Q24.22) WILD-TYPE" "AMP PEAK  7(8Q24.22) WILD-TYPE" 
                    TCGA-G6-A8L7                     TCGA-MM-A563 
"AMP PEAK  7(8Q24.22) WILD-TYPE" "AMP PEAK  7(8Q24.22) WILD-TYPE" 
                    TCGA-MM-A84U                     TCGA-T7-A92I 
"AMP PEAK  7(8Q24.22) WILD-TYPE" "AMP PEAK  7(8Q24.22) WILD-TYPE" 
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(8Q24.22) MUTATED       2                         5    69
  AMP PEAK  7(8Q24.22) WILD-TYPE     6                        51   388
D7V11, multiclass
                           clus
vv                          AMP PEAK  7(8Q24.22) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               69
                           clus
vv                          AMP PEAK  7(8Q24.22) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             51
  WHITE                                                388
[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"
D7V12, binary
                                cls
clus                               0   1
  AMP PEAK  7(8Q24.22) MUTATED     1  50
  AMP PEAK  7(8Q24.22) WILD-TYPE  25 300
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q24.22) MUTATED      1   50
  AMP PEAK  7(8Q24.22) WILD-TYPE   25  300
                        clus
vv                       AMP PEAK  7(8Q24.22) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           50
                        clus
vv                       AMP PEAK  7(8Q24.22) WILD-TYPE
  HISPANIC OR LATINO                                 25
  NOT HISPANIC OR LATINO                            300
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(10P14) MUTATION ANALYSIS
D8V1, survival
                              sevent
clus2                            0   1
  AMP PEAK  8(10P14) MUTATED    13   7
  AMP PEAK  8(10P14) WILD-TYPE 338 168
  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE 
                          20                          506 
  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE 
                           7                          168 
$`AMP PEAK  8(10P14) MUTATED`
TCGA-A3-3316 TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-5109 TCGA-B4-5832 
       49.08        83.21         3.32         1.41        19.30         5.10 
TCGA-B4-5838 TCGA-B8-4143 TCGA-BP-4338 TCGA-BP-4342 TCGA-BP-4768 TCGA-BP-4781 
        5.46        23.31        93.99        74.17        13.15        68.38 
TCGA-BP-4986 TCGA-BP-5175 TCGA-CJ-5675 TCGA-CW-5588 TCGA-CZ-4854 TCGA-CZ-4866 
       25.81        30.64       129.40        66.31        46.16        61.41 
TCGA-CZ-5454 TCGA-EU-5905 
       23.74         3.91 

$`AMP PEAK  8(10P14) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        78.64        40.01        49.28        94.29 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
       28.47        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73        57.70        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        10.52        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80       129.67       133.94        15.78        70.68        85.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       86.47       119.38       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       91.46       126.05        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        31.66        24.82        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       16.67        12.00         5.75         0.85         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.36         0.23        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       12.23        31.89        11.31        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
       61.97        60.59        13.51        56.91        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        31.30        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
        1.74        74.20        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95       115.00        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
      108.56        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
      122.83        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        73.18        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       74.66         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       25.45         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       14.66       107.54        63.39        93.04         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82        79.53        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        94.45        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        13.28        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ 
       37.15        66.28        56.84        23.90        53.46        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       81.21        18.12         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        23.01 
TCGA-MW-A4EC TCGA-T7-A92I 
       16.37        11.70 

  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE 
                        1.41                         0.07 
  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE 
                      129.40                       149.16 
  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE 
                      28.225                       38.515 
[1] "1.4 - 129.4 (28.2)" "0.1 - 149.2 (38.5)"
[1] "hr=" "1.1"
D8V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  8(10P14) MUTATED         9        4         2        5
  AMP PEAK  8(10P14) WILD-TYPE     254       53       123       78
D8V3, multiclass
           clus
vv          AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE
  STAGE I                            9                          254
  STAGE II                           4                           53
  STAGE III                          2                          123
  STAGE IV                           5                           78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK  8(10P14) MUTATED     9   5   4   2
  AMP PEAK  8(10P14) WILD-TYPE 259  64 176   9
D8V4, multiclass
    clus
vv   AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE
  T1                          9                          259
  T2                          5                           64
  T3                          4                          176
  T4                          2                            9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                              cls
clus                             0   1
  AMP PEAK  8(10P14) MUTATED    10   2
  AMP PEAK  8(10P14) WILD-TYPE 224  15
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK  8(10P14) MUTATED     10    2
  AMP PEAK  8(10P14) WILD-TYPE  224   15
   clus
vv  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE
  0                         10                          224
  1                          2                           15
[1] 2 2
[1] FALSE
D8V6, binary
                              cls
clus                             0   1
  AMP PEAK  8(10P14) MUTATED    16   4
  AMP PEAK  8(10P14) WILD-TYPE 402  74
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK  8(10P14) MUTATED     16    4
  AMP PEAK  8(10P14) WILD-TYPE  402   74
   clus
vv  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE
  0                         16                          402
  1                          4                           74
[1] 2 2
[1] FALSE
D8V7, binary
                              cls
clus                             0   1
  AMP PEAK  8(10P14) MUTATED     6  14
  AMP PEAK  8(10P14) WILD-TYPE 183 325
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK  8(10P14) MUTATED      6   14
  AMP PEAK  8(10P14) WILD-TYPE  183  325
        clus
vv       AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE
  FEMALE                          6                          183
  MALE                           14                          325
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
D8V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(10P14) MUTATED       0                         0    20
  AMP PEAK  8(10P14) WILD-TYPE     8                        56   437
D8V11, multiclass
                           clus
vv                          AMP PEAK  8(10P14) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             20
                           clus
vv                          AMP PEAK  8(10P14) WILD-TYPE
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                           56
  WHITE                                              437
[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"
D8V12, binary
                              cls
clus                             0   1
  AMP PEAK  8(10P14) MUTATED     1  12
  AMP PEAK  8(10P14) WILD-TYPE  25 338
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK  8(10P14) MUTATED      1   12
  AMP PEAK  8(10P14) WILD-TYPE   25  338
                        clus
vv                       AMP PEAK  8(10P14) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         12
                        clus
vv                       AMP PEAK  8(10P14) WILD-TYPE
  HISPANIC OR LATINO                               25
  NOT HISPANIC OR LATINO                          338
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(XP22.2) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(XP22.2) MUTATED    18  13
  AMP PEAK  9(XP22.2) WILD-TYPE 333 162
  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE 
                           31                           495 
  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE 
                           13                           162 
$`AMP PEAK  9(XP22.2) MUTATED`
TCGA-A3-3346 TCGA-A3-3382 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3453 
        4.50        18.87       109.41       109.51        78.64        83.21 
TCGA-B0-5109 TCGA-BP-4162 TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4343 
       19.30       101.06        61.78         0.07        93.99        62.86 
TCGA-BP-4346 TCGA-BP-4352 TCGA-BP-4756 TCGA-BP-4770 TCGA-BP-4799 TCGA-BP-4969 
       49.08        11.31        12.30        10.82        37.25        58.98 
TCGA-BP-4989 TCGA-CJ-4642 TCGA-CJ-4644 TCGA-CJ-4885 TCGA-CJ-4899 TCGA-CJ-5681 
        3.88       105.37        11.05       113.46        50.24        18.15 
TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-5456 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-DV-A4VX 
       74.66        46.16        79.63        69.96         1.94        53.46 
TCGA-EU-5905 
        3.91 

$`AMP PEAK  9(XP22.2) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       34.29        31.07        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       20.71        18.64        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 
      109.91        29.10       117.80        73.08        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 
      112.08        68.61        94.19        46.78        48.36        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       49.28        94.29        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
       90.48        52.54        30.48        58.59        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       46.39        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         0.85         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       85.51        94.72        90.28        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 
        0.43        89.36        23.05        77.03        62.24        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 
       80.68        37.25        21.21        15.16        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 
       74.17        54.77        44.94        12.23        31.89        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       33.99        31.33        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       44.15        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       36.39        10.98        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.74        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 
       14.17       106.16       114.41        54.61        58.95        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4900 
       50.01        24.66        27.65        39.45       109.84        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        22.32        25.25       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       67.00        53.26       118.85        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 
       85.78        73.18        66.31        78.18         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 
       83.90       103.43        18.77        25.45         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66       107.54        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       12.00        81.21        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       23.01        16.37        11.70 

  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE 
                         0.07                          0.10 
  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE 
                       113.46                        149.16 
  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE 
                        50.24                         38.30 
[1] "0.1 - 113.5 (50.2)" "0.1 - 149.2 (38.3)"
[1] "hr=" "1.1"
D9V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  9(XP22.2) MUTATED         9        5         7       10
  AMP PEAK  9(XP22.2) WILD-TYPE     254       52       118       73
D9V3, multiclass
           clus
vv          AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE
  STAGE I                             9                           254
  STAGE II                            5                            52
  STAGE III                           7                           118
  STAGE IV                           10                            73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  9(XP22.2) MUTATED     9   6  15   1
  AMP PEAK  9(XP22.2) WILD-TYPE 259  63 165  10
D9V4, multiclass
    clus
vv   AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE
  T1                           9                           259
  T2                           6                            63
  T3                          15                           165
  T4                           1                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
                               cls
clus                              0   1
  AMP PEAK  9(XP22.2) MUTATED    18   1
  AMP PEAK  9(XP22.2) WILD-TYPE 216  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(XP22.2) MUTATED     18    1
  AMP PEAK  9(XP22.2) WILD-TYPE  216   16
   clus
vv  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE
  0                          18                           216
  1                           1                            16
[1] 2 2
[1] FALSE
D9V6, binary
                               cls
clus                              0   1
  AMP PEAK  9(XP22.2) MUTATED    22   8
  AMP PEAK  9(XP22.2) WILD-TYPE 396  70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(XP22.2) MUTATED     22    8
  AMP PEAK  9(XP22.2) WILD-TYPE  396   70
   clus
vv  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE
  0                          22                           396
  1                           8                            70
[1] 2 2
[1] FALSE
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(XP22.2) MUTATED    11  20
  AMP PEAK  9(XP22.2) WILD-TYPE 178 319
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(XP22.2) MUTATED     11   20
  AMP PEAK  9(XP22.2) WILD-TYPE  178  319
        clus
vv       AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE
  FEMALE                          11                           178
  MALE                            20                           319
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
[1] "Remove cluster labels:"      "AMP PEAK  9(XP22.2) MUTATED"
clus
  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE 
                            2                            19 
                   TCGA-A3-A8CQ                    TCGA-A3-A8OV 
"AMP PEAK  9(XP22.2) WILD-TYPE" "AMP PEAK  9(XP22.2) WILD-TYPE" 
                   TCGA-A3-A8OW                    TCGA-AK-3451 
"AMP PEAK  9(XP22.2) WILD-TYPE" "AMP PEAK  9(XP22.2) WILD-TYPE" 
                   TCGA-B2-A4SR                    TCGA-B8-4146 
"AMP PEAK  9(XP22.2) WILD-TYPE" "AMP PEAK  9(XP22.2) WILD-TYPE" 
                   TCGA-B8-4621                    TCGA-B8-5158 
"AMP PEAK  9(XP22.2) WILD-TYPE" "AMP PEAK  9(XP22.2) WILD-TYPE" 
                   TCGA-B8-5164                    TCGA-B8-5550 
"AMP PEAK  9(XP22.2) WILD-TYPE" "AMP PEAK  9(XP22.2) WILD-TYPE" 
                   TCGA-B8-A54E                    TCGA-B8-A54F 
"AMP PEAK  9(XP22.2) WILD-TYPE" "AMP PEAK  9(XP22.2) WILD-TYPE" 
                   TCGA-B8-A54G                    TCGA-B8-A8YJ 
"AMP PEAK  9(XP22.2) WILD-TYPE" "AMP PEAK  9(XP22.2) WILD-TYPE" 
                   TCGA-DV-A4W0                    TCGA-G6-A5PC 
"AMP PEAK  9(XP22.2) WILD-TYPE" "AMP PEAK  9(XP22.2) WILD-TYPE" 
                   TCGA-G6-A8L7                    TCGA-MM-A563 
"AMP PEAK  9(XP22.2) WILD-TYPE" "AMP PEAK  9(XP22.2) WILD-TYPE" 
                   TCGA-T7-A92I 
"AMP PEAK  9(XP22.2) WILD-TYPE" 
D9V10, continuous
[1] "Remove cluster labels:"      "AMP PEAK  9(XP22.2) MUTATED"
clus
  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE 
                            1                            11 
                   TCGA-A3-A8OV                    TCGA-A3-A8OW 
"AMP PEAK  9(XP22.2) WILD-TYPE" "AMP PEAK  9(XP22.2) WILD-TYPE" 
                   TCGA-AK-3451                    TCGA-B2-A4SR 
"AMP PEAK  9(XP22.2) WILD-TYPE" "AMP PEAK  9(XP22.2) WILD-TYPE" 
                   TCGA-B8-5158                    TCGA-B8-5550 
"AMP PEAK  9(XP22.2) WILD-TYPE" "AMP PEAK  9(XP22.2) WILD-TYPE" 
                   TCGA-DV-A4W0                    TCGA-G6-A8L7 
"AMP PEAK  9(XP22.2) WILD-TYPE" "AMP PEAK  9(XP22.2) WILD-TYPE" 
                   TCGA-MM-A563                    TCGA-MM-A84U 
"AMP PEAK  9(XP22.2) WILD-TYPE" "AMP PEAK  9(XP22.2) WILD-TYPE" 
                   TCGA-T7-A92I 
"AMP PEAK  9(XP22.2) WILD-TYPE" 
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(XP22.2) MUTATED       2                         1    28
  AMP PEAK  9(XP22.2) WILD-TYPE     6                        55   429
D9V11, multiclass
                           clus
vv                          AMP PEAK  9(XP22.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              28
                           clus
vv                          AMP PEAK  9(XP22.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            55
  WHITE                                               429
[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"
D9V12, binary
                               cls
clus                              0   1
  AMP PEAK  9(XP22.2) MUTATED     0  16
  AMP PEAK  9(XP22.2) WILD-TYPE  26 334
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(XP22.2) MUTATED      0   16
  AMP PEAK  9(XP22.2) WILD-TYPE   26  334
                        clus
vv                       AMP PEAK  9(XP22.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          16
                        clus
vv                       AMP PEAK  9(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                26
  NOT HISPANIC OR LATINO                           334
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(XP11.4) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(XP11.4) MUTATED    20  13
  AMP PEAK 10(XP11.4) WILD-TYPE 331 162
  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE 
                           33                           493 
  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE 
                           13                           162 
$`AMP PEAK 10(XP11.4) MUTATED`
TCGA-A3-3325 TCGA-A3-3382 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3453 
       38.47        18.87       109.41       109.51        78.64        83.21 
TCGA-B0-4696 TCGA-B0-5109 TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4174 TCGA-BP-4337 
       28.47        19.30         4.93       101.06        61.78         0.07 
TCGA-BP-4338 TCGA-BP-4352 TCGA-BP-4756 TCGA-BP-4770 TCGA-BP-4799 TCGA-BP-4969 
       93.99        11.31        12.30        10.82        37.25        58.98 
TCGA-BP-4989 TCGA-BP-5178 TCGA-BP-5199 TCGA-CJ-4644 TCGA-CJ-4885 TCGA-CJ-4899 
        3.88        62.86        44.55        11.05       113.46        50.24 
TCGA-CJ-4902 TCGA-CJ-5681 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-5456 TCGA-CZ-5464 
       49.97        18.15        74.66        46.16        79.63        69.96 
TCGA-CZ-5468 TCGA-DV-A4VX TCGA-EU-5905 
        1.94        53.46         3.91 

$`AMP PEAK 10(XP11.4) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       36.36        38.99        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       20.71        18.64        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 
      109.91        29.10       117.80        73.08        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 
      112.08        68.61        94.19        46.78        48.36        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       49.28        94.29        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 
        1.41         4.57         2.53         3.48        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       57.70        43.96         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       52.54        30.48        58.59        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       24.82        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         8.42        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       23.05        77.03        62.24        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
       21.21        15.16        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 
       54.77        49.08        44.94        12.23        31.89        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       33.99        31.33        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       44.15        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       36.39        10.98        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        1.74        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       24.62        33.47        19.82        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
      115.00        46.55        63.25        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61       105.37        58.95        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        10.72        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 
       64.27        71.87        66.21        61.91        57.83        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        27.65        39.45       109.84        56.35        47.67 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       25.25       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       66.31        78.18         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       18.77        25.45         0.59        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
        6.77        14.66       107.54        63.39        93.04         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 
       21.76        84.30        22.52         2.40        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        13.28        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-DV-A4W0 
       37.15        66.28        56.84        23.90        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
       18.12         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        23.01        16.37 
TCGA-T7-A92I 
       11.70 

  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE 
                         0.07                          0.10 
  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE 
                       113.46                        149.16 
  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE 
                        46.16                         38.30 
[1] "0.1 - 113.5 (46.2)" "0.1 - 149.2 (38.3)"
[1] "hr=" "1.1"
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 10(XP11.4) MUTATED        10        5         7       11
  AMP PEAK 10(XP11.4) WILD-TYPE     253       52       118       72
D10V3, multiclass
           clus
vv          AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE
  STAGE I                            10                           253
  STAGE II                            5                            52
  STAGE III                           7                           118
  STAGE IV                           11                            72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 10(XP11.4) MUTATED    10   6  16   1
  AMP PEAK 10(XP11.4) WILD-TYPE 258  63 164  10
D10V4, multiclass
    clus
vv   AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE
  T1                          10                           258
  T2                           6                            63
  T3                          16                           164
  T4                           1                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                               cls
clus                              0   1
  AMP PEAK 10(XP11.4) MUTATED    18   1
  AMP PEAK 10(XP11.4) WILD-TYPE 216  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(XP11.4) MUTATED     18    1
  AMP PEAK 10(XP11.4) WILD-TYPE  216   16
   clus
vv  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE
  0                          18                           216
  1                           1                            16
[1] 2 2
[1] FALSE
D10V6, binary
                               cls
clus                              0   1
  AMP PEAK 10(XP11.4) MUTATED    22   9
  AMP PEAK 10(XP11.4) WILD-TYPE 396  69
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(XP11.4) MUTATED     22    9
  AMP PEAK 10(XP11.4) WILD-TYPE  396   69
   clus
vv  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE
  0                          22                           396
  1                           9                            69
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(XP11.4) MUTATED    11  22
  AMP PEAK 10(XP11.4) WILD-TYPE 178 317
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(XP11.4) MUTATED     11   22
  AMP PEAK 10(XP11.4) WILD-TYPE  178  317
        clus
vv       AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE
  FEMALE                          11                           178
  MALE                            22                           317
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
[1] "Remove cluster labels:"      "AMP PEAK 10(XP11.4) MUTATED"
clus
  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE 
                            2                            19 
                   TCGA-A3-A8CQ                    TCGA-A3-A8OV 
"AMP PEAK 10(XP11.4) WILD-TYPE" "AMP PEAK 10(XP11.4) WILD-TYPE" 
                   TCGA-A3-A8OW                    TCGA-AK-3451 
"AMP PEAK 10(XP11.4) WILD-TYPE" "AMP PEAK 10(XP11.4) WILD-TYPE" 
                   TCGA-B2-A4SR                    TCGA-B8-4146 
"AMP PEAK 10(XP11.4) WILD-TYPE" "AMP PEAK 10(XP11.4) WILD-TYPE" 
                   TCGA-B8-4621                    TCGA-B8-5158 
"AMP PEAK 10(XP11.4) WILD-TYPE" "AMP PEAK 10(XP11.4) WILD-TYPE" 
                   TCGA-B8-5164                    TCGA-B8-5550 
"AMP PEAK 10(XP11.4) WILD-TYPE" "AMP PEAK 10(XP11.4) WILD-TYPE" 
                   TCGA-B8-A54E                    TCGA-B8-A54F 
"AMP PEAK 10(XP11.4) WILD-TYPE" "AMP PEAK 10(XP11.4) WILD-TYPE" 
                   TCGA-B8-A54G                    TCGA-B8-A8YJ 
"AMP PEAK 10(XP11.4) WILD-TYPE" "AMP PEAK 10(XP11.4) WILD-TYPE" 
                   TCGA-DV-A4W0                    TCGA-G6-A5PC 
"AMP PEAK 10(XP11.4) WILD-TYPE" "AMP PEAK 10(XP11.4) WILD-TYPE" 
                   TCGA-G6-A8L7                    TCGA-MM-A563 
"AMP PEAK 10(XP11.4) WILD-TYPE" "AMP PEAK 10(XP11.4) WILD-TYPE" 
                   TCGA-T7-A92I 
"AMP PEAK 10(XP11.4) WILD-TYPE" 
D10V10, continuous
[1] "Remove cluster labels:"      "AMP PEAK 10(XP11.4) MUTATED"
clus
  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE 
                            1                            11 
                   TCGA-A3-A8OV                    TCGA-A3-A8OW 
"AMP PEAK 10(XP11.4) WILD-TYPE" "AMP PEAK 10(XP11.4) WILD-TYPE" 
                   TCGA-AK-3451                    TCGA-B2-A4SR 
"AMP PEAK 10(XP11.4) WILD-TYPE" "AMP PEAK 10(XP11.4) WILD-TYPE" 
                   TCGA-B8-5158                    TCGA-B8-5550 
"AMP PEAK 10(XP11.4) WILD-TYPE" "AMP PEAK 10(XP11.4) WILD-TYPE" 
                   TCGA-DV-A4W0                    TCGA-G6-A8L7 
"AMP PEAK 10(XP11.4) WILD-TYPE" "AMP PEAK 10(XP11.4) WILD-TYPE" 
                   TCGA-MM-A563                    TCGA-MM-A84U 
"AMP PEAK 10(XP11.4) WILD-TYPE" "AMP PEAK 10(XP11.4) WILD-TYPE" 
                   TCGA-T7-A92I 
"AMP PEAK 10(XP11.4) WILD-TYPE" 
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(XP11.4) MUTATED       2                         2    29
  AMP PEAK 10(XP11.4) WILD-TYPE     6                        54   428
D10V11, multiclass
                           clus
vv                          AMP PEAK 10(XP11.4) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              29
                           clus
vv                          AMP PEAK 10(XP11.4) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            54
  WHITE                                               428
[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"
D10V12, binary
                               cls
clus                              0   1
  AMP PEAK 10(XP11.4) MUTATED     0  20
  AMP PEAK 10(XP11.4) WILD-TYPE  26 330
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(XP11.4) MUTATED      0   20
  AMP PEAK 10(XP11.4) WILD-TYPE   26  330
                        clus
vv                       AMP PEAK 10(XP11.4) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          20
                        clus
vv                       AMP PEAK 10(XP11.4) WILD-TYPE
  HISPANIC OR LATINO                                26
  NOT HISPANIC OR LATINO                           330
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(XQ11.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(XQ11.2) MUTATED    19  10
  AMP PEAK 11(XQ11.2) WILD-TYPE 332 165
  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE 
                           29                           497 
  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE 
                           10                           165 
$`AMP PEAK 11(XQ11.2) MUTATED`
TCGA-A3-3363 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3453 TCGA-B0-4696 TCGA-B0-5109 
       10.49       109.41       109.51        83.21        28.47        19.30 
TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4352 
        4.93       101.06        61.78         0.07        93.99        11.31 
TCGA-BP-4762 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4799 TCGA-BP-4969 TCGA-BP-4989 
       44.15        61.68        61.97        37.25        58.98         3.88 
TCGA-BP-5176 TCGA-CJ-4644 TCGA-CJ-4885 TCGA-CJ-4899 TCGA-CW-5591 TCGA-CZ-4854 
       52.27        11.05       113.46        50.24        74.66        46.16 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5464 TCGA-DV-A4VX TCGA-EU-5905 
       79.63        91.69        69.96        53.46         3.91 

$`AMP PEAK 11(XQ11.2) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 
       18.44        88.37        42.97        82.32        51.25        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 
       10.62       109.91        29.10       117.80        73.08        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       73.68       112.08        68.61        94.19        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 
       78.64        40.01        49.28        94.29        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73        57.70        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       58.45        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.90         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       90.87        90.48        52.54        30.48        58.59        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       48.82        46.39        56.98        42.41       111.52       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
      119.38       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
      126.05        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        31.66        24.82        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       12.00         5.75         5.10         0.85         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        8.42        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       85.51        94.72        90.28        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 
        0.43        89.36        23.05        77.03        62.24        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 
       80.68        37.25        21.21        15.16        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.98        77.62         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       13.15        10.82         5.33        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       20.38        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         6.90        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
       27.22        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5178 
       79.30         1.74        74.20        30.64         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17       106.16       114.41        54.61       105.37        58.95 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       57.83        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45       109.84 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.25       108.56        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
       62.10        73.35        67.00        53.26       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
        0.59        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
      107.54        63.39        93.04         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5459 
       58.82        79.53        23.74        18.44        90.54        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       94.45        10.85        10.22        21.76        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        13.28 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 
       56.84        23.90        12.00        81.21        18.12         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.43        19.96        23.01        16.37        11.70 

  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE 
                         0.07                          0.10 
  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE 
                       113.46                        149.16 
  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE 
                        53.46                         37.48 
[1] "0.1 - 113.5 (53.5)" "0.1 - 149.2 (37.5)"
[1] "hr=" "1.2"
D11V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 11(XQ11.2) MUTATED        11        5         6        7
  AMP PEAK 11(XQ11.2) WILD-TYPE     252       52       119       76
D11V3, multiclass
           clus
vv          AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE
  STAGE I                            11                           252
  STAGE II                            5                            52
  STAGE III                           6                           119
  STAGE IV                            7                            76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 11(XQ11.2) MUTATED    11   6  12   0
  AMP PEAK 11(XQ11.2) WILD-TYPE 257  63 168  11
D11V4, multiclass
    clus
vv   AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE
  T1                          11                           257
  T2                           6                            63
  T3                          12                           168
  T4                           0                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                               cls
clus                              0   1
  AMP PEAK 11(XQ11.2) MUTATED    16   1
  AMP PEAK 11(XQ11.2) WILD-TYPE 218  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(XQ11.2) MUTATED     16    1
  AMP PEAK 11(XQ11.2) WILD-TYPE  218   16
   clus
vv  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE
  0                          16                           218
  1                           1                            16
[1] 2 2
[1] FALSE
D11V6, binary
                               cls
clus                              0   1
  AMP PEAK 11(XQ11.2) MUTATED    21   6
  AMP PEAK 11(XQ11.2) WILD-TYPE 397  72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(XQ11.2) MUTATED     21    6
  AMP PEAK 11(XQ11.2) WILD-TYPE  397   72
   clus
vv  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE
  0                          21                           397
  1                           6                            72
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(XQ11.2) MUTATED    10  19
  AMP PEAK 11(XQ11.2) WILD-TYPE 179 320
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(XQ11.2) MUTATED     10   19
  AMP PEAK 11(XQ11.2) WILD-TYPE  179  320
        clus
vv       AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE
  FEMALE                          10                           179
  MALE                            19                           320
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
[1] "Remove cluster labels:"      "AMP PEAK 11(XQ11.2) MUTATED"
clus
  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE 
                            1                            20 
                   TCGA-A3-A8CQ                    TCGA-A3-A8OV 
"AMP PEAK 11(XQ11.2) WILD-TYPE" "AMP PEAK 11(XQ11.2) WILD-TYPE" 
                   TCGA-A3-A8OW                    TCGA-AK-3445 
"AMP PEAK 11(XQ11.2) WILD-TYPE" "AMP PEAK 11(XQ11.2) WILD-TYPE" 
                   TCGA-AK-3451                    TCGA-B2-A4SR 
"AMP PEAK 11(XQ11.2) WILD-TYPE" "AMP PEAK 11(XQ11.2) WILD-TYPE" 
                   TCGA-B8-4146                    TCGA-B8-4621 
"AMP PEAK 11(XQ11.2) WILD-TYPE" "AMP PEAK 11(XQ11.2) WILD-TYPE" 
                   TCGA-B8-5158                    TCGA-B8-5164 
"AMP PEAK 11(XQ11.2) WILD-TYPE" "AMP PEAK 11(XQ11.2) WILD-TYPE" 
                   TCGA-B8-5550                    TCGA-B8-A54E 
"AMP PEAK 11(XQ11.2) WILD-TYPE" "AMP PEAK 11(XQ11.2) WILD-TYPE" 
                   TCGA-B8-A54F                    TCGA-B8-A54G 
"AMP PEAK 11(XQ11.2) WILD-TYPE" "AMP PEAK 11(XQ11.2) WILD-TYPE" 
                   TCGA-B8-A8YJ                    TCGA-DV-A4W0 
"AMP PEAK 11(XQ11.2) WILD-TYPE" "AMP PEAK 11(XQ11.2) WILD-TYPE" 
                   TCGA-G6-A5PC                    TCGA-G6-A8L7 
"AMP PEAK 11(XQ11.2) WILD-TYPE" "AMP PEAK 11(XQ11.2) WILD-TYPE" 
                   TCGA-MM-A563                    TCGA-T7-A92I 
"AMP PEAK 11(XQ11.2) WILD-TYPE" "AMP PEAK 11(XQ11.2) WILD-TYPE" 
D11V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(XQ11.2) MUTATED       2                         2    25
  AMP PEAK 11(XQ11.2) WILD-TYPE     6                        54   432
D11V11, multiclass
                           clus
vv                          AMP PEAK 11(XQ11.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              25
                           clus
vv                          AMP PEAK 11(XQ11.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            54
  WHITE                                               432
[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"
D11V12, binary
                               cls
clus                              0   1
  AMP PEAK 11(XQ11.2) MUTATED     0  15
  AMP PEAK 11(XQ11.2) WILD-TYPE  26 335
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(XQ11.2) MUTATED      0   15
  AMP PEAK 11(XQ11.2) WILD-TYPE   26  335
                        clus
vv                       AMP PEAK 11(XQ11.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          15
                        clus
vv                       AMP PEAK 11(XQ11.2) WILD-TYPE
  HISPANIC OR LATINO                                26
  NOT HISPANIC OR LATINO                           335
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(XQ28) MUTATION ANALYSIS
D12V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 12(XQ28) MUTATED    25  12
  AMP PEAK 12(XQ28) WILD-TYPE 326 163
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                         37                         489 
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                         12                         163 
$`AMP PEAK 12(XQ28) MUTATED`
TCGA-A3-3317 TCGA-A3-3336 TCGA-A3-3383 TCGA-AK-3428 TCGA-AK-3436 TCGA-AK-3453 
       49.02        34.29        28.31        73.08       109.51        83.21 
TCGA-B0-4688 TCGA-B0-4713 TCGA-B0-4827 TCGA-B0-5080 TCGA-B0-5109 TCGA-B0-5120 
        3.32         6.64        29.10        11.24        19.30        38.43 
TCGA-B0-5705 TCGA-B8-5159 TCGA-B8-A54D TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4174 
      149.16        23.74        27.29         4.93       101.06        61.78 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4352 TCGA-BP-4799 TCGA-BP-4959 TCGA-BP-4969 
        0.07        93.99        11.31        37.25        87.45        58.98 
TCGA-BP-4989 TCGA-BP-5176 TCGA-CJ-4885 TCGA-CW-5591 TCGA-CW-6088 TCGA-CZ-4854 
        3.88        52.27       113.46        74.66       105.93        46.16 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-DV-A4VX TCGA-EU-5905 
       79.63        91.69        10.85        69.96        53.46         3.91 
TCGA-MM-A84U 
       23.01 

$`AMP PEAK 12(XQ28) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.08        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 
       38.99        38.47        37.38        48.82        62.01        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.76        24.16        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.64        18.87        65.52        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       22.65         0.10         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
       29.10       117.80       109.41        15.78        73.68       112.08 
TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       68.61        94.19        46.78        48.36        78.64        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       49.28        94.29        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 
       82.45        72.89        12.13        40.70         1.41         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70        43.96         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 
        6.02        40.44        36.53        14.93        54.48        10.09 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       78.44        68.71        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       43.30        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       48.82        46.39        56.98        42.41       111.52       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5706 
      119.38       126.28        80.91        71.41        73.84       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.66        24.82        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         0.85         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       20.91         1.18        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K 
       29.88        17.06         1.74         8.42        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       77.03        62.24        64.27        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       15.16        18.48        52.24        74.17        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       44.15        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       20.38        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
        1.74        74.20        30.64         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95       115.00        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       57.83        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
      122.83        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       78.18         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
        0.59        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
      107.54        63.39        93.04         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5459 
       58.82        79.53        23.74        18.44        90.54        55.33 
TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       94.45        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 
       23.90        12.00        81.21        18.12         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       19.96        16.37        11.70 

  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                       0.07                        0.10 
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                     149.16                      133.94 
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                      46.16                       38.40 
[1] "0.1 - 149.2 (46.2)" "0.1 - 133.9 (38.4)"
[1] "hr=" "1.2"
D12V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 12(XQ28) MUTATED        15        4         9        9
  AMP PEAK 12(XQ28) WILD-TYPE     248       53       116       74
D12V3, multiclass
           clus
vv          AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  STAGE I                          15                         248
  STAGE II                          4                          53
  STAGE III                         9                         116
  STAGE IV                          9                          74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 12(XQ28) MUTATED    16   5  15   1
  AMP PEAK 12(XQ28) WILD-TYPE 252  64 165  10
D12V4, multiclass
    clus
vv   AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  T1                        16                         252
  T2                         5                          64
  T3                        15                         165
  T4                         1                          10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                             cls
clus                            0   1
  AMP PEAK 12(XQ28) MUTATED    21   1
  AMP PEAK 12(XQ28) WILD-TYPE 213  16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(XQ28) MUTATED     21    1
  AMP PEAK 12(XQ28) WILD-TYPE  213   16
   clus
vv  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  0                        21                         213
  1                         1                          16
[1] 2 2
[1] FALSE
D12V6, binary
                             cls
clus                            0   1
  AMP PEAK 12(XQ28) MUTATED    25   8
  AMP PEAK 12(XQ28) WILD-TYPE 393  70
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(XQ28) MUTATED     25    8
  AMP PEAK 12(XQ28) WILD-TYPE  393   70
   clus
vv  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  0                        25                         393
  1                         8                          70
[1] 2 2
[1] FALSE
D12V7, binary
                             cls
clus                            0   1
  AMP PEAK 12(XQ28) MUTATED    14  23
  AMP PEAK 12(XQ28) WILD-TYPE 175 316
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(XQ28) MUTATED     14   23
  AMP PEAK 12(XQ28) WILD-TYPE  175  316
        clus
vv       AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  FEMALE                        14                         175
  MALE                          23                         316
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
[1] "Remove cluster labels:"    "AMP PEAK 12(XQ28) MUTATED"
clus
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                          1                          20 
                 TCGA-A3-A8CQ                  TCGA-A3-A8OV 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-A3-A8OW                  TCGA-AK-3445 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-AK-3451                  TCGA-B2-A4SR 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-B8-4146                  TCGA-B8-4621 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-B8-5158                  TCGA-B8-5164 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-B8-5550                  TCGA-B8-A54E 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-B8-A54F                  TCGA-B8-A54G 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-B8-A8YJ                  TCGA-DV-A4W0 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-G6-A5PC                  TCGA-G6-A8L7 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-MM-A563                  TCGA-T7-A92I 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
D12V10, continuous
[1] "Remove cluster labels:"    "AMP PEAK 12(XQ28) MUTATED"
clus
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                          1                          11 
                 TCGA-A3-A8OV                  TCGA-A3-A8OW 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-AK-3445                  TCGA-AK-3451 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-B2-A4SR                  TCGA-B8-5158 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-B8-5550                  TCGA-DV-A4W0 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-G6-A8L7                  TCGA-MM-A563 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-T7-A92I 
"AMP PEAK 12(XQ28) WILD-TYPE" 
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(XQ28) MUTATED       0                         4    32
  AMP PEAK 12(XQ28) WILD-TYPE     8                        52   425
D12V11, multiclass
                           clus
vv                          AMP PEAK 12(XQ28) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         4
  WHITE                                            32
                           clus
vv                          AMP PEAK 12(XQ28) WILD-TYPE
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                          52
  WHITE                                             425
[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"
D12V12, binary
                             cls
clus                            0   1
  AMP PEAK 12(XQ28) MUTATED     0  24
  AMP PEAK 12(XQ28) WILD-TYPE  26 326
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(XQ28) MUTATED      0   24
  AMP PEAK 12(XQ28) WILD-TYPE   26  326
                        clus
vv                       AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             0                          26
  NOT HISPANIC OR LATINO                        24                         326
[1] 2 2
[1] FALSE

Clustering(13) Variable = DEL PEAK  1(1P36.23) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.23) MUTATED    57  46
  DEL PEAK  1(1P36.23) WILD-TYPE 294 129
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                           103                            423 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            46                            129 
$`DEL PEAK  1(1P36.23) MUTATED`
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3347 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3380 
       24.16        49.08        52.93        53.29        43.20        18.64 
TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3453 
      117.80       112.08       109.51        94.19        40.01        83.21 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4698 TCGA-B0-4699 
       12.13        40.70         1.41         4.57         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4834 
       65.10        58.45         0.59        40.44        36.53        68.71 
TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5084 TCGA-B0-5092 
       10.52        65.29        36.85        70.52         7.30        15.09 
TCGA-B0-5098 TCGA-B0-5102 TCGA-B0-5117 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5709 
       52.08        90.87        52.87        80.91        73.84       130.65 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 
       32.61         1.68        21.57         5.10         0.53         5.46 
TCGA-B8-4143 TCGA-B8-4619 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5549 TCGA-B8-5550 
       23.31        17.19         1.18         0.85         6.38        48.53 
TCGA-B8-5551 TCGA-BP-4176 TCGA-BP-4334 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4342 
        0.53        64.27        21.21        93.99        18.48        74.17 
TCGA-BP-4343 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4775 
       62.86        11.31        12.33        13.15         5.33        60.59 
TCGA-BP-4781 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4989 
       68.38        61.51        57.40        31.30        25.81         3.88 
TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5173 TCGA-BP-5185 TCGA-BP-5201 TCGA-CJ-4635 
       43.00        37.02         1.74        37.22        31.27        46.55 
TCGA-CJ-4637 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4869 TCGA-CJ-4876 TCGA-CJ-4894 
       73.22       114.41        54.61        83.97        64.27        27.65 
TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5678 TCGA-CJ-5679 
      109.84        47.67        51.25        49.28        18.87        22.32 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5588 
      118.85        75.58        62.66         7.36        64.57        66.31 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4864 TCGA-CZ-4866 
       83.90        18.77        47.08         6.77        93.04        61.41 
TCGA-CZ-5457 TCGA-CZ-5462 TCGA-CZ-5469 TCGA-EU-5907 TCGA-G6-A8L8 TCGA-GK-A6C7 
       90.54        10.22        31.10         4.18        35.87         2.01 
TCGA-T7-A92I 
       11.70 

$`DEL PEAK  1(1P36.23) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.47        37.38        48.82        62.01        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
        4.50        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       24.16        55.76        20.71        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3429 
       11.18        10.62       109.91        29.10        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       15.78        73.68        68.61        46.78        48.36        78.64 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       49.28        94.29        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4693 TCGA-B0-4694 
       82.45        72.89         1.41         3.32         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
       28.47        19.00         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 
       57.70        43.96         6.64         3.25        15.72        46.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4844 
       45.30        27.42        53.88         6.71        56.68        10.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-5075 TCGA-B0-5077 
       39.45        26.07        29.03         2.27        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5094 TCGA-B0-5095 
       11.24        11.90        25.32        18.51        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 
        2.24        21.86        15.95        62.89        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       41.88        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       42.41       111.52       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 
       70.68        85.78        86.47       119.38       126.28        71.41 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      149.16       105.37        79.89       131.15        89.49        91.46 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
      126.05        35.90        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       24.82        32.98        16.67        12.00         5.75         0.85 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        4.64         0.36         0.23        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        25.55        25.91        50.14        20.91 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 
       23.74        27.02        24.23        50.14        16.60        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       61.78        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4341 
       62.07        80.68        37.25        15.16         0.07        52.24 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 
       54.77        49.08        44.94        12.23        31.89        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       61.97        13.51        56.91        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4969 
       63.62        58.68        60.30        61.22         6.74        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 
       53.65        14.93        36.07        33.34        46.45        36.95 
TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
       27.22        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       41.62        18.51        38.70        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
       36.23        28.87        48.10         6.35        79.30        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       38.30        42.44        37.25        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
       19.82        44.55        34.95         0.95       115.00        63.25 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       14.17       106.16       105.37        58.95        11.05        21.24 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        10.72        74.27        75.06       116.84 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4904 
       24.66        39.45        50.24        56.35        49.97       108.56 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       25.71        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
       67.00        53.26        53.42       119.64        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
        5.39        85.78        73.18        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 
      105.93       103.43        25.45        46.16         0.59        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-5451 
       58.75        14.66       107.54        63.39         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        79.63        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       55.33        94.45        10.85        21.76        69.96        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
       22.52         2.40         1.94        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        13.28 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 
       56.84        23.90        53.46        12.00        81.21        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-MM-A563 
        3.91         6.77         7.96        10.29        70.13        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       19.96        23.01        16.37 

  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                          0.53                           0.07 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                        130.65                         149.16 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                         40.44                          38.40 
[1] "0.5 - 130.7 (40.4)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1.5"
D13V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  1(1P36.23) MUTATED        45       12        24       22
  DEL PEAK  1(1P36.23) WILD-TYPE     218       45       101       61
D13V3, multiclass
           clus
vv          DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  STAGE I                             45                            218
  STAGE II                            12                             45
  STAGE III                           24                            101
  STAGE IV                            22                             61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  1(1P36.23) MUTATED    48  17  33   5
  DEL PEAK  1(1P36.23) WILD-TYPE 220  52 147   6
D13V4, multiclass
    clus
vv   DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  T1                           48                            220
  T2                           17                             52
  T3                           33                            147
  T4                            5                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.23) MUTATED    50   4
  DEL PEAK  1(1P36.23) WILD-TYPE 184  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     50    4
  DEL PEAK  1(1P36.23) WILD-TYPE  184   13
   clus
vv  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  0                           50                            184
  1                            4                             13
[1] 2 2
[1] FALSE
D13V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.23) MUTATED    80  20
  DEL PEAK  1(1P36.23) WILD-TYPE 338  58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     80   20
  DEL PEAK  1(1P36.23) WILD-TYPE  338   58
   clus
vv  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  0                           80                            338
  1                           20                             58
[1] 2 2
[1] FALSE
D13V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.23) MUTATED    31  72
  DEL PEAK  1(1P36.23) WILD-TYPE 158 267
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     31   72
  DEL PEAK  1(1P36.23) WILD-TYPE  158  267
        clus
vv       DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  FEMALE                           31                            158
  MALE                             72                            267
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
D13V10, continuous
[1] "Remove cluster labels:"       "DEL PEAK  1(1P36.23) MUTATED"
clus
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                             2                             10 
                    TCGA-A3-A8OV                     TCGA-A3-A8OW 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-AK-3445                     TCGA-AK-3451 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-B2-A4SR                     TCGA-B8-5158 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-DV-A4W0                     TCGA-G6-A8L7 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-MM-A563                     TCGA-MM-A84U 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.23) MUTATED       1                        10    91
  DEL PEAK  1(1P36.23) WILD-TYPE     7                        46   366
D13V11, multiclass
                           clus
vv                          DEL PEAK  1(1P36.23) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                               91
                           clus
vv                          DEL PEAK  1(1P36.23) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             46
  WHITE                                                366
[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"
D13V12, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.23) MUTATED     8  71
  DEL PEAK  1(1P36.23) WILD-TYPE  18 279
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      8   71
  DEL PEAK  1(1P36.23) WILD-TYPE   18  279
                        clus
vv                       DEL PEAK  1(1P36.23) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           71
                        clus
vv                       DEL PEAK  1(1P36.23) WILD-TYPE
  HISPANIC OR LATINO                                 18
  NOT HISPANIC OR LATINO                            279
[1] 2 2
[1] FALSE

Clustering(14) Variable = DEL PEAK  2(1P31.1) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P31.1) MUTATED    47  30
  DEL PEAK  2(1P31.1) WILD-TYPE 304 145
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                           77                           449 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                           30                           145 
$`DEL PEAK  2(1P31.1) MUTATED`
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3380 
       24.16        49.08        37.15        53.29        43.20        18.64 
TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 
      117.80       112.08       109.51        94.19        40.01        12.13 
TCGA-AS-3777 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4712 TCGA-B0-4718 TCGA-B0-4814 
       40.70         1.38         3.62        43.96        58.45         5.52 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4834 TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-5084 
       40.44        36.53        68.71        65.29        36.85         7.30 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5098 TCGA-B0-5102 TCGA-B0-5109 TCGA-B0-5117 
       15.09        10.95        52.08        90.87        19.30        52.87 
TCGA-B0-5402 TCGA-B0-5703 TCGA-B2-3923 TCGA-B2-4098 TCGA-B4-5832 TCGA-B4-5835 
       42.41        73.84        32.61         1.68         5.10         0.53 
TCGA-B4-5838 TCGA-B8-4619 TCGA-B8-5549 TCGA-BP-4176 TCGA-BP-4334 TCGA-BP-4340 
        5.46        17.19         6.38        64.27        21.21        18.48 
TCGA-BP-4342 TCGA-BP-4353 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4968 
       74.17        12.33        13.15        60.59        68.38        57.40 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5173 
       46.45        31.30        25.81        43.00        37.02         1.74 
TCGA-BP-5175 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4869 TCGA-CJ-4876 
       30.64        31.27        46.55       114.41        83.97        64.27 
TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-5678 TCGA-CJ-5679 
       27.65       109.84        47.67        49.28        18.87        22.32 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6090 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5457 
       66.31        74.66        83.90         6.77        61.41        90.54 
TCGA-CZ-5462 TCGA-CZ-5469 TCGA-EU-5907 TCGA-G6-A8L8 TCGA-T7-A92I 
       10.22        31.10         4.18        35.87        11.70 

$`DEL PEAK  2(1P31.1) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       49.02        49.58        48.59        36.36        38.99        38.47 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        62.01        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       24.16        55.76        20.71        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3429 
       11.18        10.62       109.91        29.10        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       15.78        73.68        68.61        46.78        48.36        78.64 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       49.28        94.29        83.21        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       38.40        82.45        72.89         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4700 
        4.57         2.53         3.48        28.47        19.00        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4713 
        7.82         5.98         2.14        19.73        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 
        3.25        15.72        46.59         0.59        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       33.50        16.77         6.02        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 
        6.71        56.68        10.52        10.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
       29.03         2.27        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       11.90        25.32        18.51         8.05         2.24        21.86 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       15.95        62.89        90.48        52.54        30.48        58.59 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       66.05        38.63        52.73        41.88        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       48.82        46.39        56.98       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
      126.28        80.91        71.41       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
       79.89       131.15        89.49        91.46       126.05        35.90 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       31.96        21.30        31.30        31.66        24.82        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 
       21.57        16.67        12.00         5.75         0.85         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        25.55        25.91        50.14        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 
       89.36        23.05        77.03        62.24        61.78        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4341 TCGA-BP-4343 
       37.25        15.16         0.07        93.99        52.24        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       54.77        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
       10.82         5.33        61.97        13.51        56.91        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       33.34        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        6.35        79.30        74.20        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        63.25        73.22        14.17       106.16 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 
       54.61       105.37        58.95        11.05        21.24        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 
       79.66        10.72        74.27        75.06       116.84        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        26.93        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       39.45        50.24        56.35        49.97        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       25.71        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       67.00        53.26       118.85        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 
       85.78        73.18        78.18         1.35       105.93       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
       58.75        14.66       107.54        63.39        93.04         5.46 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
       91.69        55.33        94.45        10.85        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
       84.30        22.52         2.40         1.94        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       13.28        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 
       66.28        56.84        23.90        53.46        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
       18.12         3.91         6.77         7.96        10.29        70.13 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
        2.01        19.43        19.96        23.01        16.37 

  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                         0.53                          0.07 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                       117.80                        149.16 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                        37.15                         38.47 
[1] "0.5 - 117.8 (37.1)" "0.1 - 149.2 (38.5)"
[1] "hr=" "1.3"
D14V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  2(1P31.1) MUTATED        36        9        16       16
  DEL PEAK  2(1P31.1) WILD-TYPE     227       48       109       67
D14V3, multiclass
           clus
vv          DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  STAGE I                            36                           227
  STAGE II                            9                            48
  STAGE III                          16                           109
  STAGE IV                           16                            67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  2(1P31.1) MUTATED    38  12  22   5
  DEL PEAK  2(1P31.1) WILD-TYPE 230  57 158   6
D14V4, multiclass
    clus
vv   DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  T1                          38                           230
  T2                          12                            57
  T3                          22                           158
  T4                           5                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P31.1) MUTATED    34   4
  DEL PEAK  2(1P31.1) WILD-TYPE 200  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED     34    4
  DEL PEAK  2(1P31.1) WILD-TYPE  200   13
   clus
vv  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  0                          34                           200
  1                           4                            13
[1] 2 2
[1] FALSE
D14V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P31.1) MUTATED    62  13
  DEL PEAK  2(1P31.1) WILD-TYPE 356  65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED     62   13
  DEL PEAK  2(1P31.1) WILD-TYPE  356   65
   clus
vv  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  0                          62                           356
  1                          13                            65
[1] 2 2
[1] FALSE
D14V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P31.1) MUTATED    20  57
  DEL PEAK  2(1P31.1) WILD-TYPE 169 282
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED     20   57
  DEL PEAK  2(1P31.1) WILD-TYPE  169  282
        clus
vv       DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  FEMALE                          20                           169
  MALE                            57                           282
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
[1] "Remove cluster labels:"      "DEL PEAK  2(1P31.1) MUTATED"
clus
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                            1                            20 
                   TCGA-A3-A8CQ                    TCGA-A3-A8OV 
"DEL PEAK  2(1P31.1) WILD-TYPE" "DEL PEAK  2(1P31.1) WILD-TYPE" 
                   TCGA-A3-A8OW                    TCGA-AK-3445 
"DEL PEAK  2(1P31.1) WILD-TYPE" "DEL PEAK  2(1P31.1) WILD-TYPE" 
                   TCGA-AK-3451                    TCGA-B2-A4SR 
"DEL PEAK  2(1P31.1) WILD-TYPE" "DEL PEAK  2(1P31.1) WILD-TYPE" 
                   TCGA-B8-4146                    TCGA-B8-4621 
"DEL PEAK  2(1P31.1) WILD-TYPE" "DEL PEAK  2(1P31.1) WILD-TYPE" 
                   TCGA-B8-5158                    TCGA-B8-5164 
"DEL PEAK  2(1P31.1) WILD-TYPE" "DEL PEAK  2(1P31.1) WILD-TYPE" 
                   TCGA-B8-5550                    TCGA-B8-A54E 
"DEL PEAK  2(1P31.1) WILD-TYPE" "DEL PEAK  2(1P31.1) WILD-TYPE" 
                   TCGA-B8-A54F                    TCGA-B8-A54G 
"DEL PEAK  2(1P31.1) WILD-TYPE" "DEL PEAK  2(1P31.1) WILD-TYPE" 
                   TCGA-B8-A8YJ                    TCGA-DV-A4VX 
"DEL PEAK  2(1P31.1) WILD-TYPE" "DEL PEAK  2(1P31.1) WILD-TYPE" 
                   TCGA-DV-A4W0                    TCGA-G6-A5PC 
"DEL PEAK  2(1P31.1) WILD-TYPE" "DEL PEAK  2(1P31.1) WILD-TYPE" 
                   TCGA-G6-A8L7                    TCGA-MM-A563 
"DEL PEAK  2(1P31.1) WILD-TYPE" "DEL PEAK  2(1P31.1) WILD-TYPE" 
D14V10, continuous
[1] "Remove cluster labels:"      "DEL PEAK  2(1P31.1) MUTATED"
clus
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                            1                            11 
                   TCGA-A3-A8OV                    TCGA-A3-A8OW 
"DEL PEAK  2(1P31.1) WILD-TYPE" "DEL PEAK  2(1P31.1) WILD-TYPE" 
                   TCGA-AK-3445                    TCGA-AK-3451 
"DEL PEAK  2(1P31.1) WILD-TYPE" "DEL PEAK  2(1P31.1) WILD-TYPE" 
                   TCGA-B2-A4SR                    TCGA-B8-5158 
"DEL PEAK  2(1P31.1) WILD-TYPE" "DEL PEAK  2(1P31.1) WILD-TYPE" 
                   TCGA-B8-5550                    TCGA-DV-A4W0 
"DEL PEAK  2(1P31.1) WILD-TYPE" "DEL PEAK  2(1P31.1) WILD-TYPE" 
                   TCGA-G6-A8L7                    TCGA-MM-A563 
"DEL PEAK  2(1P31.1) WILD-TYPE" "DEL PEAK  2(1P31.1) WILD-TYPE" 
                   TCGA-MM-A84U 
"DEL PEAK  2(1P31.1) WILD-TYPE" 
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P31.1) MUTATED       2                         8    66
  DEL PEAK  2(1P31.1) WILD-TYPE     6                        48   391
D14V11, multiclass
                           clus
vv                          DEL PEAK  2(1P31.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           8
  WHITE                                              66
                           clus
vv                          DEL PEAK  2(1P31.1) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            48
  WHITE                                               391
[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"
D14V12, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P31.1) MUTATED     7  50
  DEL PEAK  2(1P31.1) WILD-TYPE  19 300
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED      7   50
  DEL PEAK  2(1P31.1) WILD-TYPE   19  300
                        clus
vv                       DEL PEAK  2(1P31.1) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                          50
                        clus
vv                       DEL PEAK  2(1P31.1) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           300
[1] 2 2
[1] FALSE

Clustering(15) Variable = DEL PEAK  3(1Q43) MUTATION ANALYSIS
D15V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  3(1Q43) MUTATED    27  15
  DEL PEAK  3(1Q43) WILD-TYPE 324 160
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         42                         484 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         15                         160 
$`DEL PEAK  3(1Q43) MUTATED`
TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-A8OV TCGA-AK-3427 TCGA-AK-3433 
       74.76        43.20        18.64        11.18       117.80       112.08 
TCGA-AK-3440 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 
       94.19        12.13        40.70        28.47         1.38         3.62 
TCGA-B0-4821 TCGA-B0-4834 TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-5102 TCGA-B0-5117 
       40.44        68.71        65.29        36.85        90.87        52.87 
TCGA-B0-5703 TCGA-B2-3923 TCGA-B4-5838 TCGA-B8-4619 TCGA-B8-5549 TCGA-BP-4329 
       73.84        32.61         5.46        17.19         6.38        27.78 
TCGA-BP-4334 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4968 
       21.21        11.31        12.33        13.15        60.59        57.40 
TCGA-BP-4994 TCGA-CJ-4878 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CW-5585 
       43.00        71.87       109.84        47.67        49.28        85.78 
TCGA-CW-5588 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5469 TCGA-G6-A8L8 
       66.31         6.77        61.41        90.54        31.10        35.87 

$`DEL PEAK  3(1Q43) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        38.47        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       28.70        74.63        24.16        53.29        55.76        20.71 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.87        28.31        65.52        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
       22.65         0.10         0.10        10.62       109.91        29.10 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        78.64        40.01        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        3.48        19.00        65.10         7.82         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 
       53.88         6.71        56.68        10.52        10.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       26.07        29.03         2.27        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       62.89        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       66.05        38.63        52.73        41.88        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       48.82        46.39        56.98        42.41       111.52       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 
      119.38       126.28        80.91        71.41       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       24.82        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
        5.10         0.85         0.53         4.64         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        42.71        25.05        45.37 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        50.14        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 
       27.02         0.85        24.23        50.14        16.60        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 
       53.42         3.58        62.07        80.68        37.25        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 
       54.77        49.08        44.94        12.23        31.89        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.33        61.97        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
        3.88        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.74        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17       106.16       114.41        54.61       105.37        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4882 
       74.27        75.06       116.84        64.27        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       50.24        56.35        49.97        51.25       108.56        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26       118.85        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
        5.39        73.18        78.18        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        69.21        58.75        14.66       107.54        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04         5.46        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       18.44        79.63        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
        1.94        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       53.46        12.00        81.21        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
        4.18         7.96        10.29        70.13         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.96        23.01        16.37        11.70 

  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                       1.38                        0.07 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                     117.80                      149.16 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                      41.85                       38.35 
[1] "1.4 - 117.8 (41.9)" "0.1 - 149.2 (38.3)"
[1] "hr=" "1"  
D15V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  3(1Q43) MUTATED        22        4         9        7
  DEL PEAK  3(1Q43) WILD-TYPE     241       53       116       76
D15V3, multiclass
           clus
vv          DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  STAGE I                          22                         241
  STAGE II                          4                          53
  STAGE III                         9                         116
  STAGE IV                          7                          76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK  3(1Q43) MUTATED    22   4  13   3
  DEL PEAK  3(1Q43) WILD-TYPE 246  65 167   8
D15V4, multiclass
    clus
vv   DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  T1                        22                         246
  T2                         4                          65
  T3                        13                         167
  T4                         3                           8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED    21   1
  DEL PEAK  3(1Q43) WILD-TYPE 213  16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED     21    1
  DEL PEAK  3(1Q43) WILD-TYPE  213   16
   clus
vv  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  0                        21                         213
  1                         1                          16
[1] 2 2
[1] FALSE
D15V6, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED    35   5
  DEL PEAK  3(1Q43) WILD-TYPE 383  73
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED     35    5
  DEL PEAK  3(1Q43) WILD-TYPE  383   73
   clus
vv  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  0                        35                         383
  1                         5                          73
[1] 2 2
[1] FALSE
D15V7, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED    15  27
  DEL PEAK  3(1Q43) WILD-TYPE 174 312
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED     15   27
  DEL PEAK  3(1Q43) WILD-TYPE  174  312
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  FEMALE                        15                         174
  MALE                          27                         312
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
[1] "Remove cluster labels:"    "DEL PEAK  3(1Q43) MUTATED"
clus
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          1                          20 
                 TCGA-A3-A8CQ                  TCGA-A3-A8OW 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-AK-3445                  TCGA-AK-3451 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-B2-A4SR                  TCGA-B8-4146 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-B8-4621                  TCGA-B8-5158 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-B8-5164                  TCGA-B8-5550 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-B8-A54E                  TCGA-B8-A54F 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-B8-A54G                  TCGA-B8-A8YJ 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-DV-A4VX                  TCGA-DV-A4W0 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-G6-A5PC                  TCGA-G6-A8L7 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-MM-A563                  TCGA-T7-A92I 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
D15V10, continuous
[1] "Remove cluster labels:"    "DEL PEAK  3(1Q43) MUTATED"
clus
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          1                          11 
                 TCGA-A3-A8OW                  TCGA-AK-3445 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-AK-3451                  TCGA-B2-A4SR 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-B8-5158                  TCGA-B8-5550 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-DV-A4W0                  TCGA-G6-A8L7 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-MM-A563                  TCGA-MM-A84U 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-T7-A92I 
"DEL PEAK  3(1Q43) WILD-TYPE" 
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q43) MUTATED       1                         4    36
  DEL PEAK  3(1Q43) WILD-TYPE     7                        52   421
D15V11, multiclass
                           clus
vv                          DEL PEAK  3(1Q43) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         4
  WHITE                                            36
                           clus
vv                          DEL PEAK  3(1Q43) WILD-TYPE
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                          52
  WHITE                                             421
[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"
D15V12, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED     3  32
  DEL PEAK  3(1Q43) WILD-TYPE  23 318
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      3   32
  DEL PEAK  3(1Q43) WILD-TYPE   23  318
                        clus
vv                       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  HISPANIC OR LATINO                             3                          23
  NOT HISPANIC OR LATINO                        32                         318
[1] 2 2
[1] FALSE

Clustering(16) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.3) MUTATED    36  14
  DEL PEAK  4(2Q37.3) WILD-TYPE 315 161
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           50                           476 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           14                           161 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-A3-3311 TCGA-A3-3323 TCGA-A3-3336 TCGA-A3-3374 TCGA-AK-3425 TCGA-AK-3433 
       39.16        36.36        34.29        43.20       109.91       112.08 
TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4696 TCGA-B0-4699 
       94.19        40.01        12.13        40.70        28.47         3.62 
TCGA-B0-4703 TCGA-B0-4821 TCGA-B0-4841 TCGA-B0-5095 TCGA-B0-5099 TCGA-B0-5116 
        5.98        40.44         6.71         8.05        15.95        41.88 
TCGA-B0-5117 TCGA-B0-5120 TCGA-B2-3923 TCGA-B2-5641 TCGA-B8-4620 TCGA-B8-5549 
       52.87        38.43        32.61        21.57        25.55         6.38 
TCGA-B8-A54F TCGA-B8-A54G TCGA-BP-4166 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4761 
       17.06         1.74         0.43        37.25        21.21         5.98 
TCGA-BP-4782 TCGA-BP-4991 TCGA-BP-4994 TCGA-BP-5008 TCGA-BP-5175 TCGA-BP-5177 
       11.64        46.45        43.00        35.21        30.64         9.63 
TCGA-BP-5199 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4881 TCGA-CJ-4902 
       44.55        58.95        21.24        49.25        66.21        49.97 
TCGA-CJ-6027 TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-5453 TCGA-CZ-5468 TCGA-CZ-5985 
      118.85        83.90        46.16        79.53         1.94        65.65 
TCGA-CZ-5988 TCGA-CZ-5989 
       22.78        62.63 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 
       12.66        11.90        36.82        47.21         0.53        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 
       49.08        49.02        37.15        49.58        48.59        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3346 
       38.47        37.38        48.82        62.01        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       24.16        53.29        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 
        0.10         0.10        11.18        10.62        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       46.78        48.36        78.64        49.28        94.29        83.21 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        82.45        72.89 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4707 
       19.00         1.38        65.10         7.82         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       57.70        43.96         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
       53.88        56.68        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 
       15.09        10.95         2.24        21.86        52.08        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 
       66.05        38.63        52.73        51.02        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
       79.89       131.15        89.49        91.46       126.05        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        31.96        21.30        31.30        31.66        24.82 
TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       32.98        16.67        12.00         5.75         5.10         0.85 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        50.14        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 
        0.85        24.23        50.14        16.60        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54H TCGA-B8-A54I 
       34.39        14.30        27.29        29.88         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       80.68        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       31.89        11.31        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       72.59        77.98        77.62        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       48.07        13.15        61.68        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 
       60.59        13.51        56.91        68.38        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       57.40        58.98        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        6.90        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       16.47         5.82        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5009 TCGA-BP-5010 
       38.70        37.02        27.62        37.48        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       48.10         6.35        79.30         1.74        74.20        52.27 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61       105.37        11.05 
TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       83.97        79.66        10.72        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       64.27        71.87        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        53.26        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
      103.43        18.77        25.45         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66       107.54        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        61.41        63.42        58.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5986 TCGA-CZ-5987 
       31.10        12.69        80.19        67.96        12.26        14.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       13.28        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 
       66.28        56.84        23.90        53.46        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        23.01 
TCGA-MW-A4EC TCGA-T7-A92I 
       16.37        11.70 

  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         0.43                          0.07 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       118.85                        149.16 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       36.805                        38.595 
[1] "0.4 - 118.8 (36.8)" "0.1 - 149.2 (38.6)"
[1] "hr=" "1.1"
D16V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  4(2Q37.3) MUTATED        24        8        13        5
  DEL PEAK  4(2Q37.3) WILD-TYPE     239       49       112       78
D16V3, multiclass
           clus
vv          DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  STAGE I                            24                           239
  STAGE II                            8                            49
  STAGE III                          13                           112
  STAGE IV                            5                            78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  4(2Q37.3) MUTATED    24   9  16   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 244  60 164  10
D16V4, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  T1                          24                           244
  T2                           9                            60
  T3                          16                           164
  T4                           1                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    23   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 211  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     23    1
  DEL PEAK  4(2Q37.3) WILD-TYPE  211   16
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                          23                           211
  1                           1                            16
[1] 2 2
[1] FALSE
D16V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    43   5
  DEL PEAK  4(2Q37.3) WILD-TYPE 375  73
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     43    5
  DEL PEAK  4(2Q37.3) WILD-TYPE  375   73
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                          43                           375
  1                           5                            73
[1] 2 2
[1] FALSE
D16V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    13  37
  DEL PEAK  4(2Q37.3) WILD-TYPE 176 302
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     13   37
  DEL PEAK  4(2Q37.3) WILD-TYPE  176  302
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                          13                           176
  MALE                            37                           302
[1] 2 2
[1] FALSE
D16V8, continuous
[1] "Remove cluster labels:"      "DEL PEAK  4(2Q37.3) MUTATED"
clus
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            1                            52 
                   TCGA-3Z-A93Z                    TCGA-A3-A6NJ 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A3-A6NL                    TCGA-A3-A8CQ 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-AK-3426                    TCGA-AK-3430 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B0-4838                    TCGA-B2-5639 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B4-5377                    TCGA-B4-5378 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B4-5832                    TCGA-B4-5834 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B4-5835                    TCGA-B4-5836 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B4-5838                    TCGA-B4-5843 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B4-5844                    TCGA-B8-4143 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B8-4622                    TCGA-B8-5158 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-CJ-6028                    TCGA-CZ-4856 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-CZ-4858                    TCGA-CZ-4860 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-CZ-4861                    TCGA-CZ-4862 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-CZ-5456                    TCGA-CZ-5457 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-CZ-5458                    TCGA-CZ-5465 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-CZ-5469                    TCGA-CZ-5982 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DV-5565                    TCGA-DV-5566 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DV-5567                    TCGA-DV-5568 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DV-5569                    TCGA-DV-5573 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DV-5574                    TCGA-DV-5575 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DV-5576                    TCGA-DV-A4VX 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DV-A4VZ                    TCGA-DV-A4W0 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-EU-5904                    TCGA-EU-5905 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-EU-5906                    TCGA-EU-5907 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G6-A8L6                    TCGA-G6-A8L7 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G6-A8L8                    TCGA-T7-A92I 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
D16V9, continuous
[1] "Remove cluster labels:"      "DEL PEAK  4(2Q37.3) MUTATED"
clus
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            2                            19 
                   TCGA-A3-A8CQ                    TCGA-A3-A8OV 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A3-A8OW                    TCGA-AK-3445 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-AK-3451                    TCGA-B2-A4SR 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B8-4146                    TCGA-B8-4621 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B8-5158                    TCGA-B8-5164 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B8-5550                    TCGA-B8-A54E 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B8-A8YJ                    TCGA-DV-A4VX 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DV-A4W0                    TCGA-G6-A5PC 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G6-A8L7                    TCGA-MM-A563 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-T7-A92I 
"DEL PEAK  4(2Q37.3) WILD-TYPE" 
D16V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED       1                         5    43
  DEL PEAK  4(2Q37.3) WILD-TYPE     7                        51   414
D16V11, multiclass
                           clus
vv                          DEL PEAK  4(2Q37.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              43
                           clus
vv                          DEL PEAK  4(2Q37.3) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            51
  WHITE                                               414
[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"
D16V12, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     1  34
  DEL PEAK  4(2Q37.3) WILD-TYPE  25 316
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      1   34
  DEL PEAK  4(2Q37.3) WILD-TYPE   25  316
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          34
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                25
  NOT HISPANIC OR LATINO                           316
[1] 2 2
[1] FALSE

Clustering(17) Variable = DEL PEAK  5(3P26.3) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(3P26.3) MUTATED   304 150
  DEL PEAK  5(3P26.3) WILD-TYPE  47  25
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                          454                            72 
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                          150                            25 
$`DEL PEAK  5(3P26.3) MUTATED`
TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        36.82        47.21         0.53        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        82.32        51.25        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        28.31        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       73.08       109.41        15.78        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
      109.51        48.36        78.64        49.28        94.29        28.73 
TCGA-AK-3455 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 
       22.45        38.40        82.45        72.89         1.41         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4701 
        4.57         2.53         3.48        28.47        19.00         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73        57.70        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       40.70        45.30        27.42         6.71        56.68        10.52 
TCGA-B0-4845 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       65.29        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       15.09        10.95         8.05        21.86        52.08        15.95 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
       90.87        90.48        30.48        58.59        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        41.88        51.02        38.43        48.82        46.39 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       42.41       111.52       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4099 
      131.15        89.49        91.46       126.05        35.90        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       21.30        31.30        31.66        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.05        45.37        25.55        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 
       27.02         0.85        24.23         6.38         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       14.30        27.29        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       17.36        16.27       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        32.61         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       77.03        61.78        64.27        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 
       27.78        62.07        80.68        37.25        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       93.99        18.48        52.24        74.17        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       49.08        44.94        12.23        31.89        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 
       33.99        31.33        72.59        77.98         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4774 
       41.75        71.80        48.07        13.15         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       60.59        13.51        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.90        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
       33.34        46.45        31.30        25.81        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.74 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       13.35        27.02        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
      115.00        46.55        63.25        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      114.41        54.61       105.37        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        10.72        74.27        75.06 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       64.18        30.64        51.52        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5671 
       54.48        38.56        45.14         3.06        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       25.25       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4853 
       66.31        78.18        74.66       105.93        83.90        25.45 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
        0.59        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        94.45        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       62.63        13.28        45.96        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-A4VX TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 
       66.28        56.84        53.46        81.21        18.12         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       19.43        19.96        23.01        16.37 

$`DEL PEAK  5(3P26.3) WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3440 
       11.90        10.49        43.20        65.52       117.80        94.19 
TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 
       46.78        40.01        83.21        37.58        12.13        40.70 
TCGA-B0-4688 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4834 TCGA-B0-4839 
        3.32         1.38         3.62        65.10        68.71        53.88 
TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-5080 TCGA-B0-5096 TCGA-B0-5100 TCGA-B0-5106 
       10.29        39.45        11.24         2.24        62.89        52.54 
TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5400 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-5635 
       19.30        52.87        56.98        32.61         1.68        24.82 
TCGA-B4-5378 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5545 TCGA-B8-5546 
        5.75        17.19        25.91        50.14        50.14        16.60 
TCGA-B8-5550 TCGA-B8-A54E TCGA-B8-A54K TCGA-B8-A8YJ TCGA-BP-4165 TCGA-BP-4173 
       48.53        29.88        15.42        14.17        99.85        62.24 
TCGA-BP-4177 TCGA-BP-4334 TCGA-BP-4756 TCGA-BP-4760 TCGA-BP-4769 TCGA-BP-4770 
       54.90        21.21        12.30        77.62        61.68        10.82 
TCGA-BP-4784 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4967 TCGA-BP-4976 
       60.95        20.38        37.25        47.97         6.74        53.65 
TCGA-BP-4988 TCGA-BP-4994 TCGA-BP-5191 TCGA-CJ-4875 TCGA-CJ-4889 TCGA-CJ-4890 
       27.22        43.00        31.79       116.84        63.98       115.69 
TCGA-CJ-4920 TCGA-CJ-5681 TCGA-CW-6087 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4854 
        4.57        18.15         1.35       103.43        18.77        46.16 
TCGA-CZ-4862 TCGA-DV-5567 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-EU-5905 TCGA-T7-A92I 
      107.54        65.88        23.90        12.00         3.91        11.70 

  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                         0.07                          1.35 
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                       149.16                        117.80 
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                       38.515                        37.415 
[1] "0.1 - 149.2 (38.5)" "1.4 - 117.8 (37.4)"
[1] "hr=" "1.2"
D17V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  5(3P26.3) MUTATED       220       50       115       70
  DEL PEAK  5(3P26.3) WILD-TYPE      43        7        10       13
D17V3, multiclass
           clus
vv          DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  STAGE I                           220                            43
  STAGE II                           50                             7
  STAGE III                         115                            10
  STAGE IV                           70                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  5(3P26.3) MUTATED   225  62 162   6
  DEL PEAK  5(3P26.3) WILD-TYPE  43   7  18   5
D17V4, multiclass
    clus
vv   DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  T1                         225                            43
  T2                          62                             7
  T3                         162                            18
  T4                           6                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P26.3) MUTATED   201  14
  DEL PEAK  5(3P26.3) WILD-TYPE  33   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.3) MUTATED    201   14
  DEL PEAK  5(3P26.3) WILD-TYPE   33    3
   clus
vv  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  0                         201                            33
  1                          14                             3
[1] 2 2
[1] FALSE
D17V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P26.3) MUTATED   363  67
  DEL PEAK  5(3P26.3) WILD-TYPE  55  11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.3) MUTATED    363   67
  DEL PEAK  5(3P26.3) WILD-TYPE   55   11
   clus
vv  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  0                         363                            55
  1                          67                            11
[1] 2 2
[1] FALSE
D17V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P26.3) MUTATED   164 291
  DEL PEAK  5(3P26.3) WILD-TYPE  25  48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.3) MUTATED    164  291
  DEL PEAK  5(3P26.3) WILD-TYPE   25   48
        clus
vv       DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE
  FEMALE                         164                            25
  MALE                           291                            48
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
D17V10, continuous
[1] "Remove cluster labels:"        "DEL PEAK  5(3P26.3) WILD-TYPE"
clus
  DEL PEAK  5(3P26.3) MUTATED DEL PEAK  5(3P26.3) WILD-TYPE 
                           10                             2 
                 TCGA-A3-A8OV                  TCGA-A3-A8OW 
"DEL PEAK  5(3P26.3) MUTATED" "DEL PEAK  5(3P26.3) MUTATED" 
                 TCGA-AK-3445                  TCGA-AK-3451 
"DEL PEAK  5(3P26.3) MUTATED" "DEL PEAK  5(3P26.3) MUTATED" 
                 TCGA-B2-A4SR                  TCGA-B8-5158 
"DEL PEAK  5(3P26.3) MUTATED" "DEL PEAK  5(3P26.3) MUTATED" 
                 TCGA-DV-A4W0                  TCGA-G6-A8L7 
"DEL PEAK  5(3P26.3) MUTATED" "DEL PEAK  5(3P26.3) MUTATED" 
                 TCGA-MM-A563                  TCGA-MM-A84U 
"DEL PEAK  5(3P26.3) MUTATED" "DEL PEAK  5(3P26.3) MUTATED" 
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P26.3) MUTATED       6                        38   404
  DEL PEAK  5(3P26.3) WILD-TYPE     2                        18    53
D17V11, multiclass
                           clus
vv                          DEL PEAK  5(3P26.3) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          38
  WHITE                                             404
                           clus
vv                          DEL PEAK  5(3P26.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            18
  WHITE                                                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P26.3) MUTATED    24 295
  DEL PEAK  5(3P26.3) WILD-TYPE   2  55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.3) MUTATED     24  295
  DEL PEAK  5(3P26.3) WILD-TYPE    2   55
                        clus
vv                       DEL PEAK  5(3P26.3) MUTATED
  HISPANIC OR LATINO                              24
  NOT HISPANIC OR LATINO                         295
                        clus
vv                       DEL PEAK  5(3P26.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            55
[1] 2 2
[1] FALSE

Clustering(18) Variable = DEL PEAK  6(3P22.2) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P22.2) MUTATED   306 158
  DEL PEAK  6(3P22.2) WILD-TYPE  45  17
  DEL PEAK  6(3P22.2) MUTATED DEL PEAK  6(3P22.2) WILD-TYPE 
                          464                            62 
  DEL PEAK  6(3P22.2) MUTATED DEL PEAK  6(3P22.2) WILD-TYPE 
                          158                            17 
$`DEL PEAK  6(3P22.2) MUTATED`
TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        36.82        47.21         0.53        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        82.32        51.25        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        28.31        20.28        33.47        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       73.08       109.41        15.78        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
      109.51        48.36        78.64        49.28        94.29        28.73 
TCGA-AK-3455 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 
       22.45        38.40        82.45        72.89         1.41         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4701 
        4.57         2.53         3.48        28.47        19.00         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73        57.70        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       40.70        45.30        27.42         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5084 
       36.85        70.52        20.94        43.30        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5107 
       21.86        52.08        15.95        90.87        90.48        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       58.59        66.05        38.63        52.73        41.88        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       38.43        48.82        46.39        42.41       111.52       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
       35.90        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       21.57        16.67        12.00         5.10         0.85         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4622 
       27.16        42.71        25.05        45.37        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
       17.06         1.74         8.42         4.93        17.36        16.27 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       61.78        64.27        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       93.99        18.48        52.24        74.17        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       49.08        44.94        12.23        31.89        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 
       33.99        31.33        72.59        77.98         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4774 
       41.75        71.80        48.07        13.15         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       60.59        13.51        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.90        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
       33.34        46.45        31.30        25.81        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.74 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       13.35        27.02        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
      115.00        46.55        63.25        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      114.41        54.61       105.37        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4891 TCGA-CJ-4892 
      113.46        64.18        30.64        51.52        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       50.33        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       22.32        25.25       122.83        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 
       73.18        66.31        78.18        74.66       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75         6.77        14.66        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        13.28 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       45.96        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-A4VX TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       53.46        81.21        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC 
       23.01        16.37 

$`DEL PEAK  6(3P22.2) WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3440 
       11.90        10.49        43.20        65.52       117.80        94.19 
TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 
       46.78        40.01        83.21        37.58        12.13        40.70 
TCGA-B0-4688 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4834 TCGA-B0-4839 
        3.32         1.38         3.62        65.10        68.71        53.88 
TCGA-B0-5080 TCGA-B0-5100 TCGA-B0-5106 TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5400 
       11.24        62.89        52.54        19.30        52.87        56.98 
TCGA-B0-5691 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-5635 TCGA-B4-5378 TCGA-B8-4619 
      112.80        32.61         1.68        24.82         5.75        17.19 
TCGA-B8-4621 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-A54E TCGA-B8-A54K TCGA-B8-A8YJ 
       25.91        50.14        16.60        29.88        15.42        14.17 
TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4756 TCGA-BP-4760 TCGA-BP-4769 TCGA-BP-4770 
       62.24        54.90        12.30        77.62        61.68        10.82 
TCGA-BP-4784 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4967 TCGA-BP-4976 
       60.95        20.38        37.25        47.97         6.74        53.65 
TCGA-BP-4988 TCGA-BP-4994 TCGA-BP-5191 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4912 
       27.22        43.00        31.79        63.98       115.69        54.48 
TCGA-CJ-5681 TCGA-CW-6087 TCGA-CZ-4862 TCGA-DV-5567 TCGA-DV-5576 TCGA-DV-A4VZ 
       18.15         1.35       107.54        65.88        23.90        12.00 
TCGA-EU-5905 TCGA-T7-A92I 
        3.91        11.70 

  DEL PEAK  6(3P22.2) MUTATED DEL PEAK  6(3P22.2) WILD-TYPE 
                         0.07                          1.35 
  DEL PEAK  6(3P22.2) MUTATED DEL PEAK  6(3P22.2) WILD-TYPE 
                       149.16                        117.80 
  DEL PEAK  6(3P22.2) MUTATED DEL PEAK  6(3P22.2) WILD-TYPE 
                       38.515                        37.415 
[1] "0.1 - 149.2 (38.5)" "1.4 - 117.8 (37.4)"
[1] "hr=" "1.1"
D18V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  6(3P22.2) MUTATED       223       49       119       74
  DEL PEAK  6(3P22.2) WILD-TYPE      40        8         6        9
D18V3, multiclass
           clus
vv          DEL PEAK  6(3P22.2) MUTATED DEL PEAK  6(3P22.2) WILD-TYPE
  STAGE I                           223                            40
  STAGE II                           49                             8
  STAGE III                         119                             6
  STAGE IV                           74                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  6(3P22.2) MUTATED   228  61 170   6
  DEL PEAK  6(3P22.2) WILD-TYPE  40   8  10   5
D18V4, multiclass
    clus
vv   DEL PEAK  6(3P22.2) MUTATED DEL PEAK  6(3P22.2) WILD-TYPE
  T1                         228                            40
  T2                          61                             8
  T3                         170                            10
  T4                           6                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P22.2) MUTATED   206  15
  DEL PEAK  6(3P22.2) WILD-TYPE  28   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P22.2) MUTATED    206   15
  DEL PEAK  6(3P22.2) WILD-TYPE   28    2
   clus
vv  DEL PEAK  6(3P22.2) MUTATED DEL PEAK  6(3P22.2) WILD-TYPE
  0                         206                            28
  1                          15                             2
[1] 2 2
[1] FALSE
D18V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P22.2) MUTATED   369  71
  DEL PEAK  6(3P22.2) WILD-TYPE  49   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P22.2) MUTATED    369   71
  DEL PEAK  6(3P22.2) WILD-TYPE   49    7
   clus
vv  DEL PEAK  6(3P22.2) MUTATED DEL PEAK  6(3P22.2) WILD-TYPE
  0                         369                            49
  1                          71                             7
[1] 2 2
[1] FALSE
D18V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P22.2) MUTATED   166 299
  DEL PEAK  6(3P22.2) WILD-TYPE  23  40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P22.2) MUTATED    166  299
  DEL PEAK  6(3P22.2) WILD-TYPE   23   40
        clus
vv       DEL PEAK  6(3P22.2) MUTATED DEL PEAK  6(3P22.2) WILD-TYPE
  FEMALE                         166                            23
  MALE                           299                            40
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
D18V10, continuous
[1] "Remove cluster labels:"        "DEL PEAK  6(3P22.2) WILD-TYPE"
clus
  DEL PEAK  6(3P22.2) MUTATED DEL PEAK  6(3P22.2) WILD-TYPE 
                           11                             1 
                 TCGA-A3-A8OV                  TCGA-A3-A8OW 
"DEL PEAK  6(3P22.2) MUTATED" "DEL PEAK  6(3P22.2) MUTATED" 
                 TCGA-AK-3445                  TCGA-AK-3451 
"DEL PEAK  6(3P22.2) MUTATED" "DEL PEAK  6(3P22.2) MUTATED" 
                 TCGA-B2-A4SR                  TCGA-B8-5158 
"DEL PEAK  6(3P22.2) MUTATED" "DEL PEAK  6(3P22.2) MUTATED" 
                 TCGA-B8-5550                  TCGA-DV-A4W0 
"DEL PEAK  6(3P22.2) MUTATED" "DEL PEAK  6(3P22.2) MUTATED" 
                 TCGA-G6-A8L7                  TCGA-MM-A563 
"DEL PEAK  6(3P22.2) MUTATED" "DEL PEAK  6(3P22.2) MUTATED" 
                 TCGA-MM-A84U 
"DEL PEAK  6(3P22.2) MUTATED" 
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P22.2) MUTATED       6                        38   414
  DEL PEAK  6(3P22.2) WILD-TYPE     2                        18    43
D18V11, multiclass
                           clus
vv                          DEL PEAK  6(3P22.2) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          38
  WHITE                                             414
                           clus
vv                          DEL PEAK  6(3P22.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            18
  WHITE                                                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P22.2) MUTATED    23 303
  DEL PEAK  6(3P22.2) WILD-TYPE   3  47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P22.2) MUTATED     23  303
  DEL PEAK  6(3P22.2) WILD-TYPE    3   47
                        clus
vv                       DEL PEAK  6(3P22.2) MUTATED
  HISPANIC OR LATINO                              23
  NOT HISPANIC OR LATINO                         303
                        clus
vv                       DEL PEAK  6(3P22.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            47
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEL PEAK  7(3P14.1) MUTATION ANALYSIS
D19V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P14.1) MUTATED   247 126
  DEL PEAK  7(3P14.1) WILD-TYPE 104  49
  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE 
                          373                           153 
  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE 
                          126                            49 
$`DEL PEAK  7(3P14.1) MUTATED`
TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       12.66        36.82        47.21        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3347 
       38.47        48.82        62.01        34.29         4.50        52.93 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3365 
       29.92        18.44        88.37        42.97        82.32        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        24.16        53.29        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.64        18.87        28.31        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       22.65         0.10         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       29.10       109.41        15.78        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 
      109.51        78.64        49.28        94.29        28.73        22.45 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4693 
       38.40        82.45        72.89         1.41         1.41         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        28.47        19.00         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
       57.70        43.96         6.64        15.72        46.59         0.59 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 
       52.21        45.07        33.50        16.77        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 
       45.30        27.42         6.71        56.68        10.52        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 
       39.45        26.07        29.03         2.27        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5084 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       43.30         7.30        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 
        2.24        21.86        52.08        15.95        90.87        90.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       58.59        66.05        38.63        52.73        41.88        51.02 
TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 
       38.43        46.39        42.41       111.52       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       15.78        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       71.41        73.84       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-5633 TCGA-B2-5639 
       89.49        91.46        35.90        31.96        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       21.57        16.67        12.00         5.10         0.85         0.53 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        4.64         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        23.74         1.18        27.02         0.85 
TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
        6.38         0.53        34.39        27.29        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
        8.42         4.93        17.36       111.02        85.51        94.72 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4329 
       77.03        61.78        64.27        97.45         3.58        27.78 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68        37.25        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 
       62.86        54.77        49.08        44.94        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4758 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       12.33        72.59         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
       13.15         5.33        61.97        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       11.64        48.95        36.39        10.98        36.95         6.71 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4965 TCGA-BP-4971 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4982 
       61.51        48.89         6.90        47.11        14.93        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       46.45        31.30        25.81        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       16.47         5.82        45.07        30.64        41.62        18.51 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.02        27.62        35.21        28.87        48.10         6.35 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
        1.74        74.20        52.27        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5189 
       38.30        42.44        37.25        37.22        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4634 TCGA-CJ-4635 
       19.82        44.55        34.95        31.27       115.00        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       63.25        73.22       114.41        54.61       105.37        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 
       11.05        21.24        83.97        49.25        79.66        74.27 
TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4886 
       75.06        64.27        71.87        66.21        61.91        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       30.64        51.52        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45        50.24        56.35        47.67        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
      108.56        50.33        45.14       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 
      133.71        25.71        18.87        22.32       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6032 
       73.35        53.26       118.85        53.42        75.58       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5588 
        7.36        64.57        81.83         5.39        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66       105.93        83.90        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39        93.04         5.46        63.42        58.82        79.53 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       18.44        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 
       10.22        21.76        69.96        84.30        22.52         1.94 
TCGA-CZ-5469 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       31.10        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5573 
       22.78        62.63        13.28        45.96        12.16        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-A4VX TCGA-DV-A4W0 TCGA-EU-5906 TCGA-EU-5907 
       66.28        56.84        53.46        81.21         6.77         4.18 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       10.29        35.87         2.01        19.43        19.96        23.01 
TCGA-MW-A4EC 
       16.37 

$`DEL PEAK  7(3P14.1) WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3326 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3362 
       11.90         0.53        37.38        31.07        45.53        51.25 
TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3440 
       10.49        43.20        65.52       117.80        73.08        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 
       46.78        48.36        40.01        83.21        37.58        12.13 
TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
       40.70         3.32         4.57         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4814 TCGA-B0-4819 TCGA-B0-4834 
        7.82         3.25        58.45         5.52         6.02        68.71 
TCGA-B0-4839 TCGA-B0-4844 TCGA-B0-4852 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 
       53.88        10.29        36.85        11.24        11.90        25.32 
TCGA-B0-5100 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5121 
       62.89        52.54        30.48        19.30        52.87        48.82 
TCGA-B0-5400 TCGA-B0-5691 TCGA-B0-5695 TCGA-B0-5705 TCGA-B0-5812 TCGA-B2-3923 
       56.98       112.80        70.68       149.16       126.05        32.61 
TCGA-B2-4098 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B4-5378 TCGA-B4-5838 
        1.68        21.30        31.30        24.82         5.75         5.46 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-5158 
       42.71        25.05        45.37        17.19        25.91        20.91 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5553 TCGA-B8-A54E 
       24.23        50.14        16.60        48.53        14.30        29.88 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4173 
       15.42        16.27        14.17        90.28       101.06        62.24 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       54.90        53.42        62.07        21.21        15.16         0.07 
TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4759 TCGA-BP-4760 
       12.23        33.99        31.33        12.30        77.98        77.62 
TCGA-BP-4762 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4775 TCGA-BP-4784 TCGA-BP-4787 
       44.15        61.68        10.82        60.59        60.95        15.78 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4964 TCGA-BP-4967 
       36.53        20.38        37.25        47.97        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4976 
       57.40        58.98        14.24        49.38        45.50        53.65 
TCGA-BP-4981 TCGA-BP-4988 TCGA-BP-4994 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5009 
       36.07        27.22        43.00        38.70        37.48        36.23 
TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5186 TCGA-BP-5202 TCGA-CJ-4638 
       79.30        30.64         9.63        22.78         0.95        14.17 
TCGA-CJ-4639 TCGA-CJ-4872 TCGA-CJ-4875 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4889 
      106.16        10.72       116.84        57.83       113.46        63.98 
TCGA-CJ-4890 TCGA-CJ-4897 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-4913 
      115.69       109.84        49.18        49.28        54.48        38.56 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5686 
        3.06         4.57        18.81        25.25        18.15        67.00 
TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-6087 TCGA-CW-6093 TCGA-CZ-4861 
       62.66        92.02        85.78         1.35       103.43        14.66 
TCGA-CZ-4862 TCGA-CZ-4866 TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5467 TCGA-CZ-5470 
      107.54        61.41        23.74        79.63         2.40        12.69 
TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       65.88        11.67        23.90        12.00        18.12         3.91 
TCGA-G6-A5PC TCGA-G6-A8L7 TCGA-T7-A92I 
        7.96        70.13        11.70 

  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE 
                       133.94                        149.16 
  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE 
                        39.45                         36.85 
[1] "0.1 - 133.9 (39.5)" "0.1 - 149.2 (36.9)"
[1] "hr=" "1"  
D19V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  7(3P14.1) MUTATED       181       41        97       54
  DEL PEAK  7(3P14.1) WILD-TYPE      82       16        28       29
D19V3, multiclass
           clus
vv          DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE
  STAGE I                           181                            82
  STAGE II                           41                            16
  STAGE III                          97                            28
  STAGE IV                           54                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  7(3P14.1) MUTATED   184  50 135   4
  DEL PEAK  7(3P14.1) WILD-TYPE  84  19  45   7
D19V4, multiclass
    clus
vv   DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE
  T1                         184                            84
  T2                          50                            19
  T3                         135                            45
  T4                           4                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.1) MUTATED   166  10
  DEL PEAK  7(3P14.1) WILD-TYPE  68   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.1) MUTATED    166   10
  DEL PEAK  7(3P14.1) WILD-TYPE   68    7
   clus
vv  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE
  0                         166                            68
  1                          10                             7
[1] 2 2
[1] FALSE
D19V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.1) MUTATED   299  52
  DEL PEAK  7(3P14.1) WILD-TYPE 119  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.1) MUTATED    299   52
  DEL PEAK  7(3P14.1) WILD-TYPE  119   26
   clus
vv  DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE
  0                         299                           119
  1                          52                            26
[1] 2 2
[1] FALSE
D19V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.1) MUTATED   116 257
  DEL PEAK  7(3P14.1) WILD-TYPE  73  82
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.1) MUTATED    116  257
  DEL PEAK  7(3P14.1) WILD-TYPE   73   82
        clus
vv       DEL PEAK  7(3P14.1) MUTATED DEL PEAK  7(3P14.1) WILD-TYPE
  FEMALE                         116                            73
  MALE                           257                            82
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
D19V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P14.1) MUTATED       5                        33   329
  DEL PEAK  7(3P14.1) WILD-TYPE     3                        23   128
D19V11, multiclass
                           clus
vv                          DEL PEAK  7(3P14.1) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                          33
  WHITE                                             329
                           clus
vv                          DEL PEAK  7(3P14.1) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                            23
  WHITE                                               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"
D19V12, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.1) MUTATED    19 245
  DEL PEAK  7(3P14.1) WILD-TYPE   7 105
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.1) MUTATED     19  245
  DEL PEAK  7(3P14.1) WILD-TYPE    7  105
                        clus
vv                       DEL PEAK  7(3P14.1) MUTATED
  HISPANIC OR LATINO                              19
  NOT HISPANIC OR LATINO                         245
                        clus
vv                       DEL PEAK  7(3P14.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           105
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK  8(3P12.2) MUTATION ANALYSIS
D20V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3P12.2) MUTATED   197 108
  DEL PEAK  8(3P12.2) WILD-TYPE 154  67
  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE 
                          305                           221 
  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE 
                          108                            67 
$`DEL PEAK  8(3P12.2) MUTATED`
TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
       12.66        36.82        39.16        24.16        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3331 
       49.58        48.59        36.36        38.99        38.47        48.82 
TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       62.01         4.50        52.93        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
       82.32        28.70        74.63        74.76        24.16        53.29 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NJ 
       20.71        18.64        18.87        28.31        20.28        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       22.65         0.10         0.10        11.18        10.62       109.91 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
      109.41        15.78        73.68       112.08        68.61       109.51 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3460 
       78.64        49.28        94.29        28.73        38.40        82.45 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
       72.89         1.41         1.41         2.53         3.48        28.47 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4810 
        5.98         2.14        19.73        43.96         6.64        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4821 TCGA-B0-4822 
       46.59         0.59        52.21        33.50        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 
       45.30        27.42         6.71        56.68        10.52        65.29 
TCGA-B0-4846 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5077 TCGA-B0-5084 
       39.45        29.03         2.27        70.52        43.30         7.30 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5102 
       15.09        10.95         8.05        52.08        15.95        90.87 
TCGA-B0-5108 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       58.59        38.63        52.73        41.88        51.02        38.43 
TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5697 
       46.39        42.41       129.67       133.94        15.78        86.47 
TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5712 
      126.28        73.84       105.37       130.65        79.89        89.49 
TCGA-B2-3924 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       35.90        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-5162 TCGA-B8-5163 
        5.10         0.85        27.16        25.55         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A54D TCGA-B8-A54F 
        0.85         6.38         0.53        34.39        27.29        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 
        1.74         8.42         4.93       111.02        94.72        32.61 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 
        0.43        23.05        77.03        61.78        64.27        97.45 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4338 TCGA-BP-4340 
        3.58        27.78        80.68        37.25        93.99        18.48 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4351 
       74.17        62.86        54.77        49.08        44.94        31.89 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4758 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4766 
       11.31        12.33        72.59         5.98        41.75        48.07 
TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4789 
       13.15         5.33        61.97        56.91        68.38        48.95 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       10.98        36.95         6.71         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4971 TCGA-BP-4974 TCGA-BP-4975 
       63.62        58.68        60.30        48.89         6.90        47.11 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       31.30        25.81        36.95         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5004 
        5.82        45.07        30.64        41.62        18.51        37.02 
TCGA-BP-5006 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5173 TCGA-BP-5174 
       27.62        35.21        28.87        48.10         1.74        74.20 
TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
       52.27        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.25        37.22        13.35        27.02        33.24        31.79 
TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4634 
       24.62        19.82        44.55        34.95        31.27       115.00 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       46.55        63.25       114.41        54.61       105.37        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4876 
       11.05        21.24        83.97        49.25        74.27        64.27 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4891 
       66.21        61.91        64.18        30.64        51.52        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        27.65        39.45        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-5671 TCGA-CJ-5672 
       47.67        49.97        51.25       108.56       131.08        72.00 
TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5689 
       25.71        22.32        18.15       122.83        62.10        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
      118.85        53.42        75.58       119.64         7.36        64.57 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
       81.83         5.39        73.18        78.18        74.66       105.93 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77        46.16         0.59        69.21        58.75 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39        93.04         5.46        63.42        58.82        79.53 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       90.54        91.69        55.33        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5982 
       69.96        84.30        22.52         1.94        31.10        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       13.28        45.96        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-A4VX TCGA-DV-A4W0 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 
       56.84        53.46        81.21         6.77         4.18        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        16.37 

$`DEL PEAK  8(3P12.2) WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3326 TCGA-A3-3336 
       11.90        47.21         0.53        49.08        37.38        34.29 
TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3374 
       31.07        45.53        29.92        51.25        10.49        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-A6NI TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       55.76        65.52        33.47        29.10       117.80        73.08 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3455 
       94.19        46.78        48.36        40.01        83.21        22.45 
TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4697 
       37.58        12.13        40.70         3.32         4.57        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4710 TCGA-B0-4714 
        1.38         3.62        65.10         7.82        57.70         3.25 
TCGA-B0-4718 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4834 
       58.45         5.52        45.07        16.77         6.02        68.71 
TCGA-B0-4839 TCGA-B0-4844 TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-5075 TCGA-B0-5080 
       53.88        10.29        26.07        36.85        20.94        11.24 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5100 
       11.90        25.32        18.51         2.24        21.86        62.89 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5117 
       90.48        52.54        30.48        19.30        66.05        52.87 
TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5695 TCGA-B0-5696 
       48.82        56.98       111.52       112.80        70.68        85.78 
TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5711 TCGA-B0-5713 
      119.38        80.91        71.41       149.16       131.15        91.46 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
      126.05        32.61         1.68        31.96        21.30        31.30 
TCGA-B2-5635 TCGA-B4-5378 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
       24.82         5.75         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        23.31        16.80        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5165 
       17.19        25.91        50.14        20.91        23.74        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5553 TCGA-B8-A54E TCGA-B8-A54J 
       50.14        16.60        48.53        14.30        29.88        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
       15.42        16.27        14.17        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4326 
       93.34        99.85        89.36        62.24        54.90        53.42 
TCGA-BP-4330 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4341 TCGA-BP-4349 
       62.07        21.21        15.16         0.07        52.24        12.23 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 
       33.99        31.33        12.30        77.98        77.62        44.15 
TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4782 
       71.80        61.68        10.82        60.59        13.51        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4799 
       60.95        15.78        36.53        20.38        36.39        37.25 
TCGA-BP-4804 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       47.97        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       14.24        49.38        45.50        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4988 TCGA-BP-4994 TCGA-BP-5001 TCGA-BP-5007 
       33.34        46.45        27.22        43.00        38.70        37.48 
TCGA-BP-5009 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5186 
       36.23         6.35        79.30        30.64         9.63        22.78 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4637 TCGA-CJ-4638 
       23.47        13.41        33.47         0.95        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 
      106.16        79.66        10.72        75.06       116.84        71.87 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4897 TCGA-CJ-4905 
       57.83       113.46        63.98       115.69       109.84        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 
        4.57        18.81       129.40       133.71        18.87        25.25 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-5588 
       73.35        67.00        62.66        92.02        85.78        66.31 
TCGA-CW-6087 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4861 
        1.35       103.43        25.45        47.08         6.77        14.66 
TCGA-CZ-4862 TCGA-CZ-4866 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5460 
      107.54        61.41        23.74        18.44        79.63        94.45 
TCGA-CZ-5467 TCGA-CZ-5470 TCGA-DV-5567 TCGA-DV-5576 TCGA-DV-A4VZ TCGA-EU-5904 
        2.40        12.69        65.88        23.90        12.00        18.12 
TCGA-EU-5905 TCGA-G6-A5PC TCGA-G6-A8L7 TCGA-MM-A84U TCGA-T7-A92I 
        3.91         7.96        70.13        23.01        11.70 

  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE 
                       133.94                        149.16 
  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE 
                        39.16                         37.25 
[1] "0.1 - 133.9 (39.2)" "0.1 - 149.2 (37.2)"
[1] "hr=" "1.1"
D20V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  8(3P12.2) MUTATED       150       34        77       44
  DEL PEAK  8(3P12.2) WILD-TYPE     113       23        48       39
D20V3, multiclass
           clus
vv          DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE
  STAGE I                           150                           113
  STAGE II                           34                            23
  STAGE III                          77                            48
  STAGE IV                           44                            39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  8(3P12.2) MUTATED   153  41 108   3
  DEL PEAK  8(3P12.2) WILD-TYPE 115  28  72   8
D20V4, multiclass
    clus
vv   DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE
  T1                         153                           115
  T2                          41                            28
  T3                         108                            72
  T4                           3                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V5, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.2) MUTATED   136   8
  DEL PEAK  8(3P12.2) WILD-TYPE  98   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.2) MUTATED    136    8
  DEL PEAK  8(3P12.2) WILD-TYPE   98    9
   clus
vv  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE
  0                         136                            98
  1                           8                             9
[1] 2 2
[1] FALSE
D20V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.2) MUTATED   244  42
  DEL PEAK  8(3P12.2) WILD-TYPE 174  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.2) MUTATED    244   42
  DEL PEAK  8(3P12.2) WILD-TYPE  174   36
   clus
vv  DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE
  0                         244                           174
  1                          42                            36
[1] 2 2
[1] FALSE
D20V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.2) MUTATED    90 215
  DEL PEAK  8(3P12.2) WILD-TYPE  99 124
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.2) MUTATED     90  215
  DEL PEAK  8(3P12.2) WILD-TYPE   99  124
        clus
vv       DEL PEAK  8(3P12.2) MUTATED DEL PEAK  8(3P12.2) WILD-TYPE
  FEMALE                          90                            99
  MALE                           215                           124
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
D20V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3P12.2) MUTATED       4                        27   269
  DEL PEAK  8(3P12.2) WILD-TYPE     4                        29   188
D20V11, multiclass
                           clus
vv                          DEL PEAK  8(3P12.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          27
  WHITE                                             269
                           clus
vv                          DEL PEAK  8(3P12.2) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            29
  WHITE                                               188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.2) MUTATED    13 203
  DEL PEAK  8(3P12.2) WILD-TYPE  13 147
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.2) MUTATED     13  203
  DEL PEAK  8(3P12.2) WILD-TYPE   13  147
                        clus
vv                       DEL PEAK  8(3P12.2) MUTATED
  HISPANIC OR LATINO                              13
  NOT HISPANIC OR LATINO                         203
                        clus
vv                       DEL PEAK  8(3P12.2) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           147
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK  9(3Q11.2) MUTATION ANALYSIS
D21V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(3Q11.2) MUTATED   108  53
  DEL PEAK  9(3Q11.2) WILD-TYPE 243 122
  DEL PEAK  9(3Q11.2) MUTATED DEL PEAK  9(3Q11.2) WILD-TYPE 
                          161                           365 
  DEL PEAK  9(3Q11.2) MUTATED DEL PEAK  9(3Q11.2) WILD-TYPE 
                           53                           122 
$`DEL PEAK  9(3Q11.2) MUTATED`
TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
       12.66        36.82        39.16        24.16        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3331 TCGA-A3-3346 
       49.58        48.59        36.36        38.99        48.82         4.50 
TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       52.93        88.37        82.32        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       24.16        18.64        18.87         0.10         0.10        11.18 
TCGA-AK-3425 TCGA-AK-3429 TCGA-AK-3433 TCGA-AK-3454 TCGA-AK-3460 TCGA-AK-3461 
      109.91       109.41       112.08        28.73        82.45        72.89 
TCGA-B0-4694 TCGA-B0-4703 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4815 
        3.48         5.98        15.72        46.59         0.59        52.21 
TCGA-B0-4817 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4828 TCGA-B0-4836 
       33.50        40.44        36.53        14.93        10.09        40.70 
TCGA-B0-4837 TCGA-B0-4841 TCGA-B0-4845 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-5084 
       45.30         6.71        65.29        29.03         2.27         7.30 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5099 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 
       10.95         8.05        15.95        52.73        41.88        38.43 
TCGA-B0-5399 TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5710 TCGA-B2-3924 
       46.39       126.28        73.84       105.37        79.89        35.90 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5832 TCGA-B8-4620 TCGA-B8-5162 
       31.66        32.98        21.57         5.10        25.55         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5549 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54H 
       27.02         0.85         6.38        27.29        17.06         8.42 
TCGA-BP-4158 TCGA-BP-4166 TCGA-BP-4176 TCGA-BP-4329 TCGA-BP-4332 TCGA-BP-4342 
      111.02         0.43        64.27        27.78        37.25        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 
       62.86        54.77        49.08        44.94        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4758 TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4774 TCGA-BP-4777 
       12.33        72.59        41.75        13.15        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4960 
       68.38        10.98        36.95         6.71         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4975 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4991 TCGA-BP-4992 
       63.62        47.11        31.30        25.81        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5008 TCGA-BP-5168 
        5.82        30.64        41.62        18.51        35.21        48.10 
TCGA-BP-5173 TCGA-BP-5180 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5195 TCGA-BP-5198 
        1.74        74.40        37.22        13.35        24.62        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4642 TCGA-CJ-4644 
       44.55        34.95        31.27        46.55       105.37        11.05 
TCGA-CJ-4868 TCGA-CJ-4873 TCGA-CJ-4888 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4902 
       21.24        74.27        51.52        26.93        50.01        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5689 
       51.25       108.56        22.32       122.83        62.10        53.26 
TCGA-CJ-6027 TCGA-CW-5580 TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4863 TCGA-CZ-4864 
      118.85        64.57       105.93        83.90        63.39        93.04 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       63.42        58.82        79.53        90.54        91.69        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       10.85        10.22        21.76         2.40         1.94        31.10 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5573 
       65.65        12.26        14.63        62.63        13.28        37.15 
TCGA-DV-5574 TCGA-EU-5907 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC 
       66.28         4.18         2.01        19.96        16.37 

$`DEL PEAK  9(3Q11.2) WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3325 TCGA-A3-3326 
       11.90        47.21         0.53        49.08        38.47        37.38 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       62.01        34.29        31.07        45.53        29.92        18.44 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       42.97        51.25        10.49        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       20.71        28.31        65.52        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 
       22.65        10.62        29.10       117.80        73.08        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       73.68        68.61       109.51        94.19        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3455 
       78.64        40.01        49.28        94.29        83.21        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       37.58        38.40        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        1.41         4.57         2.53        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
        3.62        65.10         7.82         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4814 TCGA-B0-4816 
       43.96         6.64         3.25        58.45         5.52        45.07 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 
       16.77         6.02        54.48        29.10        78.44        68.71 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 
       27.42        53.88        56.68        10.52        10.29        39.45 
TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
       26.07        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5096 TCGA-B0-5097 
       11.90        25.32        18.51        15.09         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       52.08        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5117 TCGA-B0-5119 
       58.59        19.30        66.05        38.63        52.87        51.02 
TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       48.82        56.98        42.41       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5711 TCGA-B0-5712 
       80.91        71.41       149.16       130.65       131.15        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46       126.05        32.61         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       31.30        24.82        16.67        12.00         5.75         0.85 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        42.71        25.05        45.37        17.19 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5165 TCGA-B8-5545 
       25.91        50.14        20.91        23.74        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54E 
       16.60        48.53         0.53        34.39        14.30        29.88 
TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        1.74         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       99.85        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4330 TCGA-BP-4331 
       54.90        97.45        53.42         3.58        62.07        80.68 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4759 TCGA-BP-4760 
       12.23        33.99        31.33        12.30        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
        5.98        44.15        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
        5.33        60.59        13.51        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4799 TCGA-BP-4804 
       48.95        36.53        20.38        36.39        37.25        47.97 
TCGA-BP-4959 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       87.45        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       57.40        58.98        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.90        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-5001 
       36.95        27.22         3.88        43.00        45.07        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5169 
       37.02        27.62        37.48        36.23        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
       79.30        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5189 
       49.15        38.30        42.44        37.25        22.78        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5196 TCGA-BP-5202 
       33.24        31.79        23.47        13.41        33.47         0.95 
TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        63.25        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       54.61        58.95        83.97        49.25        79.66        10.72 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4890 
       57.83       113.46        64.18        30.64        63.98       115.69 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       47.67        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 
      129.40       133.71        25.71        18.87        25.25        18.15 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       73.35        67.00        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
        7.36        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6093 TCGA-CW-6097 
       66.31        78.18        74.66         1.35       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5454 
        6.77        14.66       107.54         5.46        61.41        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       18.44        79.63        94.45        69.96        84.30        22.52 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5988 TCGA-DV-5566 TCGA-DV-5567 
       12.69        80.19        67.96        22.78        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ 
       12.16        11.67        56.84        23.90        53.46        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 
       81.21        18.12         3.91         6.77         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MM-A84U TCGA-T7-A92I 
       70.13        35.87        19.43        23.01        11.70 

  DEL PEAK  9(3Q11.2) MUTATED DEL PEAK  9(3Q11.2) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK  9(3Q11.2) MUTATED DEL PEAK  9(3Q11.2) WILD-TYPE 
                       126.28                        149.16 
  DEL PEAK  9(3Q11.2) MUTATED DEL PEAK  9(3Q11.2) WILD-TYPE 
                        36.95                         39.45 
[1] "0.1 - 126.3 (37.0)" "0.1 - 149.2 (39.5)"
[1] "hr=" "1.1"
D21V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  9(3Q11.2) MUTATED        78       22        40       21
  DEL PEAK  9(3Q11.2) WILD-TYPE     185       35        85       62
D21V3, multiclass
           clus
vv          DEL PEAK  9(3Q11.2) MUTATED DEL PEAK  9(3Q11.2) WILD-TYPE
  STAGE I                            78                           185
  STAGE II                           22                            35
  STAGE III                          40                            85
  STAGE IV                           21                            62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  9(3Q11.2) MUTATED    81  25  55   0
  DEL PEAK  9(3Q11.2) WILD-TYPE 187  44 125  11
D21V4, multiclass
    clus
vv   DEL PEAK  9(3Q11.2) MUTATED DEL PEAK  9(3Q11.2) WILD-TYPE
  T1                          81                           187
  T2                          25                            44
  T3                          55                           125
  T4                           0                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                               cls
clus                              0   1
  DEL PEAK  9(3Q11.2) MUTATED    71   3
  DEL PEAK  9(3Q11.2) WILD-TYPE 163  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3Q11.2) MUTATED     71    3
  DEL PEAK  9(3Q11.2) WILD-TYPE  163   14
   clus
vv  DEL PEAK  9(3Q11.2) MUTATED DEL PEAK  9(3Q11.2) WILD-TYPE
  0                          71                           163
  1                           3                            14
[1] 2 2
[1] FALSE
D21V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(3Q11.2) MUTATED   130  22
  DEL PEAK  9(3Q11.2) WILD-TYPE 288  56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3Q11.2) MUTATED    130   22
  DEL PEAK  9(3Q11.2) WILD-TYPE  288   56
   clus
vv  DEL PEAK  9(3Q11.2) MUTATED DEL PEAK  9(3Q11.2) WILD-TYPE
  0                         130                           288
  1                          22                            56
[1] 2 2
[1] FALSE
D21V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(3Q11.2) MUTATED    31 130
  DEL PEAK  9(3Q11.2) WILD-TYPE 158 209
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3Q11.2) MUTATED     31  130
  DEL PEAK  9(3Q11.2) WILD-TYPE  158  209
        clus
vv       DEL PEAK  9(3Q11.2) MUTATED DEL PEAK  9(3Q11.2) WILD-TYPE
  FEMALE                          31                           158
  MALE                           130                           209
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
D21V10, continuous
[1] "Remove cluster labels:"      "DEL PEAK  9(3Q11.2) MUTATED"
clus
  DEL PEAK  9(3Q11.2) MUTATED DEL PEAK  9(3Q11.2) WILD-TYPE 
                            1                            11 
                   TCGA-A3-A8OW                    TCGA-AK-3445 
"DEL PEAK  9(3Q11.2) WILD-TYPE" "DEL PEAK  9(3Q11.2) WILD-TYPE" 
                   TCGA-AK-3451                    TCGA-B2-A4SR 
"DEL PEAK  9(3Q11.2) WILD-TYPE" "DEL PEAK  9(3Q11.2) WILD-TYPE" 
                   TCGA-B8-5158                    TCGA-B8-5550 
"DEL PEAK  9(3Q11.2) WILD-TYPE" "DEL PEAK  9(3Q11.2) WILD-TYPE" 
                   TCGA-DV-A4W0                    TCGA-G6-A8L7 
"DEL PEAK  9(3Q11.2) WILD-TYPE" "DEL PEAK  9(3Q11.2) WILD-TYPE" 
                   TCGA-MM-A563                    TCGA-MM-A84U 
"DEL PEAK  9(3Q11.2) WILD-TYPE" "DEL PEAK  9(3Q11.2) WILD-TYPE" 
                   TCGA-T7-A92I 
"DEL PEAK  9(3Q11.2) WILD-TYPE" 
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3Q11.2) MUTATED       2                        11   145
  DEL PEAK  9(3Q11.2) WILD-TYPE     6                        45   312
D21V11, multiclass
                           clus
vv                          DEL PEAK  9(3Q11.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             145
                           clus
vv                          DEL PEAK  9(3Q11.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            45
  WHITE                                               312
[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"
D21V12, binary
                               cls
clus                              0   1
  DEL PEAK  9(3Q11.2) MUTATED     5  99
  DEL PEAK  9(3Q11.2) WILD-TYPE  21 251
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3Q11.2) MUTATED      5   99
  DEL PEAK  9(3Q11.2) WILD-TYPE   21  251
                        clus
vv                       DEL PEAK  9(3Q11.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          99
                        clus
vv                       DEL PEAK  9(3Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                21
  NOT HISPANIC OR LATINO                           251
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK 10(4Q34.3) MUTATION ANALYSIS
D22V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4Q34.3) MUTATED    37  41
  DEL PEAK 10(4Q34.3) WILD-TYPE 314 134
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                           78                           448 
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                           41                           134 
$`DEL PEAK 10(4Q34.3) MUTATED`
TCGA-A3-3316 TCGA-A3-3320 TCGA-A3-3346 TCGA-A3-3352 TCGA-A3-3367 TCGA-A3-3380 
       49.08        49.58         4.50        18.44        74.63        18.64 
TCGA-AK-3436 TCGA-AK-3458 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4698 TCGA-B0-4707 
      109.51        38.40         3.32         1.41         1.38        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       57.70        43.96        46.59         0.59         5.52        52.21 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-4845 
       40.44        36.53        10.09        40.70        10.29        65.29 
TCGA-B0-4852 TCGA-B0-5084 TCGA-B0-5095 TCGA-B0-5098 TCGA-B0-5113 TCGA-B0-5116 
       36.85         7.30         8.05        52.08        38.63        41.88 
TCGA-B0-5691 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5709 TCGA-B4-5838 TCGA-B8-4143 
      112.80       126.28        80.91       130.65         5.46        23.31 
TCGA-B8-4146 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5549 TCGA-BP-4161 TCGA-BP-4164 
       16.80        20.91         1.18         6.38        90.28        32.61 
TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4787 
       62.86        31.89        12.33        13.15        10.82        15.78 
TCGA-BP-4985 TCGA-BP-5173 TCGA-BP-5183 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4636 
       31.30         1.74        42.44        33.47        19.82        63.25 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4870 TCGA-CJ-4881 TCGA-CJ-4897 TCGA-CJ-4903 
       58.95        11.05        49.25        66.21       109.84        51.25 
TCGA-CJ-4907 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6028 TCGA-CW-5580 
       49.28       133.71        25.71        22.32        53.42        64.57 
TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 
       66.31        83.90        18.77        47.08        69.21         6.77 
TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-EU-5907 
       61.41        90.54        10.85        84.30        31.10         4.18 

$`DEL PEAK 10(4Q34.3) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       24.16        49.02        37.15        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.47        37.38        48.82        62.01        34.29        31.07 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       52.93        45.53        29.92        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
       51.25        10.49        28.70        74.76        24.16        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       43.20        55.76        20.71        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10       117.80        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 
      109.41        15.78        73.68       112.08        68.61        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        78.64        40.01        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 
       83.21        28.73        22.45        37.58        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       28.47        19.00         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4816 
        2.14         6.64         3.25        58.45        15.72        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       33.50        16.77         6.02        14.93        54.48        29.10 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        68.71        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       56.68        10.52        39.45        26.07        29.03         2.27 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 
       70.52        20.94        43.30        11.24        11.90        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       18.51        15.09        10.95         2.24        21.86        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       19.30        66.05        52.73        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5710 TCGA-B0-5711 
       71.41        73.84       149.16       105.37        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       31.96        21.30        31.30        31.66        24.82        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         0.85 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4148 TCGA-B8-4151 
        0.53         4.64         0.36         0.23        27.16        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 
       16.27        14.17       111.02        85.51        94.72       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       15.16         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4354 
       54.77        49.08        44.94        12.23        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 
       44.15        41.75        71.80        48.07        61.68         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       60.95        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       49.15        38.30        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17       106.16       114.41        54.61       105.37 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       21.24        83.97        79.66        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
      116.84        64.27        71.87        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        27.65        39.45        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       47.67        49.97       108.56        49.18        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       72.00       129.40        18.87        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
       62.10        73.35        67.00        53.26       118.85        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       62.66       119.64         7.36        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       85.78        73.18        78.18        74.66         1.35       105.93 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 
      103.43        25.45        46.16         0.59        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 
      107.54        63.39        93.04         5.46        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        79.63        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 
       94.45        10.22        21.76        69.96        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
        1.94        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       53.46        12.00        81.21        18.12         3.91         6.77 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.96        23.01        16.37        11.70 

  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                         0.59                          0.07 
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                       133.71                        149.16 
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                       37.625                        38.515 
[1] "0.6 - 133.7 (37.6)" "0.1 - 149.2 (38.5)"
[1] "hr=" "1.9"
D22V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 10(4Q34.3) MUTATED        19        7        30       22
  DEL PEAK 10(4Q34.3) WILD-TYPE     244       50        95       61
D22V3, multiclass
           clus
vv          DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  STAGE I                            19                           244
  STAGE II                            7                            50
  STAGE III                          30                            95
  STAGE IV                           22                            61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 10(4Q34.3) MUTATED    20   9  43   6
  DEL PEAK 10(4Q34.3) WILD-TYPE 248  60 137   5
D22V4, multiclass
    clus
vv   DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  T1                          20                           248
  T2                           9                            60
  T3                          43                           137
  T4                           6                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V5, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q34.3) MUTATED    32   3
  DEL PEAK 10(4Q34.3) WILD-TYPE 202  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q34.3) MUTATED     32    3
  DEL PEAK 10(4Q34.3) WILD-TYPE  202   14
   clus
vv  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  0                          32                           202
  1                           3                            14
[1] 2 2
[1] FALSE
D22V6, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q34.3) MUTATED    59  19
  DEL PEAK 10(4Q34.3) WILD-TYPE 359  59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q34.3) MUTATED     59   19
  DEL PEAK 10(4Q34.3) WILD-TYPE  359   59
   clus
vv  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  0                          59                           359
  1                          19                            59
[1] 2 2
[1] FALSE
D22V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q34.3) MUTATED    24  54
  DEL PEAK 10(4Q34.3) WILD-TYPE 165 285
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q34.3) MUTATED     24   54
  DEL PEAK 10(4Q34.3) WILD-TYPE  165  285
        clus
vv       DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  FEMALE                          24                           165
  MALE                            54                           285
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
[1] "Remove cluster labels:"      "DEL PEAK 10(4Q34.3) MUTATED"
clus
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                            2                            19 
                   TCGA-A3-A8CQ                    TCGA-A3-A8OV 
"DEL PEAK 10(4Q34.3) WILD-TYPE" "DEL PEAK 10(4Q34.3) WILD-TYPE" 
                   TCGA-A3-A8OW                    TCGA-AK-3445 
"DEL PEAK 10(4Q34.3) WILD-TYPE" "DEL PEAK 10(4Q34.3) WILD-TYPE" 
                   TCGA-AK-3451                    TCGA-B2-A4SR 
"DEL PEAK 10(4Q34.3) WILD-TYPE" "DEL PEAK 10(4Q34.3) WILD-TYPE" 
                   TCGA-B8-4621                    TCGA-B8-5164 
"DEL PEAK 10(4Q34.3) WILD-TYPE" "DEL PEAK 10(4Q34.3) WILD-TYPE" 
                   TCGA-B8-5550                    TCGA-B8-A54E 
"DEL PEAK 10(4Q34.3) WILD-TYPE" "DEL PEAK 10(4Q34.3) WILD-TYPE" 
                   TCGA-B8-A54F                    TCGA-B8-A54G 
"DEL PEAK 10(4Q34.3) WILD-TYPE" "DEL PEAK 10(4Q34.3) WILD-TYPE" 
                   TCGA-B8-A8YJ                    TCGA-DV-A4VX 
"DEL PEAK 10(4Q34.3) WILD-TYPE" "DEL PEAK 10(4Q34.3) WILD-TYPE" 
                   TCGA-DV-A4W0                    TCGA-G6-A5PC 
"DEL PEAK 10(4Q34.3) WILD-TYPE" "DEL PEAK 10(4Q34.3) WILD-TYPE" 
                   TCGA-G6-A8L7                    TCGA-MM-A563 
"DEL PEAK 10(4Q34.3) WILD-TYPE" "DEL PEAK 10(4Q34.3) WILD-TYPE" 
                   TCGA-T7-A92I 
"DEL PEAK 10(4Q34.3) WILD-TYPE" 
D22V10, continuous
[1] "Remove cluster labels:"      "DEL PEAK 10(4Q34.3) MUTATED"
clus
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                            1                            11 
                   TCGA-A3-A8OV                    TCGA-A3-A8OW 
"DEL PEAK 10(4Q34.3) WILD-TYPE" "DEL PEAK 10(4Q34.3) WILD-TYPE" 
                   TCGA-AK-3445                    TCGA-AK-3451 
"DEL PEAK 10(4Q34.3) WILD-TYPE" "DEL PEAK 10(4Q34.3) WILD-TYPE" 
                   TCGA-B2-A4SR                    TCGA-B8-5550 
"DEL PEAK 10(4Q34.3) WILD-TYPE" "DEL PEAK 10(4Q34.3) WILD-TYPE" 
                   TCGA-DV-A4W0                    TCGA-G6-A8L7 
"DEL PEAK 10(4Q34.3) WILD-TYPE" "DEL PEAK 10(4Q34.3) WILD-TYPE" 
                   TCGA-MM-A563                    TCGA-MM-A84U 
"DEL PEAK 10(4Q34.3) WILD-TYPE" "DEL PEAK 10(4Q34.3) WILD-TYPE" 
                   TCGA-T7-A92I 
"DEL PEAK 10(4Q34.3) WILD-TYPE" 
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(4Q34.3) MUTATED       1                         2    73
  DEL PEAK 10(4Q34.3) WILD-TYPE     7                        54   384
D22V11, multiclass
                           clus
vv                          DEL PEAK 10(4Q34.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              73
                           clus
vv                          DEL PEAK 10(4Q34.3) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            54
  WHITE                                               384
[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"
D22V12, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q34.3) MUTATED     5  54
  DEL PEAK 10(4Q34.3) WILD-TYPE  21 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q34.3) MUTATED      5   54
  DEL PEAK 10(4Q34.3) WILD-TYPE   21  296
                        clus
vv                       DEL PEAK 10(4Q34.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          54
                        clus
vv                       DEL PEAK 10(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                21
  NOT HISPANIC OR LATINO                           296
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK 11(6Q26) MUTATION ANALYSIS
D23V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 11(6Q26) MUTATED   101  50
  DEL PEAK 11(6Q26) WILD-TYPE 250 125
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                        151                         375 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                         50                         125 
$`DEL PEAK 11(6Q26) MUTATED`
TCGA-A3-3306 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
       36.82        24.16        49.08        49.02        37.15        49.58 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3374 
       62.01        34.29         4.50        52.93        18.44        43.20 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3426 TCGA-AK-3430 TCGA-AK-3433 
       18.64        18.87         0.10        29.10        15.78       112.08 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3454 TCGA-AK-3458 
       68.61       109.51        94.19        40.01        28.73        38.40 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 
       72.89        12.13        40.70         1.41         3.48        28.47 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4810 TCGA-B0-4813 
        1.38         3.62        19.73        43.96        15.72         0.59 
TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4844 
       36.53        54.48        10.09        40.70        45.30        10.29 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-5084 TCGA-B0-5102 TCGA-B0-5108 TCGA-B0-5117 
       29.03         2.27         7.30        90.87        58.59        52.87 
TCGA-B0-5119 TCGA-B0-5402 TCGA-B0-5702 TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5377 
       51.02        42.41        71.41        32.61        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4148 TCGA-B8-4620 
        5.10         0.53         5.46        23.31        27.16        25.55 
TCGA-B8-5158 TCGA-B8-A54G TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4167 TCGA-BP-4176 
       20.91         1.74        94.72        32.61        89.36        64.27 
TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4334 TCGA-BP-4342 TCGA-BP-4346 
       97.45         3.58        80.68        21.21        74.17        49.08 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4777 
       11.31        12.33         5.98        13.15        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4962 
       68.38        15.78        36.39        87.45        71.41        58.68 
TCGA-BP-4963 TCGA-BP-4968 TCGA-BP-4974 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
       60.30        57.40         6.90        46.45        25.81        36.95 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 
       16.47         5.82        43.00        18.51         6.35        30.64 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5201 
       62.86        74.40        49.15        37.22        31.79        31.27 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4643 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4876 
      115.00        46.55        58.95        79.66        10.72        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4887 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       71.87        66.21        30.64        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-5675 TCGA-CJ-5676 
      109.84        47.67       108.56        49.28       129.40       133.71 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5584 
       22.32        25.25       118.85        53.42       119.64         5.39 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4864 
       85.78        66.31        25.45        69.21        58.75        93.04 
TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5465 
       61.41        58.82        79.63        94.45        10.22        84.30 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-5565 TCGA-DV-5568 
       80.19        67.96        65.65        14.63        13.28        12.16 
TCGA-DV-5573 TCGA-DV-5575 TCGA-EU-5907 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-MM-A563 
       37.15        56.84         4.18        70.13        35.87        19.43 
TCGA-MW-A4EC 
       16.37 

$`DEL PEAK 11(6Q26) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3322 
       12.66        11.90        47.21         0.53        39.16        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 
       36.36        38.99        38.47        37.38        48.82        31.07 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       45.53        29.92        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
       10.49        28.70        74.63        74.76        24.16        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       55.76        20.71        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       15.39        22.65         0.10        11.18        10.62       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3443 TCGA-AK-3444 
      117.80        73.08       109.41        73.68        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3455 TCGA-AK-3456 
       78.64        49.28        94.29        83.21        22.45        37.58 
TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 
       82.45         1.41         3.32         4.57         2.53        19.00 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       65.10         7.82         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
        3.25        58.45        46.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4827 
       33.50        16.77         6.02        40.44        14.93        29.10 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       78.44        68.71        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-4945 
       10.52        65.29        39.45        26.07        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.24        11.90        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 
       15.95        62.89        90.48        52.54        30.48        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5121 
       66.05        38.63        52.73        41.88        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       80.91        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46       126.05        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       31.96        21.30        31.30        31.66        24.82        32.98 
TCGA-B2-A4SR TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
       16.67         5.75         0.85         4.64         0.36         0.23 
TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 
       16.80        42.71        25.05        45.37        17.19        25.91 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54H TCGA-B8-A54I 
       14.30        27.29        29.88        17.06         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 
       90.28       101.06        93.34        99.85         0.43        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       77.03        62.24        61.78        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       62.07        37.25        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       52.24        62.86        54.77        44.94        12.23        31.89 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
        5.33        61.97        13.51        11.64        60.95        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       36.53        20.38        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       47.97         6.94        63.62        61.22        61.51         6.74 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
       58.98        14.24        48.89        49.38        45.50        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4988 
       53.65        14.93        36.07        33.34        31.30        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 
        3.88        46.45        45.07        30.64        41.62        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 
       48.10        79.30         1.74        74.20        52.27         9.63 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       38.30        42.44        37.25        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
       44.55        34.95         0.95        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4644 TCGA-CJ-4868 
      106.16       114.41        54.61       105.37        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4882 
       83.97        49.25        74.27        75.06       116.84        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       57.83       113.46        64.18        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       26.93        27.65        50.24        56.35        49.97        51.25 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5677 TCGA-CJ-5678 
        4.57        18.81       131.08        72.00        25.71        18.87 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15       122.83        62.10        73.35        67.00        53.26 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       75.58        62.66         7.36        64.57        92.02        81.83 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       73.18        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4860 
      103.43        18.77        46.16         0.59        47.08         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5453 
       14.66       107.54        63.39         5.46        63.42        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 
       23.74        18.44        90.54        91.69        55.33        10.85 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        69.96        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 
       12.69        12.26        22.78        62.63        45.96        65.88 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 
       11.67        66.28        23.90        53.46        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-GK-A6C7 
       18.12         3.91         6.77         7.96        10.29         2.01 
TCGA-MM-A564 TCGA-MM-A84U TCGA-T7-A92I 
       19.96        23.01        11.70 

  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                       0.10                        0.07 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                     133.71                      149.16 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                      39.45                       38.43 
[1] "0.1 - 133.7 (39.5)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1"  
D23V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 11(6Q26) MUTATED        69       20        34       28
  DEL PEAK 11(6Q26) WILD-TYPE     194       37        91       55
D23V3, multiclass
           clus
vv          DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  STAGE I                          69                         194
  STAGE II                         20                          37
  STAGE III                        34                          91
  STAGE IV                         28                          55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 11(6Q26) MUTATED    70  22  55   4
  DEL PEAK 11(6Q26) WILD-TYPE 198  47 125   7
D23V4, multiclass
    clus
vv   DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  T1                        70                         198
  T2                        22                          47
  T3                        55                         125
  T4                         4                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V5, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q26) MUTATED    56   9
  DEL PEAK 11(6Q26) WILD-TYPE 178   8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED     56    9
  DEL PEAK 11(6Q26) WILD-TYPE  178    8
   clus
vv  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  0                        56                         178
  1                         9                           8
[1] 2 2
[1] FALSE
D23V6, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q26) MUTATED   120  25
  DEL PEAK 11(6Q26) WILD-TYPE 298  53
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED    120   25
  DEL PEAK 11(6Q26) WILD-TYPE  298   53
   clus
vv  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  0                       120                         298
  1                        25                          53
[1] 2 2
[1] FALSE
D23V7, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q26) MUTATED    43 108
  DEL PEAK 11(6Q26) WILD-TYPE 146 231
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED     43  108
  DEL PEAK 11(6Q26) WILD-TYPE  146  231
        clus
vv       DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  FEMALE                        43                         146
  MALE                         108                         231
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
D23V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q26) MUTATED       2                         9   137
  DEL PEAK 11(6Q26) WILD-TYPE     6                        47   320
D23V11, multiclass
                           clus
vv                          DEL PEAK 11(6Q26) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         9
  WHITE                                           137
                           clus
vv                          DEL PEAK 11(6Q26) WILD-TYPE
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          47
  WHITE                                             320
[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"
D23V12, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q26) MUTATED    11  97
  DEL PEAK 11(6Q26) WILD-TYPE  15 253
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED     11   97
  DEL PEAK 11(6Q26) WILD-TYPE   15  253
                        clus
vv                       DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  HISPANIC OR LATINO                            11                          15
  NOT HISPANIC OR LATINO                        97                         253
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK 12(6Q26) MUTATION ANALYSIS
D24V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 12(6Q26) MUTATED   101  50
  DEL PEAK 12(6Q26) WILD-TYPE 250 125
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        151                         375 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                         50                         125 
$`DEL PEAK 12(6Q26) MUTATED`
TCGA-A3-3306 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
       36.82        24.16        49.08        49.02        37.15        49.58 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3374 
       62.01        34.29         4.50        52.93        18.44        43.20 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3426 TCGA-AK-3430 TCGA-AK-3433 
       18.64        18.87         0.10        29.10        15.78       112.08 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3454 TCGA-AK-3458 
       68.61       109.51        94.19        40.01        28.73        38.40 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 
       72.89        12.13        40.70         1.41         3.48        28.47 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4810 TCGA-B0-4813 
        1.38         3.62        19.73        43.96        15.72         0.59 
TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4844 
       36.53        54.48        10.09        40.70        45.30        10.29 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-5084 TCGA-B0-5102 TCGA-B0-5108 TCGA-B0-5117 
       29.03         2.27         7.30        90.87        58.59        52.87 
TCGA-B0-5119 TCGA-B0-5402 TCGA-B0-5702 TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5377 
       51.02        42.41        71.41        32.61        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4148 TCGA-B8-4620 
        5.10         0.53         5.46        23.31        27.16        25.55 
TCGA-B8-5158 TCGA-B8-A54G TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4167 TCGA-BP-4176 
       20.91         1.74        94.72        32.61        89.36        64.27 
TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4334 TCGA-BP-4342 TCGA-BP-4346 
       97.45         3.58        80.68        21.21        74.17        49.08 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4777 
       11.31        12.33         5.98        13.15        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4962 
       68.38        15.78        36.39        87.45        71.41        58.68 
TCGA-BP-4963 TCGA-BP-4968 TCGA-BP-4974 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
       60.30        57.40         6.90        46.45        25.81        36.95 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 
       16.47         5.82        43.00        18.51         6.35        30.64 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5201 
       62.86        74.40        49.15        37.22        31.79        31.27 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4643 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4876 
      115.00        46.55        58.95        79.66        10.72        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4887 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       71.87        66.21        30.64        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-5675 TCGA-CJ-5676 
      109.84        47.67       108.56        49.28       129.40       133.71 
TCGA-CJ-5679 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5584 TCGA-CW-5585 
       22.32       118.85        53.42       119.64         5.39        85.78 
TCGA-CW-5588 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4864 TCGA-CZ-4866 
       66.31        25.45        69.21        58.75        93.04        61.41 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5468 
       58.82        79.63        94.45        10.22        84.30         1.94 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-5565 TCGA-DV-5568 
       80.19        67.96        65.65        14.63        13.28        12.16 
TCGA-DV-5573 TCGA-DV-5575 TCGA-EU-5907 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-MM-A563 
       37.15        56.84         4.18        70.13        35.87        19.43 
TCGA-MW-A4EC 
       16.37 

$`DEL PEAK 12(6Q26) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3322 
       12.66        11.90        47.21         0.53        39.16        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 
       36.36        38.99        38.47        37.38        48.82        31.07 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       45.53        29.92        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
       10.49        28.70        74.63        74.76        24.16        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       55.76        20.71        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       15.39        22.65         0.10        11.18        10.62       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3443 TCGA-AK-3444 
      117.80        73.08       109.41        73.68        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3455 TCGA-AK-3456 
       78.64        49.28        94.29        83.21        22.45        37.58 
TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 
       82.45         1.41         3.32         4.57         2.53        19.00 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       65.10         7.82         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
        3.25        58.45        46.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4827 
       33.50        16.77         6.02        40.44        14.93        29.10 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       78.44        68.71        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-4945 
       10.52        65.29        39.45        26.07        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.24        11.90        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 
       15.95        62.89        90.48        52.54        30.48        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5121 
       66.05        38.63        52.73        41.88        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       80.91        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46       126.05        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       31.96        21.30        31.30        31.66        24.82        32.98 
TCGA-B2-A4SR TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
       16.67         5.75         0.85         4.64         0.36         0.23 
TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 
       16.80        42.71        25.05        45.37        17.19        25.91 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54H TCGA-B8-A54I 
       14.30        27.29        29.88        17.06         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 
       90.28       101.06        93.34        99.85         0.43        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       77.03        62.24        61.78        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       62.07        37.25        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       52.24        62.86        54.77        44.94        12.23        31.89 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
        5.33        61.97        13.51        11.64        60.95        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       36.53        20.38        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       47.97         6.94        63.62        61.22        61.51         6.74 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
       58.98        14.24        48.89        49.38        45.50        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4988 
       53.65        14.93        36.07        33.34        31.30        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 
        3.88        46.45        45.07        30.64        41.62        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 
       48.10        79.30         1.74        74.20        52.27         9.63 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       38.30        42.44        37.25        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
       44.55        34.95         0.95        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4644 TCGA-CJ-4868 
      106.16       114.41        54.61       105.37        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4882 
       83.97        49.25        74.27        75.06       116.84        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       57.83       113.46        64.18        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       26.93        27.65        50.24        56.35        49.97        51.25 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5677 TCGA-CJ-5678 
        4.57        18.81       131.08        72.00        25.71        18.87 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.26        75.58        62.66         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       81.83        73.18        78.18        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
       83.90       103.43        18.77        46.16         0.59        47.08 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-5451 
        6.77        14.66       107.54        63.39         5.46        63.42 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        90.54        91.69        55.33 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 
       10.85        21.76        69.96        22.52         2.40        31.10 
TCGA-CZ-5470 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 
       12.69        12.26        22.78        62.63        45.96        65.88 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 
       11.67        66.28        23.90        53.46        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-GK-A6C7 
       18.12         3.91         6.77         7.96        10.29         2.01 
TCGA-MM-A564 TCGA-MM-A84U TCGA-T7-A92I 
       19.96        23.01        11.70 

  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                       0.10                        0.07 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                     133.71                      149.16 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                      39.45                       38.43 
[1] "0.1 - 133.7 (39.5)" "0.1 - 149.2 (38.4)"
[1] "hr=" "1"  
D24V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 12(6Q26) MUTATED        69       20        34       28
  DEL PEAK 12(6Q26) WILD-TYPE     194       37        91       55
D24V3, multiclass
           clus
vv          DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  STAGE I                          69                         194
  STAGE II                         20                          37
  STAGE III                        34                          91
  STAGE IV                         28                          55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 12(6Q26) MUTATED    70  22  55   4
  DEL PEAK 12(6Q26) WILD-TYPE 198  47 125   7
D24V4, multiclass
    clus
vv   DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  T1                        70                         198
  T2                        22                          47
  T3                        55                         125
  T4                         4                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V5, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED    56   9
  DEL PEAK 12(6Q26) WILD-TYPE 178   8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     56    9
  DEL PEAK 12(6Q26) WILD-TYPE  178    8
   clus
vv  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  0                        56                         178
  1                         9                           8
[1] 2 2
[1] FALSE
D24V6, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED   120  25
  DEL PEAK 12(6Q26) WILD-TYPE 298  53
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED    120   25
  DEL PEAK 12(6Q26) WILD-TYPE  298   53
   clus
vv  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  0                       120                         298
  1                        25                          53
[1] 2 2
[1] FALSE
D24V7, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED    42 109
  DEL PEAK 12(6Q26) WILD-TYPE 147 230
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     42  109
  DEL PEAK 12(6Q26) WILD-TYPE  147  230
        clus
vv       DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  FEMALE                        42                         147
  MALE                         109                         230
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
D24V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6Q26) MUTATED       2                         9   137
  DEL PEAK 12(6Q26) WILD-TYPE     6                        47   320
D24V11, multiclass
                           clus
vv                          DEL PEAK 12(6Q26) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         9
  WHITE                                           137
                           clus
vv                          DEL PEAK 12(6Q26) WILD-TYPE
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          47
  WHITE                                             320
[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"
D24V12, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED    11  97
  DEL PEAK 12(6Q26) WILD-TYPE  15 253
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     11   97
  DEL PEAK 12(6Q26) WILD-TYPE   15  253
                        clus
vv                       DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  HISPANIC OR LATINO                            11                          15
  NOT HISPANIC OR LATINO                        97                         253
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK 13(8P23.2) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(8P23.2) MUTATED    93  61
  DEL PEAK 13(8P23.2) WILD-TYPE 258 114
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                          154                           372 
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                           61                           114 
$`DEL PEAK 13(8P23.2) MUTATED`
TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3365 TCGA-A3-3372 
       37.15        38.47        34.29         4.50        28.70        24.16 
TCGA-A3-3373 TCGA-A3-3382 TCGA-A3-A6NN TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3434 
       53.29        18.87         0.10       109.91        29.10        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3458 TCGA-AS-3777 
      109.51        94.19        78.64        40.01        38.40        40.70 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4699 TCGA-B0-4703 TCGA-B0-4707 
        3.32         1.41         4.57         3.62         5.98        19.73 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 
       43.96         6.64        58.45         0.59        52.21        45.07 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 
        6.02        40.44        36.53        40.70        27.42        53.88 
TCGA-B0-4845 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5094 TCGA-B0-5097 
       65.29         2.27        36.85        70.52        10.95        21.86 
TCGA-B0-5102 TCGA-B0-5108 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5712 TCGA-B0-5713 
       90.87        58.59        70.68        85.78        89.49        91.46 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4151 
       16.67        12.00         5.10         5.46        23.31        42.71 
TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-5551 
       20.91        27.02         0.85        50.14         6.38         0.53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-BP-4164 TCGA-BP-4169 TCGA-BP-4174 TCGA-BP-4176 
        8.42         4.93        32.61        23.05        61.78        64.27 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       53.42         3.58        93.99        18.48        52.24        62.86 
TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4768 TCGA-BP-4775 
       44.94        31.89        11.31        12.33        13.15        60.59 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 
       68.38        11.64        15.78        20.38        10.98        37.25 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
        6.94        87.45        71.41         6.74        57.40        14.24 
TCGA-BP-4973 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-4998 
       45.50        46.45        31.30        25.81        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5169 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5177 
       18.51        37.02         6.35         1.74        30.64         9.63 
TCGA-BP-5182 TCGA-BP-5196 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4637 TCGA-CJ-4640 
       38.30        33.47        34.95        31.27        73.22       114.41 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4876 TCGA-CJ-4878 
      105.37        58.95        21.24        49.25        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4894 
       66.21        57.83       113.46        51.52        63.98        27.65 
TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5672 
      109.84        51.25       108.56        49.28        54.48        72.00 
TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6033 
       25.71        22.32        53.26       118.85        75.58         7.36 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4860 TCGA-CZ-4862 TCGA-CZ-4865 
      105.93        83.90        46.16         6.77       107.54         5.46 
TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       79.53        90.54        10.22        21.76        84.30        22.52 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-5565 
        1.94        12.69        12.26        14.63        22.78        13.28 
TCGA-DV-5574 TCGA-DV-5575 TCGA-G6-A8L8 TCGA-MM-A563 
       66.28        56.84        35.87        19.43 

$`DEL PEAK 13(8P23.2) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.08        49.02        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3347 
       38.99        37.38        48.82        62.01        31.07        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3376 
       51.25        10.49        74.63        74.76        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       20.71        18.64        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 
       15.39        22.65         0.10        11.18        10.62       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3443 
       73.08       109.41        15.78        73.68       112.08        46.78 
TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       48.36        49.28        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4693 
       37.58        82.45        72.89        12.13         1.41         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 
        3.48        28.47        19.00         1.38        65.10         7.82 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 
        2.14        57.70         3.25        15.72        46.59         5.52 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       33.50        16.77        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       78.44        68.71        45.30         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-5075 TCGA-B0-5077 
       10.29        39.45        26.07        29.03        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 
        8.05         2.24        52.08        15.95        62.89        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       52.54        30.48        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       56.98        42.41       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       15.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
      126.05        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5378 
       31.30        31.66        24.82        32.98        21.57         5.75 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
        0.85         0.53         4.64         0.36         0.23        16.80 
TCGA-B8-4148 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.16        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5165 TCGA-B8-5546 TCGA-B8-5550 
       50.14        23.74         1.18        24.23        16.60        48.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       94.72        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4329 
       89.36        77.03        62.24        54.90        97.45        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 
       74.17        54.77        49.08        12.23        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 
       61.97        13.51        56.91        60.95        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 
       36.39        36.95         6.71        47.97        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4972 
       60.30        61.22        61.51        58.98        48.89        49.38 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        6.90        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       45.07        41.62        38.70        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 
       36.23        28.87        48.10        79.30        74.20        52.27 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       62.86        74.40        49.15        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5202 TCGA-CJ-4634 
       13.41        24.62        19.82        44.55         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4644 
       46.55        63.25        14.17       106.16        54.61        11.05 
TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       83.97        79.66        10.72        74.27        75.06       116.84 
TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       61.91        64.18        30.64       115.69        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       24.66        39.45        50.24        56.35        47.67        49.97 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       49.18        50.33        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 
       18.81       131.08       129.40       133.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       62.66       119.64        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       85.78        73.18        66.31        78.18        74.66         1.35 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
      103.43        18.77        25.45         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
       58.75        14.66        63.39        93.04        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 
       58.82        23.74        18.44        79.63        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5982 
       94.45        10.85        69.96         2.40        31.10        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       67.96        65.65        62.63        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 
       11.67        37.15        23.90        53.46        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       70.13         2.01        19.96        23.01        16.37        11.70 

  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                       118.85                        149.16 
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                        36.69                         39.45 
[1] "0.1 - 118.8 (36.7)" "0.1 - 149.2 (39.5)"
[1] "hr=" "1.4"
D25V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 13(8P23.2) MUTATED        64       18        43       29
  DEL PEAK 13(8P23.2) WILD-TYPE     199       39        82       54
D25V3, multiclass
           clus
vv          DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE
  STAGE I                            64                           199
  STAGE II                           18                            39
  STAGE III                          43                            82
  STAGE IV                           29                            54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 13(8P23.2) MUTATED    65  22  63   4
  DEL PEAK 13(8P23.2) WILD-TYPE 203  47 117   7
D25V4, multiclass
    clus
vv   DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE
  T1                          65                           203
  T2                          22                            47
  T3                          63                           117
  T4                           4                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                               cls
clus                              0   1
  DEL PEAK 13(8P23.2) MUTATED    67   4
  DEL PEAK 13(8P23.2) WILD-TYPE 167  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.2) MUTATED     67    4
  DEL PEAK 13(8P23.2) WILD-TYPE  167   13
   clus
vv  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE
  0                          67                           167
  1                           4                            13
[1] 2 2
[1] FALSE
D25V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(8P23.2) MUTATED   120  29
  DEL PEAK 13(8P23.2) WILD-TYPE 298  49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.2) MUTATED    120   29
  DEL PEAK 13(8P23.2) WILD-TYPE  298   49
   clus
vv  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE
  0                         120                           298
  1                          29                            49
[1] 2 2
[1] FALSE
D25V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(8P23.2) MUTATED    49 105
  DEL PEAK 13(8P23.2) WILD-TYPE 140 234
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.2) MUTATED     49  105
  DEL PEAK 13(8P23.2) WILD-TYPE  140  234
        clus
vv       DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE
  FEMALE                          49                           140
  MALE                           105                           234
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
D25V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(8P23.2) MUTATED       4                        10   137
  DEL PEAK 13(8P23.2) WILD-TYPE     4                        46   320
D25V11, multiclass
                           clus
vv                          DEL PEAK 13(8P23.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                             137
                           clus
vv                          DEL PEAK 13(8P23.2) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            46
  WHITE                                               320
[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"
D25V12, binary
                               cls
clus                              0   1
  DEL PEAK 13(8P23.2) MUTATED    12  89
  DEL PEAK 13(8P23.2) WILD-TYPE  14 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.2) MUTATED     12   89
  DEL PEAK 13(8P23.2) WILD-TYPE   14  261
                        clus
vv                       DEL PEAK 13(8P23.2) MUTATED
  HISPANIC OR LATINO                              12
  NOT HISPANIC OR LATINO                          89
                        clus
vv                       DEL PEAK 13(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           261
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK 14(9P23) MUTATION ANALYSIS
D26V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 14(9P23) MUTATED    78  73
  DEL PEAK 14(9P23) WILD-TYPE 273 102
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                        151                         375 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                         73                         102 
$`DEL PEAK 14(9P23) MUTATED`
TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3325 
       36.82        39.16        49.08        49.02        37.15        38.47 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3425 
        4.50        52.93        18.44        24.16        18.87       109.91 
TCGA-AK-3426 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 TCGA-AS-3777 TCGA-B0-4690 
       29.10       109.51        78.64        49.28        40.70         1.41 
TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4698 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        4.57         3.48         1.38        19.73        57.70        43.96 
TCGA-B0-4811 TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       46.59        52.21        33.50         6.02        40.44        36.53 
TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4842 TCGA-B0-4845 TCGA-B0-4848 TCGA-B0-5094 
       10.09        40.70        56.68        65.29        29.03        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5107 
        8.05         2.24        21.86        52.08        62.89        30.48 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5402 TCGA-B0-5694 TCGA-B0-5701 TCGA-B2-5633 
       38.63        41.88        42.41        15.78        80.91        31.66 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       21.57         5.10         5.46        25.55        50.14        20.91 
TCGA-B8-5549 TCGA-B8-5551 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4167 TCGA-BP-4176 
        6.38         0.53        90.28        32.61        89.36        64.27 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4763 
       74.17        62.86        31.89        11.31        12.33        41.75 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4797 TCGA-BP-4798 
       48.07        13.15        68.38        11.64        36.39        10.98 
TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4973 
        6.71        71.41        58.68        60.30        61.22        45.50 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-5000 
       46.45        31.30        25.81        43.00        45.07        18.51 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 
       36.23        28.87         6.35        30.64        62.86        74.40 
TCGA-BP-5183 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 
       42.44        27.02        31.79        33.47        19.82        31.27 
TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4871 TCGA-CJ-4881 TCGA-CJ-4888 TCGA-CJ-4890 
       46.55        14.17        79.66        66.21        51.52       115.69 
TCGA-CJ-4891 TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4908 
       26.93        39.45        56.35        47.67        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5677 
       54.48        38.56         4.57       131.08       133.71        25.71 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
       22.32        25.25       122.83        53.26       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-5588 
       75.58        62.66         7.36        64.57         5.39        66.31 
TCGA-CW-5591 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 
       74.66        83.90        18.77        46.16        47.08        69.21 
TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 
        6.77        79.63        10.85        10.22        84.30        22.52 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 
        1.94        31.10        12.69        67.96        65.65        14.63 
TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4W0 TCGA-G6-A5PC TCGA-G6-A8L7 TCGA-MM-A563 
       23.90        53.46        81.21         7.96        70.13        19.43 
TCGA-MM-A84U 
       23.01 

$`DEL PEAK 14(9P23) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3320 
       12.66        11.90        47.21         0.53        24.16        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       48.59        36.36        38.99        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 
       34.29        31.07        45.53        29.92        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 
       53.29        43.20        55.76        20.71        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
        0.10        11.18        10.62       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68       112.08        68.61        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       48.36        40.01        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 
       37.58        38.40        82.45        72.89        12.13         1.41 
TCGA-B0-4688 TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4699 TCGA-B0-4700 
        3.32         2.53        28.47        19.00         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        7.82         5.98         2.14         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4823 
       15.72         0.59         5.52        45.07        16.77        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 
       54.48        29.10        78.44        68.71        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 
       53.88         6.71        10.52        10.29        39.45        26.07 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5099 
       11.90         7.30        25.32        18.51        15.09        15.95 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.87        90.48        52.54        58.59        19.30        66.05 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
       56.98       111.52       112.80       129.67       133.94        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       119.38       126.28        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       91.46       126.05        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 
       21.30        31.30        24.82        32.98        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
        5.75         0.85         0.53         4.64         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       17.19        25.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
       24.23        50.14        16.60        48.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 
       94.72       101.06        93.34        99.85         0.43        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       77.03        62.24        61.78        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 
       15.16         0.07        93.99        18.48        52.24        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       49.08        44.94        12.23        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4765 
       72.59        77.98        77.62         5.98        44.15        71.80 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       56.91        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 
       37.25        36.95        47.97         6.94        87.45        63.62 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       49.38         6.90        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       33.34        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
        5.82        30.64        41.62        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       37.48        35.21        48.10        79.30         1.74        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 
       52.27         9.63        49.15        38.30        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 
       44.55        34.95         0.95       115.00        63.25        73.22 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
      106.16       114.41        54.61       105.37        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       21.24        83.97        49.25        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
      116.84        64.27        71.87        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       64.18        30.64        63.98        50.01        24.66        27.65 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
      109.84        50.24        49.97        51.25       108.56        49.18 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 
       45.14         3.06        18.81        72.00       129.40        18.87 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5581 
       18.15        62.10        73.35        67.00       119.64        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 
       81.83        85.78        73.18        78.18         1.35       105.93 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
      103.43        25.45         0.59        58.75        14.66       107.54 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5982 TCGA-CZ-5986 
       94.45        21.76        69.96         2.40        80.19        12.26 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        13.28        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-A4VZ TCGA-EU-5904 
       11.67        37.15        66.28        56.84        12.00        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 
        3.91         6.77         4.18        10.29        35.87         2.01 
TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       19.96        16.37        11.70 

  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                       0.53                        0.07 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                     133.71                      149.16 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                      38.63                       38.30 
[1] "0.5 - 133.7 (38.6)" "0.1 - 149.2 (38.3)"
[1] "hr=" "1.9"
D26V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 14(9P23) MUTATED        52       12        50       38
  DEL PEAK 14(9P23) WILD-TYPE     211       45        75       45
D26V3, multiclass
           clus
vv          DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  STAGE I                          52                         211
  STAGE II                         12                          45
  STAGE III                        50                          75
  STAGE IV                         38                          45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 14(9P23) MUTATED    55  16  76   5
  DEL PEAK 14(9P23) WILD-TYPE 213  53 104   6
D26V4, multiclass
    clus
vv   DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  T1                        55                         213
  T2                        16                          53
  T3                        76                         104
  T4                         5                           6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V5, binary
                             cls
clus                            0   1
  DEL PEAK 14(9P23) MUTATED    61   8
  DEL PEAK 14(9P23) WILD-TYPE 173   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(9P23) MUTATED     61    8
  DEL PEAK 14(9P23) WILD-TYPE  173    9
   clus
vv  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  0                        61                         173
  1                         8                           9
[1] 2 2
[1] FALSE
D26V6, binary
                             cls
clus                            0   1
  DEL PEAK 14(9P23) MUTATED   111  35
  DEL PEAK 14(9P23) WILD-TYPE 307  43
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(9P23) MUTATED    111   35
  DEL PEAK 14(9P23) WILD-TYPE  307   43
   clus
vv  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  0                       111                         307
  1                        35                          43
[1] 2 2
[1] FALSE
D26V7, binary
                             cls
clus                            0   1
  DEL PEAK 14(9P23) MUTATED    39 113
  DEL PEAK 14(9P23) WILD-TYPE 150 226
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(9P23) MUTATED     39  113
  DEL PEAK 14(9P23) WILD-TYPE  150  226
        clus
vv       DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  FEMALE                        39                         150
  MALE                         113                         226
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
D26V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(9P23) MUTATED       2                        11   134
  DEL PEAK 14(9P23) WILD-TYPE     6                        45   323
D26V11, multiclass
                           clus
vv                          DEL PEAK 14(9P23) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                        11
  WHITE                                           134
                           clus
vv                          DEL PEAK 14(9P23) WILD-TYPE
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          45
  WHITE                                             323
[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"
D26V12, binary
                             cls
clus                            0   1
  DEL PEAK 14(9P23) MUTATED     6 101
  DEL PEAK 14(9P23) WILD-TYPE  20 249
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(9P23) MUTATED      6  101
  DEL PEAK 14(9P23) WILD-TYPE   20  249
                        clus
vv                       DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  HISPANIC OR LATINO                             6                          20
  NOT HISPANIC OR LATINO                       101                         249
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK 15(9P21.3) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(9P21.3) MUTATED    79  79
  DEL PEAK 15(9P21.3) WILD-TYPE 272  96
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                          158                           368 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                           79                            96 
$`DEL PEAK 15(9P21.3) MUTATED`
TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3325 
       36.82        39.16        49.08        49.02        37.15        38.47 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3425 
        4.50        52.93        18.44        24.16        18.87       109.91 
TCGA-AK-3426 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 TCGA-AS-3777 TCGA-B0-4688 
       29.10       109.51        78.64        49.28        40.70         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4707 
        1.41         4.57         3.48        28.47         1.38        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4811 TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4819 
       57.70        43.96        46.59        52.21        33.50         6.02 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4842 TCGA-B0-4845 
       40.44        36.53        10.09        40.70        56.68        65.29 
TCGA-B0-4848 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       29.03        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5100 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5121 
       62.89        30.48        19.30        38.63        41.88        48.82 
TCGA-B0-5402 TCGA-B0-5694 TCGA-B0-5701 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5832 
       42.41        15.78        80.91        31.66        21.57         5.10 
TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5549 
        5.46        23.31        25.55        50.14        20.91         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4167 
       48.53         0.53        94.72        90.28        32.61        89.36 
TCGA-BP-4176 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       64.27        74.17        62.86        31.89        11.31        12.33 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4782 
        5.98        41.75        48.07        13.15        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4962 
       15.78        36.39        10.98         6.71        71.41        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4994 
       60.30        61.22        45.50        31.30        25.81        43.00 
TCGA-BP-4995 TCGA-BP-5000 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5175 
       45.07        18.51        36.23        28.87         6.35        30.64 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5196 
       62.86        74.40        42.44        27.02        31.79        33.47 
TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4868 TCGA-CJ-4871 
       19.82        31.27        46.55        14.17        21.24        79.66 
TCGA-CJ-4881 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4895 TCGA-CJ-4900 
       66.21        51.52       115.69        26.93        39.45        56.35 
TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 
       47.67        49.28        50.33        54.48        38.56         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 
       18.81       131.08       133.71        25.71        22.32        25.25 
TCGA-CJ-5682 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
      122.83        53.26       118.85        53.42        75.58        62.66 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 
        7.36        64.57         5.39        66.31        83.90        18.77 
TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5461 
       46.16        47.08        69.21         6.77        79.63        10.85 
TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 
       10.22        84.30        22.52         1.94        31.10        67.96 
TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-G6-A5PC TCGA-G6-A8L7 
       65.65        14.63        23.90        81.21         7.96        70.13 
TCGA-MM-A563 TCGA-MM-A84U 
       19.43        23.01 

$`DEL PEAK 15(9P21.3) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3320 
       12.66        11.90        47.21         0.53        24.16        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       48.59        36.36        38.99        37.38        48.82        62.01 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 
       34.29        31.07        45.53        29.92        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 
       53.29        43.20        55.76        20.71        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
        0.10        11.18        10.62       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68       112.08        68.61        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       48.36        40.01        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 
       37.58        38.40        82.45        72.89        12.13         1.41 
TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
        2.53        19.00         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 
        2.14         6.64         3.25        58.45        15.72         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        5.52        45.07        16.77        14.93        54.48        29.10 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        68.71        45.30        27.42        53.88         6.71 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 
       10.52        10.29        39.45        26.07         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 
       25.32        18.51        15.09        15.95        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
       52.54        58.59        66.05        52.73        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       38.43        46.39        56.98       111.52       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
      133.94        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 
        1.68        31.96        21.30        31.30        24.82        32.98 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       16.67        12.00         5.75         0.85         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.36         0.23        16.80        27.16        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       45.37        17.19        25.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 
        0.85        24.23        50.14        16.60        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 
      101.06        93.34        99.85         0.43        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       62.24        61.78        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4346 
        0.07        93.99        18.48        52.24        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       44.94        12.23        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 
       77.98        77.62        44.15        71.80        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 
        5.33        61.97        60.59        13.51        56.91        60.95 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 
       48.95        36.53        20.38        37.25        36.95        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        6.94        87.45        63.62        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 
       58.98        14.24        48.89        49.38         6.90        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 
       53.65        14.93        36.07        33.34        46.45        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4998 
       27.22         3.88        46.45        16.47         5.82        30.64 
TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       41.62        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 
       48.10        79.30         1.74        74.20        52.27         9.63 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       49.15        38.30        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 
       33.24        23.47        13.41        24.62        44.55        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 
        0.95       115.00        63.25        73.22       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61       105.37        58.95        11.05        83.97        49.25 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       10.72        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 
       61.91        57.83       113.46        64.18        30.64        63.98 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 
       50.01        24.66        27.65       109.84        50.24        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-5672 
       51.25       108.56        49.18        45.14         3.06        72.00 
TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
      129.40        18.87        18.15        62.10        73.35        67.00 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
      119.64        92.02        81.83        85.78        73.18        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 
       74.66         1.35       105.93       103.43        25.45         0.59 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
       58.75        14.66       107.54        63.39        93.04         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5464 
       90.54        91.69        55.33        94.45        21.76        69.96 
TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
        2.40        12.69        80.19        12.26        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       13.28        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       66.28        56.84        53.46        12.00        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 
        6.77         4.18        10.29        35.87         2.01        19.96 
TCGA-MW-A4EC TCGA-T7-A92I 
       16.37        11.70 

  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                         0.53                          0.07 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                       133.71                        149.16 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                       36.985                        38.845 
[1] "0.5 - 133.7 (37.0)" "0.1 - 149.2 (38.8)"
[1] "hr=" "2.1"
D27V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 15(9P21.3) MUTATED        53       11        54       41
  DEL PEAK 15(9P21.3) WILD-TYPE     210       46        71       42
D27V3, multiclass
           clus
vv          DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  STAGE I                            53                           210
  STAGE II                           11                            46
  STAGE III                          54                            71
  STAGE IV                           41                            42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 15(9P21.3) MUTATED    56  15  82   6
  DEL PEAK 15(9P21.3) WILD-TYPE 212  54  98   5
D27V4, multiclass
    clus
vv   DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  T1                          56                           212
  T2                          15                            54
  T3                          82                            98
  T4                           6                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V5, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED    66  10
  DEL PEAK 15(9P21.3) WILD-TYPE 168   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED     66   10
  DEL PEAK 15(9P21.3) WILD-TYPE  168    7
   clus
vv  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  0                          66                           168
  1                          10                             7
[1] 2 2
[1] FALSE
D27V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED   115  39
  DEL PEAK 15(9P21.3) WILD-TYPE 303  39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED    115   39
  DEL PEAK 15(9P21.3) WILD-TYPE  303   39
   clus
vv  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  0                         115                           303
  1                          39                            39
[1] 2 2
[1] FALSE
D27V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED    40 119
  DEL PEAK 15(9P21.3) WILD-TYPE 149 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED     40  119
  DEL PEAK 15(9P21.3) WILD-TYPE  149  220
        clus
vv       DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  FEMALE                          40                           149
  MALE                           119                           220
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
D27V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(9P21.3) MUTATED       1                        10   144
  DEL PEAK 15(9P21.3) WILD-TYPE     7                        46   313
D27V11, multiclass
                           clus
vv                          DEL PEAK 15(9P21.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                             144
                           clus
vv                          DEL PEAK 15(9P21.3) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            46
  WHITE                                               313
[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"
D27V12, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED     7 107
  DEL PEAK 15(9P21.3) WILD-TYPE  19 243
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED      7  107
  DEL PEAK 15(9P21.3) WILD-TYPE   19  243
                        clus
vv                       DEL PEAK 15(9P21.3) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         107
                        clus
vv                       DEL PEAK 15(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           243
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK 16(10Q23.31) MUTATION ANALYSIS
D28V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 16(10Q23.31) MUTATED    60  36
  DEL PEAK 16(10Q23.31) WILD-TYPE 291 139
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             96                             430 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             36                             139 
$`DEL PEAK 16(10Q23.31) MUTATED`
TCGA-A3-3316 TCGA-A3-3331 TCGA-A3-3346 TCGA-A3-3352 TCGA-A3-3374 TCGA-A3-3380 
       49.08        48.82         4.50        18.44        43.20        18.64 
TCGA-A3-A6NN TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3458 
        0.10        15.78       112.08        94.19        46.78        38.40 
TCGA-AK-3461 TCGA-AK-3465 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 
       72.89        12.13         3.32         1.41         3.48        28.47 
TCGA-B0-4699 TCGA-B0-4712 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4819 TCGA-B0-4828 
        3.62        43.96        58.45        46.59         6.02        10.09 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-5099 
       40.70        45.30        10.52        10.29        65.29        15.95 
TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5703 TCGA-B0-5706 TCGA-B2-3923 TCGA-B2-5641 
       52.87        42.41        73.84       105.37        32.61        21.57 
TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-5158 TCGA-B8-5549 TCGA-B8-5550 
        0.53         5.46        23.31        20.91         6.38        48.53 
TCGA-B8-A7U6 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4329 
       16.27        90.28        32.61         0.43        89.36        27.78 
TCGA-BP-4334 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4766 TCGA-BP-4770 
       21.21        74.17        62.86        31.89        48.07        10.82 
TCGA-BP-4775 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4973 TCGA-BP-4985 
       60.59        36.39         6.71        71.41        45.50        31.30 
TCGA-BP-4994 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5173 TCGA-BP-5180 TCGA-BP-5185 
       43.00        28.87         6.35         1.74        74.40        37.22 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4642 TCGA-CJ-4644 
       33.47        19.82        31.27        46.55       105.37        11.05 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4882 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 
       10.72        75.06        61.91        24.66       109.84        47.67 
TCGA-CJ-4907 TCGA-CJ-4923 TCGA-CJ-5676 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-6090 
       49.28        18.81       133.71       119.64         7.36        83.90 
TCGA-CZ-4860 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 
        6.77        90.54        94.45        84.30         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-DV-5565 TCGA-DV-5566 TCGA-EU-5907 TCGA-G6-A8L8 
       12.69        80.19        13.28        45.96         4.18        35.87 

$`DEL PEAK 16(10Q23.31) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.99        38.47        37.38        62.01        34.29        31.07 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       52.93        45.53        29.92        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       53.29        55.76        20.71        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        33.47        15.39        22.65         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10       117.80        73.08       109.41 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       73.68        68.61       109.51        48.36        78.64        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       49.28        94.29        83.21        28.73        22.45        37.58 
TCGA-AK-3460 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 
       82.45        40.70         1.41         4.57         2.53        19.00 
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        1.38        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 
       57.70         6.64         3.25        15.72         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 
       52.21        45.07        33.50        16.77        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4838 
       14.93        54.48        29.10        78.44        68.71        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       53.88         6.71        56.68        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.90         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        21.86        52.08        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       38.63        52.73        41.88        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98       111.52       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       80.91        71.41       149.16       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46       126.05        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR 
       21.30        31.30        31.66        24.82        32.98        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 
       12.00         5.75         5.10         0.85         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        16.80        27.16        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 
       17.19        25.55        25.91        50.14        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 
       27.02         0.85        24.23        50.14        16.60         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A8YJ TCGA-BP-4158 
        8.42         4.93        17.36        15.42        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4169 
       85.51        94.72       101.06        93.34        99.85        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 
       53.42         3.58        62.07        80.68        37.25        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4346 
        0.07        93.99        18.48        52.24        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        11.31        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 
       41.75        71.80        13.15        61.68         5.33        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       48.95        36.53        20.38        10.98        37.25        36.95 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        87.45        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       48.89        49.38         6.90        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       36.07        33.34        46.45        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
        3.88        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
       35.21        36.23        48.10        79.30        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
       52.27         9.63        62.86        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.25        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 
       23.47        13.41        24.62        44.55        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        63.25        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       54.61        58.95        21.24        83.97        49.25        79.66 
TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 
       74.27       116.84        64.27        71.87        66.21        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       26.93        50.01        27.65        39.45        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.25       108.56        49.18        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 
       38.56        45.14         3.06         4.57       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      129.40        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
      122.83        62.10        73.35        67.00        53.26       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       53.42        75.58        62.66        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        5.39        85.78        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
        1.35       105.93       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66       107.54 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        79.63        91.69        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        69.96        22.52         2.40 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       23.90        53.46        12.00        81.21        18.12         3.91 
TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
        6.77         7.96        10.29        70.13         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-T7-A92I 
       19.96        23.01        16.37        11.70 

  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                           0.10                            0.07 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                         133.71                          149.16 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                         33.040                          39.075 
[1] "0.1 - 133.7 (33.0)" "0.1 - 149.2 (39.1)"
[1] "hr=" "1.3"
D28V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 16(10Q23.31) MUTATED        34       11        31       20
  DEL PEAK 16(10Q23.31) WILD-TYPE     229       46        94       63
D28V3, multiclass
           clus
vv          DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  STAGE I                              34                             229
  STAGE II                             11                              46
  STAGE III                            31                              94
  STAGE IV                             20                              63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 16(10Q23.31) MUTATED    34  12  44   6
  DEL PEAK 16(10Q23.31) WILD-TYPE 234  57 136   5
D28V4, multiclass
    clus
vv   DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  T1                            34                             234
  T2                            12                              57
  T3                            44                             136
  T4                             6                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V5, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q23.31) MUTATED    40   3
  DEL PEAK 16(10Q23.31) WILD-TYPE 194  14
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     40    3
  DEL PEAK 16(10Q23.31) WILD-TYPE  194   14
   clus
vv  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  0                            40                             194
  1                             3                              14
[1] 2 2
[1] FALSE
D28V6, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q23.31) MUTATED    76  17
  DEL PEAK 16(10Q23.31) WILD-TYPE 342  61
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     76   17
  DEL PEAK 16(10Q23.31) WILD-TYPE  342   61
   clus
vv  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  0                            76                             342
  1                            17                              61
[1] 2 2
[1] FALSE
D28V7, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q23.31) MUTATED    26  70
  DEL PEAK 16(10Q23.31) WILD-TYPE 163 269
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     26   70
  DEL PEAK 16(10Q23.31) WILD-TYPE  163  269
        clus
vv       DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  FEMALE                            26                             163
  MALE                              70                             269
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
[1] "Remove cluster labels:"        "DEL PEAK 16(10Q23.31) MUTATED"
clus
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                              2                              19 
                     TCGA-A3-A8CQ                      TCGA-A3-A8OV 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                     TCGA-A3-A8OW                      TCGA-AK-3445 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                     TCGA-AK-3451                      TCGA-B2-A4SR 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                     TCGA-B8-4146                      TCGA-B8-4621 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                     TCGA-B8-5164                      TCGA-B8-A54E 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                     TCGA-B8-A54F                      TCGA-B8-A54G 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                     TCGA-B8-A8YJ                      TCGA-DV-A4VX 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                     TCGA-DV-A4W0                      TCGA-G6-A5PC 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                     TCGA-G6-A8L7                      TCGA-MM-A563 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                     TCGA-T7-A92I 
"DEL PEAK 16(10Q23.31) WILD-TYPE" 
D28V10, continuous
[1] "Remove cluster labels:"        "DEL PEAK 16(10Q23.31) MUTATED"
clus
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                              2                              10 
                     TCGA-A3-A8OV                      TCGA-A3-A8OW 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                     TCGA-AK-3445                      TCGA-AK-3451 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                     TCGA-B2-A4SR                      TCGA-DV-A4W0 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                     TCGA-G6-A8L7                      TCGA-MM-A563 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                     TCGA-MM-A84U                      TCGA-T7-A92I 
"DEL PEAK 16(10Q23.31) WILD-TYPE" "DEL PEAK 16(10Q23.31) WILD-TYPE" 
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(10Q23.31) MUTATED       0                         6    87
  DEL PEAK 16(10Q23.31) WILD-TYPE     8                        50   370
D28V11, multiclass
                           clus
vv                          DEL PEAK 16(10Q23.31) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                87
                           clus
vv                          DEL PEAK 16(10Q23.31) WILD-TYPE
  ASIAN                                                   8
  BLACK OR AFRICAN AMERICAN                              50
  WHITE                                                 370
[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"
D28V12, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q23.31) MUTATED     6  60
  DEL PEAK 16(10Q23.31) WILD-TYPE  20 290
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED      6   60
  DEL PEAK 16(10Q23.31) WILD-TYPE   20  290
                        clus
vv                       DEL PEAK 16(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            60
                        clus
vv                       DEL PEAK 16(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  20
  NOT HISPANIC OR LATINO                             290
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK 17(13Q14.2) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(13Q14.2) MUTATED    43  38
  DEL PEAK 17(13Q14.2) WILD-TYPE 308 137
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                            81                            445 
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                            38                            137 
$`DEL PEAK 17(13Q14.2) MUTATED`
TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3370 TCGA-A3-3374 TCGA-AK-3426 
       37.15         4.50        52.93        74.76        43.20        29.10 
TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4688 
      112.08        94.19        78.64        12.13        40.70         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 
        1.41         4.57        28.47         1.38         3.62        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-5092 
       57.70        43.96         6.64        52.21         6.02        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5099 TCGA-B0-5113 TCGA-B0-5117 TCGA-B0-5696 
       10.95         8.05        15.95        38.63        52.87        85.78 
TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-5163 
        5.10         0.53         5.46        23.31        16.80        27.02 
TCGA-B8-5549 TCGA-BP-4167 TCGA-BP-4334 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 
        6.38        89.36        21.21        62.86        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4787 
       33.99         5.98        71.80        13.15        10.82        15.78 
TCGA-BP-4797 TCGA-BP-4964 TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4994 
       36.39        61.22        57.40        45.50        31.30        43.00 
TCGA-BP-5004 TCGA-BP-5175 TCGA-BP-5191 TCGA-BP-5196 TCGA-CJ-4639 TCGA-CJ-4868 
       37.02        30.64        31.79        33.47       106.16        21.24 
TCGA-CJ-4881 TCGA-CJ-4901 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6028 TCGA-CW-5588 
       66.21        47.67        25.71        22.32        53.42        66.31 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4863 
       83.90        18.77        46.16        47.08         6.77        63.39 
TCGA-CZ-4866 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 
       61.41        18.44        90.54        84.30         1.94        31.10 
TCGA-CZ-5984 TCGA-DV-5568 TCGA-G6-A8L7 
       67.96        12.16        70.13 

$`DEL PEAK 17(13Q14.2) WILD-TYPE`
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        11.90        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.08        49.02        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        38.47        37.38        48.82        62.01        34.29 
TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       31.07        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3372 
       82.32        51.25        10.49        28.70        74.63        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
       53.29        55.76        20.71        18.64        18.87        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
        0.10        11.18        10.62       109.91       117.80        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 
      109.41        15.78        73.68        68.61       109.51        46.78 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       48.36        40.01        49.28        94.29        83.21        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 
       22.45        37.58        38.40        82.45        72.89         1.41 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
        2.53         3.48        19.00        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        2.14         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 
        5.52        45.07        33.50        16.77        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5096 TCGA-B0-5097 
       11.90         7.30        25.32        18.51         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       52.08        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       58.59        19.30        66.05        52.73        41.88        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5697 
      112.80       129.67       133.94        15.78        70.68        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
      119.38       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
      126.05        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        31.66        24.82        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
       12.00         5.75         0.85         4.64         0.36         0.23 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 
       25.91        50.14        20.91        23.74         1.18         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       24.23        50.14        16.60        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       99.85         0.43        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        80.68        37.25        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        74.17        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.23        12.33        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 
       77.62        44.15        41.75        48.07        61.68         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 
       60.95        48.95        36.53        20.38        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 
       63.62        58.68        60.30        61.51         6.74        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       14.24        48.89        49.38         6.90        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 
       30.64        41.62        18.51        38.70        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
        1.74        74.20        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       13.35        27.02        33.24        23.47        13.41        24.62 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        63.25        73.22        14.17       114.41        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
      105.37        58.95        11.05        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       10.72        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45       109.84        50.24        56.35        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
      108.56        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
      129.40       133.71        18.87        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
       62.10        73.35        67.00        53.26       118.85        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
        5.39        85.78        73.18        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
      105.93       103.43        25.45         0.59        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 
       14.66       107.54        93.04         5.46        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       79.53        23.74        79.63        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        69.96        22.52         2.40 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       12.69        80.19        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5573 
       62.63        13.28        45.96        65.88        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-DV-A4W0 
       66.28        56.84        23.90        53.46        12.00        81.21 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        23.01        16.37 
TCGA-T7-A92I 
       11.70 

  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                          0.53                           0.07 
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                        112.08                         149.16 
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                         31.79                          39.45 
[1] "0.5 - 112.1 (31.8)" "0.1 - 149.2 (39.5)"
[1] "hr=" "1.8"
D29V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 17(13Q14.2) MUTATED        27        3        30       22
  DEL PEAK 17(13Q14.2) WILD-TYPE     236       54        95       61
D29V3, multiclass
           clus
vv          DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  STAGE I                             27                            236
  STAGE II                             3                             54
  STAGE III                           30                             95
  STAGE IV                            22                             61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 17(13Q14.2) MUTATED    29   4  42   7
  DEL PEAK 17(13Q14.2) WILD-TYPE 239  65 138   4
D29V4, multiclass
    clus
vv   DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  T1                           29                            239
  T2                            4                             65
  T3                           42                            138
  T4                            7                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V5, binary
                                cls
clus                               0   1
  DEL PEAK 17(13Q14.2) MUTATED    39   5
  DEL PEAK 17(13Q14.2) WILD-TYPE 195  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(13Q14.2) MUTATED     39    5
  DEL PEAK 17(13Q14.2) WILD-TYPE  195   12
   clus
vv  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  0                           39                            195
  1                            5                             12
[1] 2 2
[1] FALSE
D29V6, binary
                                cls
clus                               0   1
  DEL PEAK 17(13Q14.2) MUTATED    61  19
  DEL PEAK 17(13Q14.2) WILD-TYPE 357  59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(13Q14.2) MUTATED     61   19
  DEL PEAK 17(13Q14.2) WILD-TYPE  357   59
   clus
vv  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  0                           61                            357
  1                           19                             59
[1] 2 2
[1] FALSE
D29V7, binary
                                cls
clus                               0   1
  DEL PEAK 17(13Q14.2) MUTATED    29  53
  DEL PEAK 17(13Q14.2) WILD-TYPE 160 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(13Q14.2) MUTATED     29   53
  DEL PEAK 17(13Q14.2) WILD-TYPE  160  286
        clus
vv       DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  FEMALE                           29                            160
  MALE                             53                            286
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
D29V10, continuous
[1] "Remove cluster labels:"       "DEL PEAK 17(13Q14.2) MUTATED"
clus
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                             2                             10 
                    TCGA-A3-A8OV                     TCGA-A3-A8OW 
"DEL PEAK 17(13Q14.2) WILD-TYPE" "DEL PEAK 17(13Q14.2) WILD-TYPE" 
                    TCGA-AK-3451                     TCGA-B2-A4SR 
"DEL PEAK 17(13Q14.2) WILD-TYPE" "DEL PEAK 17(13Q14.2) WILD-TYPE" 
                    TCGA-B8-5158                     TCGA-B8-5550 
"DEL PEAK 17(13Q14.2) WILD-TYPE" "DEL PEAK 17(13Q14.2) WILD-TYPE" 
                    TCGA-DV-A4W0                     TCGA-MM-A563 
"DEL PEAK 17(13Q14.2) WILD-TYPE" "DEL PEAK 17(13Q14.2) WILD-TYPE" 
                    TCGA-MM-A84U                     TCGA-T7-A92I 
"DEL PEAK 17(13Q14.2) WILD-TYPE" "DEL PEAK 17(13Q14.2) WILD-TYPE" 
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(13Q14.2) MUTATED       0                         4    77
  DEL PEAK 17(13Q14.2) WILD-TYPE     8                        52   380
D29V11, multiclass
                           clus
vv                          DEL PEAK 17(13Q14.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               77
                           clus
vv                          DEL PEAK 17(13Q14.2) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             52
  WHITE                                                380
[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"
D29V12, binary
                                cls
clus                               0   1
  DEL PEAK 17(13Q14.2) MUTATED     2  56
  DEL PEAK 17(13Q14.2) WILD-TYPE  24 294
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(13Q14.2) MUTATED      2   56
  DEL PEAK 17(13Q14.2) WILD-TYPE   24  294
                        clus
vv                       DEL PEAK 17(13Q14.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           56
                        clus
vv                       DEL PEAK 17(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 24
  NOT HISPANIC OR LATINO                            294
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK 18(14Q31.1) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(14Q31.1) MUTATED   130  97
  DEL PEAK 18(14Q31.1) WILD-TYPE 221  78
  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                           227                            299 
  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                            97                             78 
$`DEL PEAK 18(14Q31.1) MUTATED`
TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
       12.66        36.82        39.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3324 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3347 
       49.58        38.99        62.01        34.29         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3387 
       45.53        29.92        88.37        20.71        18.87        20.28 
TCGA-A3-A6NI TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       33.47        29.10       117.80       109.41        15.78        73.68 
TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 
      109.51        78.64        49.28        94.29        28.73        22.45 
TCGA-AK-3458 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4712 
       38.40         4.57         3.48         5.98        19.73        43.96 
TCGA-B0-4713 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4828 
        6.64         5.52        52.21        33.50         6.02        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4842 TCGA-B0-4847 
       78.44        40.70        27.42        53.88        56.68        26.07 
TCGA-B0-4848 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5081 TCGA-B0-5084 
       29.03        36.85        70.52        20.94        11.90         7.30 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5106 TCGA-B0-5107 
       15.09        10.95         2.24        21.86        52.54        30.48 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5400 TCGA-B0-5692 TCGA-B0-5694 TCGA-B0-5697 
       66.05        38.63        56.98       129.67        15.78        86.47 
TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-4098 
      119.38        80.91        79.89       131.15        89.49         1.68 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5832 
       31.30        31.66        24.82        32.98        21.57         5.10 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-4619 TCGA-B8-5158 
        4.64         5.46         0.36        23.31        17.19        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5553 
       23.74         1.18         0.85        48.53         0.53        14.30 
TCGA-B8-A54D TCGA-B8-A54G TCGA-B8-A54I TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4167 
       27.29         1.74         4.93        93.34        32.61        89.36 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4331 TCGA-BP-4343 TCGA-BP-4346 
       62.24        61.78        64.27        80.68        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4761 TCGA-BP-4763 
       44.94        11.31        12.33        33.99         5.98        41.75 
TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 
       13.15         5.33        56.91        68.38        15.78        36.39 
TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4962 TCGA-BP-4965 TCGA-BP-4970 
       10.98         6.71        87.45        58.68        61.51        14.24 
TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4983 TCGA-BP-4986 
       48.89        45.50        14.93        36.07        46.45        25.81 
TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5009 TCGA-BP-5169 
        3.88        16.47        18.51        37.02        36.23         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 
       79.30         1.74        74.20        30.64        62.86        74.40 
TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5195 
       42.44        37.22        27.02        33.24        31.79        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
       33.47        19.82        31.27        63.25        73.22        14.17 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61       105.37        11.05        21.24        83.97 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4881 
       79.66        74.27        75.06       116.84        64.27        66.21 
TCGA-CJ-4884 TCGA-CJ-4888 TCGA-CJ-4891 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 
       57.83        51.52        26.93        24.66        27.65       109.84 
TCGA-CJ-4900 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       56.35        51.25       108.56        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       38.56        45.14         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5682 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6033 
      122.83        67.00        53.26       118.85        75.58         7.36 
TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-6087 TCGA-CW-6090 
       64.57         5.39        73.18        66.31         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 
       18.77        46.16        69.21         6.77        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5461 
       93.04        61.41        58.82        18.44        79.63        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       10.22        21.76        84.30         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-5573 
       12.69        67.96        65.65        14.63        62.63        37.15 
TCGA-DV-A4VX TCGA-G6-A5PC TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MM-A84U 
       53.46         7.96        35.87        19.43        23.01 

$`DEL PEAK 18(14Q31.1) WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3322 TCGA-A3-3323 
       11.90        47.21         0.53        24.16        48.59        36.36 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3352 TCGA-A3-3358 
       38.47        37.38        48.82        31.07        18.44        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 
       24.16        53.29        43.20        55.76        18.64        28.31 
TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       65.52        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 
       10.62       109.91        73.08       112.08        68.61        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3460 
       46.78        48.36        40.01        83.21        37.58        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       72.89        12.13        40.70         1.41         3.32         1.41 
TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        2.53        28.47        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        7.82         2.14        57.70         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 
       46.59         0.59        45.07        16.77        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4841 
       14.93        54.48        29.10        68.71        45.30         6.71 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4849 TCGA-B0-5077 
       10.52        10.29        65.29        39.45         2.27        43.30 
TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5095 TCGA-B0-5098 TCGA-B0-5099 
       11.24        25.32        18.51         8.05        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5115 
       62.89        90.87        90.48        58.59        19.30        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
       42.41       111.52       112.80       133.94        70.68        85.78 
TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
      126.28        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 
       91.46       126.05        32.61        35.90        31.96        21.30 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5844 
       16.67        12.00         5.75         0.85         0.53         0.23 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 
       16.80        27.16        42.71        25.05        45.37        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       25.91        50.14        27.02        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5552 TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54H TCGA-B8-A54J 
        6.38        34.39        29.88        17.06         8.42        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 
       90.28       101.06        99.85         0.43        23.05        77.03 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4355 
       52.24        74.17        54.77        12.23        31.89        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4765 
       12.30        72.59        77.98        77.62        44.15        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       48.07        61.68        10.82        61.97        60.59        13.51 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4799 
       11.64        60.95        48.95        36.53        20.38        37.25 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 
       36.95        47.97         6.94        71.41        63.62        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4974 
       61.22         6.74        57.40        58.98        49.38         6.90 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 
       47.11        53.65        33.34        31.30        36.95        27.22 
TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5168 
       38.70        27.62        37.48        35.21        28.87        48.10 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 
       52.27         9.63        49.15        38.30        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 
       13.35        23.47        13.41        44.55        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4870 TCGA-CJ-4872 
      115.00        46.55       106.16        58.95        49.25        10.72 
TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 
       71.87        61.91       113.46        64.18        30.64        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
      115.69        50.01        39.45        50.24        47.67        49.97 
TCGA-CJ-4905 TCGA-CJ-4918 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6028 
       49.18         3.06        18.15        62.10        73.35        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5589 
       62.66       119.64        92.02        81.83        85.78        78.18 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 
       74.66       105.93       103.43        25.45         0.59        47.08 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 
       58.75       107.54         5.46        63.42        79.53        23.74 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5466 
       90.54        91.69        55.33        94.45        69.96        22.52 
TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       80.19        12.26        22.78        13.28        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4VZ 
       12.16        11.67        66.28        56.84        23.90        12.00 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 
       81.21        18.12         3.91         6.77         4.18        10.29 
TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       70.13         2.01        19.96        16.37        11.70 

  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                          0.36                           0.07 
  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                        133.71                         149.16 
  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                         36.39                          41.62 
[1] "0.4 - 133.7 (36.4)" "0.1 - 149.2 (41.6)"
[1] "hr=" "1.7"
D30V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 18(14Q31.1) MUTATED        86       27        66       49
  DEL PEAK 18(14Q31.1) WILD-TYPE     177       30        59       34
D30V3, multiclass
           clus
vv          DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE
  STAGE I                             86                            177
  STAGE II                            27                             30
  STAGE III                           66                             59
  STAGE IV                            49                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 18(14Q31.1) MUTATED    91  35  98   4
  DEL PEAK 18(14Q31.1) WILD-TYPE 177  34  82   7
D30V4, multiclass
    clus
vv   DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE
  T1                           91                            177
  T2                           35                             34
  T3                           98                             82
  T4                            4                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V5, binary
                                cls
clus                               0   1
  DEL PEAK 18(14Q31.1) MUTATED   100  15
  DEL PEAK 18(14Q31.1) WILD-TYPE 134   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(14Q31.1) MUTATED    100   15
  DEL PEAK 18(14Q31.1) WILD-TYPE  134    2
   clus
vv  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE
  0                          100                            134
  1                           15                              2
[1] 2 2
[1] FALSE
D30V6, binary
                                cls
clus                               0   1
  DEL PEAK 18(14Q31.1) MUTATED   171  48
  DEL PEAK 18(14Q31.1) WILD-TYPE 247  30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(14Q31.1) MUTATED    171   48
  DEL PEAK 18(14Q31.1) WILD-TYPE  247   30
   clus
vv  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE
  0                          171                            247
  1                           48                             30
[1] 2 2
[1] FALSE
D30V7, binary
                                cls
clus                               0   1
  DEL PEAK 18(14Q31.1) MUTATED    74 154
  DEL PEAK 18(14Q31.1) WILD-TYPE 115 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(14Q31.1) MUTATED     74  154
  DEL PEAK 18(14Q31.1) WILD-TYPE  115  185
        clus
vv       DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE
  FEMALE                           74                            115
  MALE                            154                            185
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, continuous
D30V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(14Q31.1) MUTATED       2                        16   206
  DEL PEAK 18(14Q31.1) WILD-TYPE     6                        40   251
D30V11, multiclass
                           clus
vv                          DEL PEAK 18(14Q31.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              206
                           clus
vv                          DEL PEAK 18(14Q31.1) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             40
  WHITE                                                251
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, binary
                                cls
clus                               0   1
  DEL PEAK 18(14Q31.1) MUTATED    12 159
  DEL PEAK 18(14Q31.1) WILD-TYPE  14 191
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(14Q31.1) MUTATED     12  159
  DEL PEAK 18(14Q31.1) WILD-TYPE   14  191
                        clus
vv                       DEL PEAK 18(14Q31.1) MUTATED
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          159
                        clus
vv                       DEL PEAK 18(14Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            191
[1] 2 2
[1] FALSE
