[1] "ofn"        "-oTTGCT-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/TGCT-TP/15092576/TGCT-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/TGCT-TP/15101915/transformed.cor.cli.txt"

nPatients in clinical file=133, in cluster file=150, common to both=133
[1]  47 133
[1] "AMP PEAK  1(1Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                           62                            71 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                           62                            71 
[1] "AMP PEAK  2(2P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE 
                           53                            80 
  AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE 
                           53                            80 
[1] "AMP PEAK  3(3Q27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                           40                            93 
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                           40                            93 
[1] "AMP PEAK  4(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                         19                         114 
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                         19                         114 
[1] "AMP PEAK  5(7P22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE 
                          115                            18 
  AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE 
                          115                            18 
[1] "AMP PEAK  6(7Q11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE 
                           109                             24 
  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE 
                           109                             24 
[1] "AMP PEAK  7(8Q11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE 
                           113                             20 
  AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE 
                           113                             20 
[1] "AMP PEAK  8(8Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE 
                          100                            33 
  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE 
                          100                            33 
[1] "AMP PEAK  9(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE 
                            128                               5 
  AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE 
                            128                               5 
[1] "AMP PEAK 10(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE 
                           130                              3 
  AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE 
                           130                              3 
[1] "AMP PEAK 11(12P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(12P11.21) MUTATED AMP PEAK 11(12P11.21) WILD-TYPE 
                            127                               6 
  AMP PEAK 11(12P11.21) MUTATED AMP PEAK 11(12P11.21) WILD-TYPE 
                            127                               6 
[1] "AMP PEAK 12(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                          89                           44 
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                          89                           44 
[1] "AMP PEAK 13(16Q21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE 
                          18                          115 
  AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE 
                          18                          115 
[1] "AMP PEAK 14(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE 
                             41                              92 
  AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE 
                             41                              92 
[1] "AMP PEAK 15(22Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE 
                             53                              80 
  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE 
                             53                              80 
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            29                            104 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            29                            104 
[1] "DEL PEAK  2(1P31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                           26                           107 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                           26                           107 
[1] "DEL PEAK  3(1Q42.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE 
                             9                            124 
  DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE 
                             9                            124 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           13                           120 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           13                           120 
[1] "DEL PEAK  5(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE 
                           40                            93 
  DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE 
                           40                            93 
[1] "DEL PEAK  6(4Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE 
                           99                            34 
  DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE 
                           99                            34 
[1] "DEL PEAK  7(5P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE 
                           91                            42 
  DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE 
                           91                            42 
[1] "DEL PEAK  8(5P14.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE 
                           92                            41 
  DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE 
                           92                            41 
[1] "DEL PEAK  9(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           94                            39 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           94                            39 
[1] "DEL PEAK 10(6P22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE 
                           19                           114 
  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE 
                           19                           114 
[1] "DEL PEAK 11(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                         22                         111 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                         22                         111 
[1] "DEL PEAK 12(7Q11.22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE 
                             3                            130 
  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE 
                             3                            130 
[1] "DEL PEAK 13(7Q36.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE 
                           14                           119 
  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE 
                           14                           119 
[1] "DEL PEAK 14(9P24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE 
                           62                            71 
  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE 
                           62                            71 
[1] "DEL PEAK 15(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                         58                          75 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                         58                          75 
[1] "DEL PEAK 16(9Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE 
                           52                            81 
  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE 
                           52                            81 
[1] "DEL PEAK 17(9Q34.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE 
                           52                            81 
  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE 
                           52                            81 
[1] "DEL PEAK 18(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                            71                             62 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                            71                             62 
[1] "DEL PEAK 19(10Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE 
                            62                             71 
  DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE 
                            62                             71 
[1] "DEL PEAK 20(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                            65                             68 
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                            65                             68 
[1] "DEL PEAK 21(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                            84                             49 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                            84                             49 
[1] "DEL PEAK 22(11P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE 
                          89                           44 
  DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE 
                          89                           44 
[1] "DEL PEAK 23(11Q12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE 
                           103                             30 
  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE 
                           103                             30 
[1] "DEL PEAK 24(11Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE 
                           109                             24 
  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE 
                           109                             24 
[1] "DEL PEAK 25(13Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                         101                           32 
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                         101                           32 
[1] "DEL PEAK 26(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            60                             73 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            60                             73 
[1] "DEL PEAK 27(18P11.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE 
                            105                              28 
  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE 
                            105                              28 
[1] "DEL PEAK 28(18Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE 
                           112                             21 
  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE 
                           112                             21 
[1] "DEL PEAK 29(19Q13.41) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE 
                             47                              86 
  DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE 
                             47                              86 
[1] "DEL PEAK 30(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            27                            106 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            27                            106 
[1] "DEL PEAK 31(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE 
                           23                           110 
  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE 
                           23                           110 
[1] "DEL PEAK 32(XQ27.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE 
                           25                           108 
  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE 
                           25                           108 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATION_THERAPY"                     
[12] "RADIATIONS_RADIATION_REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 133 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=38,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=4,	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=127,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              12-3-2015 26-3-2015
freq.values   "1"       "132"    
freq.contrast "132"     "1"      
both >= 3     "FALSE"   "FALSE"  
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH_NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER excluded in the analysis because there is no case of (both >= 3) in the table below"
              B430.15.0 B430.16.0
freq.values   "1"       "132"    
freq.contrast "132"     "1"      
both >= 3     "FALSE"   "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 133 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"        "NEOPLASM_DISEASESTAGE" "PATHOLOGY_T_STAGE"    
[4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "RACE"                 
[7] "ETHNICITY"            
YEARS_TO_BIRTH, nv=38, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 
75 51  6 
[1] "table(vv)"
vv
T1 T2 T3 
75 51  6 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 
75 51  6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T1 T2 T3 
75 51  6 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
46 11  2 
[1] "table(vv)"
vv
   N0 N1+N2 
   46    13 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
46 11  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 46

$Class1_nSamples
[1] 13

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   46    13 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q21.2) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  1(1Q21.2) MUTATED   60  2
  AMP PEAK  1(1Q21.2) WILD-TYPE 69  2
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                           62                            71 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                            2                             2 
$`AMP PEAK  1(1Q21.2) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF8 TCGA-2G-AAFH TCGA-2G-AAFI 
       20.32        30.35        59.70       122.40        36.99        14.14 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAG0 
        9.57        14.86        16.50        40.70        36.13        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGI 
       52.37        72.20        61.71        68.38        67.96        92.09 
TCGA-2G-AAGK TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAH2 
      108.16       120.62        59.28        61.45        80.94        59.84 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHT TCGA-2G-AAKM TCGA-2G-AAL5 
       61.84        98.53        59.80         6.08       229.22       184.41 
TCGA-2G-AAL7 TCGA-4K-AA1G TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X 
      131.21         3.52         9.14         1.38        16.31        10.26 
TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AE TCGA-W4-A7U4 TCGA-WZ-A7V5 
       17.23        37.18        36.79        23.90        24.26         0.16 
TCGA-XE-A8H1 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AAO3 TCGA-XE-AAO4 
        6.87        40.01        34.22        65.98        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOL TCGA-XY-A9T9 TCGA-YU-A90P 
        7.89         8.88        67.66         0.43         6.90        57.90 
TCGA-YU-A90W TCGA-YU-A94D TCGA-YU-A94I TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
       21.96        58.88         7.96        37.02        39.35        27.55 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

$`AMP PEAK  1(1Q21.2) WILD-TYPE`
TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFJ TCGA-2G-AAFL 
       38.30       102.35       154.59       191.31        14.56        17.16 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       36.89        71.24        63.22        63.32        68.22        72.85 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGT 
       79.76        75.09        59.64       106.39       115.00       124.57 
TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH4 
      128.94       170.33        60.16        60.26        59.90       125.69 
TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKG 
       59.74        59.80        91.43       176.15       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H 
      161.72        95.67        70.59         2.73         0.13         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SN-A84W 
        0.10         4.83        20.68        18.15        13.58         9.63 
TCGA-SO-A8JP TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U2 
        3.52        37.68        24.99        35.61        33.07        41.52 
TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H4 
        4.90         3.65         5.06         0.82        28.14        18.38 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B 
        0.46        53.03        16.87        41.69        50.96         8.32 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90Y TCGA-YU-A912 
       12.92        20.12        54.35        31.92         0.56         5.29 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       40.96         8.15        17.39        16.41        11.34 

  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                         0.16                          0.10 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                       229.22                        212.65 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                         37.1                          38.3 
[1] "0.2 - 229.2 (37.1)" "0.1 - 212.7 (38.3)"
[1] "hr=" "1.8"
D1V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  1(1Q21.2) MUTATED         6       11        5        1         4
  AMP PEAK  1(1Q21.2) WILD-TYPE      13       14        6        4         2
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  1(1Q21.2) MUTATED           1         1         0          0
  AMP PEAK  1(1Q21.2) WILD-TYPE         0         0         2          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  AMP PEAK  1(1Q21.2) MUTATED            3          2       26
  AMP PEAK  1(1Q21.2) WILD-TYPE          3          3       20
D1V3, multiclass
            clus
vv           AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  STAGE I                              6                            13
  STAGE IA                            11                            14
  STAGE IB                             5                             6
  STAGE II                             1                             4
  STAGE IIA                            4                             2
  STAGE IIB                            1                             0
  STAGE IIC                            1                             0
  STAGE III                            0                             2
  STAGE IIIA                           0                             1
  STAGE IIIB                           3                             3
  STAGE IIIC                           2                             3
  STAGE IS                            26                            20
[1] 12  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
  AMP PEAK  1(1Q21.2) MUTATED   34 25  3
  AMP PEAK  1(1Q21.2) WILD-TYPE 41 26  3
D1V4, multiclass
    clus
vv   AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  T1                          34                            41
  T2                          25                            26
  T3                           3                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  AMP PEAK  1(1Q21.2) MUTATED   22     8
  AMP PEAK  1(1Q21.2) WILD-TYPE 24     5
D1V5, multiclass
       clus
vv      AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  N0                             22                            24
  N1+N2                           8                             5
[1] 2 2
[1] FALSE
D1V6, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q21.2) MUTATED   56  1
  AMP PEAK  1(1Q21.2) WILD-TYPE 58  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED     56    1
  AMP PEAK  1(1Q21.2) WILD-TYPE   58    3
   clus
vv  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  0                          56                            58
  1                           1                             3
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q21.2) MUTATED       1                         1    57
  AMP PEAK  1(1Q21.2) WILD-TYPE     3                         5    61
D1V7, multiclass
                           clus
vv                          AMP PEAK  1(1Q21.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              57
                           clus
vv                          AMP PEAK  1(1Q21.2) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                61
[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"
D1V8, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q21.2) MUTATED    8 50
  AMP PEAK  1(1Q21.2) WILD-TYPE  3 61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED      8   50
  AMP PEAK  1(1Q21.2) WILD-TYPE    3   61
                        clus
vv                       AMP PEAK  1(1Q21.2) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                          50
                        clus
vv                       AMP PEAK  1(1Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            61
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(2P24.1) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(2P24.1) MUTATED   52  1
  AMP PEAK  2(2P24.1) WILD-TYPE 77  3
  AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE 
                           53                            80 
  AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE 
                            1                             3 
$`AMP PEAK  2(2P24.1) MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ 
       59.70       102.35       122.40        36.99        14.14        14.56 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG7 TCGA-2G-AAG8 
       16.50        40.70        36.89        52.37        61.71        63.22 
TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM 
       68.38        67.96        92.09        75.09       108.16        59.64 
TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAHC 
      120.62       124.57        61.45        80.94        59.84        59.74 
TCGA-2G-AAHP TCGA-2G-AAKL TCGA-4K-AA1G TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
      176.15        95.67         3.52         4.83        20.68        18.15 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 
        9.14        13.58         1.38        10.26         3.52        37.18 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AAO6 
        5.06         0.16        28.14        18.38        40.01         7.89 
TCGA-XE-AAOC TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P 
        8.88        41.69         0.43        12.92        20.12        57.90 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-A94I TCGA-ZM-AA06 
       21.96         0.56        58.88         7.96        39.35 

$`AMP PEAK  2(2P24.1) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFL 
       20.32        30.35        38.30       154.59       191.31        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 
        9.57        14.86        36.13        40.01        71.24        72.20 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGN TCGA-2G-AAGO 
       63.32        68.22        72.85        79.76       106.39       115.00 
TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH3 
       59.28       128.94       170.33        60.16        60.26        59.90 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
      125.69        61.84        98.53        59.80        59.80        91.43 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM TCGA-2G-AAL5 
        6.08       122.50       212.65       161.72       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I 
      131.21        70.59         2.73         0.13         7.00         0.10 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB 
       16.31         9.63        17.23        36.79        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 
       35.61        33.07        23.90        41.52         4.90        24.26 
TCGA-WZ-A7V3 TCGA-WZ-A8D5 TCGA-XE-A8H1 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        3.65         0.82         6.87        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOJ 
       53.03        93.93        12.07        16.87        67.66        50.96 
TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A912 TCGA-YU-AA4L 
        8.32         6.90        54.35        31.92         5.29        40.96 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
        8.15        37.02        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

  AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE 
                         0.16                          0.10 
  AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE 
                       176.15                        229.22 
  AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE 
                        37.18                         37.99 
[1] "0.2 - 176.2 (37.2)" "0.1 - 229.2 (38.0)"
[1] "hr=" "1.2"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  2(2P24.1) MUTATED         7       11        4        1         2
  AMP PEAK  2(2P24.1) WILD-TYPE      12       14        7        4         4
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  2(2P24.1) MUTATED           1         0         1          0
  AMP PEAK  2(2P24.1) WILD-TYPE         0         1         1          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  AMP PEAK  2(2P24.1) MUTATED            1          2       22
  AMP PEAK  2(2P24.1) WILD-TYPE          5          3       24
D2V3, multiclass
            clus
vv           AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE
  STAGE I                              7                            12
  STAGE IA                            11                            14
  STAGE IB                             4                             7
  STAGE II                             1                             4
  STAGE IIA                            2                             4
  STAGE IIB                            1                             0
  STAGE IIC                            0                             1
  STAGE III                            1                             1
  STAGE IIIA                           0                             1
  STAGE IIIB                           1                             5
  STAGE IIIC                           2                             3
  STAGE IS                            22                            24
[1] 12  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
  AMP PEAK  2(2P24.1) MUTATED   31 17  4
  AMP PEAK  2(2P24.1) WILD-TYPE 44 34  2
D2V4, multiclass
    clus
vv   AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE
  T1                          31                            44
  T2                          17                            34
  T3                           4                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  AMP PEAK  2(2P24.1) MUTATED   22     4
  AMP PEAK  2(2P24.1) WILD-TYPE 24     9
D2V5, multiclass
       clus
vv      AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE
  N0                             22                            24
  N1+N2                           4                             9
[1] 2 2
[1] FALSE
D2V6, binary
                               cls
clus                             0  1
  AMP PEAK  2(2P24.1) MUTATED   44  2
  AMP PEAK  2(2P24.1) WILD-TYPE 70  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P24.1) MUTATED     44    2
  AMP PEAK  2(2P24.1) WILD-TYPE   70    2
   clus
vv  AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE
  0                          44                            70
  1                           2                             2
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(2P24.1) MUTATED       2                         3    45
  AMP PEAK  2(2P24.1) WILD-TYPE     2                         3    73
D2V7, multiclass
                           clus
vv                          AMP PEAK  2(2P24.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              45
                           clus
vv                          AMP PEAK  2(2P24.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                73
[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"
D2V8, binary
                               cls
clus                             0  1
  AMP PEAK  2(2P24.1) MUTATED    3 45
  AMP PEAK  2(2P24.1) WILD-TYPE  8 66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P24.1) MUTATED      3   45
  AMP PEAK  2(2P24.1) WILD-TYPE    8   66
                        clus
vv                       AMP PEAK  2(2P24.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          45
                        clus
vv                       AMP PEAK  2(2P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                            66
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(3Q27.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  3(3Q27.3) MUTATED   39  1
  AMP PEAK  3(3Q27.3) WILD-TYPE 90  3
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                           40                            93 
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                            1                             3 
$`AMP PEAK  3(3Q27.3) MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAFI TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFZ 
       59.70        14.14        14.86        16.50        40.70        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       40.01        63.22        68.22        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGW TCGA-2G-AAGY 
       75.09       108.16        59.64       120.62        61.45        80.94 
TCGA-2G-AAHC TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-4K-AAAL TCGA-SB-A6J6 
       59.74       122.50       212.65        95.67         4.83        13.58 
TCGA-SN-A84X TCGA-VF-A8A8 TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       10.26        37.18         4.90         3.65         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-AANJ TCGA-XE-AANV TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XY-A8S2 
        6.87        65.98        53.03         7.89         8.88        12.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94I TCGA-ZM-AA0N 
       21.96         0.56         7.96        10.85 

$`AMP PEAK  3(3Q27.3) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        38.30       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFY 
      191.31        36.99        14.56        17.16         9.57        36.13 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGC 
       52.37        71.24        72.20        61.71        63.32        72.85 
TCGA-2G-AAGE TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
       68.38       106.39       115.00        59.28       124.57       128.94 
TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      170.33        60.16        60.26        59.84        59.90       125.69 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       61.84        98.53        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKH TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
        6.08       161.72       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-S6-A8JW 
        2.73         0.13         3.52         7.00         0.10        20.68 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y 
       18.15         9.14         1.38        16.31         9.63        17.23 
TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
        3.52        36.79        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-XE-A8H4 
       23.90        41.52        24.26         5.06         0.16        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB 
       40.01        34.22         0.46        93.93        12.07        16.87 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S3 
       67.66        41.69        50.96         0.43         8.32        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A912 TCGA-YU-A94D 
        6.90        57.90        54.35        31.92         5.29        58.88 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       40.96         8.15        37.02        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       16.41        11.34        46.88 

  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                         0.56                          0.10 
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                       212.65                        229.22 
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                       38.595                        37.680 
[1] "0.6 - 212.7 (38.6)" "0.1 - 229.2 (37.7)"
[1] "hr=" "1.3"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  3(3Q27.3) MUTATED         4        7        4        1         3
  AMP PEAK  3(3Q27.3) WILD-TYPE      15       18        7        4         3
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  3(3Q27.3) MUTATED           0         0         2          0
  AMP PEAK  3(3Q27.3) WILD-TYPE         1         1         0          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  AMP PEAK  3(3Q27.3) MUTATED            1          2       14
  AMP PEAK  3(3Q27.3) WILD-TYPE          5          3       32
D3V3, multiclass
            clus
vv           AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  STAGE I                              4                            15
  STAGE IA                             7                            18
  STAGE IB                             4                             7
  STAGE II                             1                             4
  STAGE IIA                            3                             3
  STAGE IIB                            0                             1
  STAGE IIC                            0                             1
  STAGE III                            2                             0
  STAGE IIIA                           0                             1
  STAGE IIIB                           1                             5
  STAGE IIIC                           2                             3
  STAGE IS                            14                            32
[1] 12  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
  AMP PEAK  3(3Q27.3) MUTATED   19 17  4
  AMP PEAK  3(3Q27.3) WILD-TYPE 56 34  2
D3V4, multiclass
    clus
vv   AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  T1                          19                            56
  T2                          17                            34
  T3                           4                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  AMP PEAK  3(3Q27.3) MUTATED   16     5
  AMP PEAK  3(3Q27.3) WILD-TYPE 30     8
D3V5, multiclass
       clus
vv      AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  N0                             16                            30
  N1+N2                           5                             8
[1] 2 2
[1] FALSE
D3V6, binary
                               cls
clus                             0  1
  AMP PEAK  3(3Q27.3) MUTATED   33  2
  AMP PEAK  3(3Q27.3) WILD-TYPE 81  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q27.3) MUTATED     33    2
  AMP PEAK  3(3Q27.3) WILD-TYPE   81    2
   clus
vv  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  0                          33                            81
  1                           2                             2
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(3Q27.3) MUTATED       0                         2    36
  AMP PEAK  3(3Q27.3) WILD-TYPE     4                         4    82
D3V7, multiclass
                           clus
vv                          AMP PEAK  3(3Q27.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              36
                           clus
vv                          AMP PEAK  3(3Q27.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                82
[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"
D3V8, binary
                               cls
clus                             0  1
  AMP PEAK  3(3Q27.3) MUTATED    4 32
  AMP PEAK  3(3Q27.3) WILD-TYPE  7 79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q27.3) MUTATED      4   32
  AMP PEAK  3(3Q27.3) WILD-TYPE    7   79
                        clus
vv                       AMP PEAK  3(3Q27.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          32
                        clus
vv                       AMP PEAK  3(3Q27.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            79
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(4Q12) MUTATION ANALYSIS
D4V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  4(4Q12) MUTATED    19   0
  AMP PEAK  4(4Q12) WILD-TYPE 110   4
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                         19                         114 
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                          0                           4 
$`AMP PEAK  4(4Q12) MUTATED`
TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFO TCGA-2G-AAG3 TCGA-2G-AAG6 
      122.40       154.59       191.31        16.50        52.37        72.20 
TCGA-2G-AAGO TCGA-2G-AAGW TCGA-2G-AAHL TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2X-A9D5 
      115.00        61.45        59.80         6.08       122.50         2.73 
TCGA-4K-AAAL TCGA-S6-A8JY TCGA-SN-A6IS TCGA-XE-AAOL TCGA-XY-A9T9 TCGA-YU-A90P 
        4.83         9.14        16.31         0.43         6.90        57.90 
TCGA-ZM-AA0N 
       10.85 

$`AMP PEAK  4(4Q12) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFH 
       20.32        30.35        38.30        59.70       102.35        36.99 
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFV 
       14.14        14.56        17.16         9.57        14.86        40.70 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        36.89        40.01        71.24        61.71        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       63.32        68.22        72.85        68.38        79.76        67.96 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGP 
       92.09        75.09       108.16        59.64       106.39       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
       59.28       124.57       128.94       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKG TCGA-2G-AAKH 
       59.74        59.80        91.43       176.15       212.65       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D6 
       95.67       229.22       184.41       131.21        70.59         0.13 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 
        3.52         7.00         0.10        20.68        18.15        13.58 
TCGA-SB-A76C TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
        1.38         9.63        10.26        17.23         3.52        37.18 
TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       36.79        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       41.52         4.90        24.26         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B 
       16.87         8.88        67.66        41.69        50.96         8.32 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
       12.92        20.12        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 

  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                       0.43                        0.10 
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                     191.31                      229.22 
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                      52.37                       37.43 
[1] "0.4 - 191.3 (52.4)" "0.1 - 229.2 (37.4)"
[1] "hr="     "8.1e+07"
D4V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  4(4Q12) MUTATED         3        2        1        0         2
  AMP PEAK  4(4Q12) WILD-TYPE      16       23       10        5         4
                             vv
clus                          STAGE IIB STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  4(4Q12) MUTATED           0         0         1          0
  AMP PEAK  4(4Q12) WILD-TYPE         1         1         1          1
                             vv
clus                          STAGE IIIB STAGE IIIC STAGE IS
  AMP PEAK  4(4Q12) MUTATED            0          0       10
  AMP PEAK  4(4Q12) WILD-TYPE          6          5       36
D4V3, multiclass
            clus
vv           AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  STAGE I                            3                          16
  STAGE IA                           2                          23
  STAGE IB                           1                          10
  STAGE II                           0                           5
  STAGE IIA                          2                           4
  STAGE IIB                          0                           1
  STAGE IIC                          0                           1
  STAGE III                          1                           1
  STAGE IIIA                         0                           1
  STAGE IIIB                         0                           6
  STAGE IIIC                         0                           5
  STAGE IS                          10                          36
[1] 12  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
  AMP PEAK  4(4Q12) MUTATED   11  8  0
  AMP PEAK  4(4Q12) WILD-TYPE 64 43  6
D4V4, multiclass
    clus
vv   AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  T1                        11                          64
  T2                         8                          43
  T3                         0                           6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1+N2
  AMP PEAK  4(4Q12) MUTATED    8     2
  AMP PEAK  4(4Q12) WILD-TYPE 38    11
D4V5, multiclass
       clus
vv      AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  N0                            8                          38
  N1+N2                         2                          11
[1] 2 2
[1] FALSE
D4V6, binary
                             cls
clus                           0  1
  AMP PEAK  4(4Q12) MUTATED   18  0
  AMP PEAK  4(4Q12) WILD-TYPE 96  4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(4Q12) MUTATED     18    0
  AMP PEAK  4(4Q12) WILD-TYPE   96    4
   clus
vv  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  0                        18                          96
  1                         0                           4
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(4Q12) MUTATED       0                         1    18
  AMP PEAK  4(4Q12) WILD-TYPE     4                         5   100
D4V7, multiclass
                           clus
vv                          AMP PEAK  4(4Q12) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            18
                           clus
vv                          AMP PEAK  4(4Q12) WILD-TYPE
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                             100
[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"
D4V8, binary
                             cls
clus                           0  1
  AMP PEAK  4(4Q12) MUTATED    1 17
  AMP PEAK  4(4Q12) WILD-TYPE 10 94
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(4Q12) MUTATED      1   17
  AMP PEAK  4(4Q12) WILD-TYPE   10   94
                        clus
vv                       AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             1                          10
  NOT HISPANIC OR LATINO                        17                          94
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(7P22.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(7P22.1) MUTATED   112   3
  AMP PEAK  5(7P22.1) WILD-TYPE  17   1
  AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE 
                          115                            18 
  AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE 
                            3                             1 
$`AMP PEAK  5(7P22.1) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE 
       20.32        30.35        38.30        59.70       102.35       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
      191.31        36.99        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       72.20        61.71        63.22        63.32        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.38        79.76        67.96        92.09        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH2 
      128.94        61.45       170.33        80.94        60.26        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL 
       59.90       125.69        61.84        98.53        59.74        59.80 
TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
       91.43         6.08       122.50       212.65       161.72        95.67 
TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I 
      229.22       131.21        70.59         0.13         3.52         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 
       16.31        10.26        17.23         3.52        37.18        36.79 
TCGA-VF-A8AA TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 
       37.68        35.61        33.07        23.90        41.52        24.26 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       18.38        40.01        34.22         0.46        53.03        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
       12.07         7.89        67.66        50.96         0.43         8.32 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       12.92        20.12         6.90        57.90        54.35        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 
       21.96         0.56         5.29         7.96        40.96        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

$`AMP PEAK  5(7P22.1) WILD-TYPE`
TCGA-2G-AAF8 TCGA-2G-AAFI TCGA-2G-AAG5 TCGA-2G-AAGZ TCGA-2G-AAHG TCGA-2G-AAHP 
      122.40        14.14        71.24        60.16        59.80       176.15 
TCGA-2G-AAL5 TCGA-2X-A9D5 TCGA-4K-AA1H TCGA-SN-A84W TCGA-VF-A8AB TCGA-W4-A7U3 
      184.41         2.73         7.00         9.63        24.99         4.90 
TCGA-XE-AANJ TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOF TCGA-YU-A94D TCGA-YU-AA61 
       65.98        16.87         8.88        41.69        58.88         8.15 

  AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE 
                         0.10                          2.73 
  AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE 
                       229.22                        184.41 
  AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE 
                        37.68                         33.34 
[1] "0.1 - 229.2 (37.7)" "2.7 - 184.4 (33.3)"
[1] "hr=" "3.5"
D5V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  5(7P22.1) MUTATED        16       20       10        5         6
  AMP PEAK  5(7P22.1) WILD-TYPE       3        5        1        0         0
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  5(7P22.1) MUTATED           1         1         2          0
  AMP PEAK  5(7P22.1) WILD-TYPE         0         0         0          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  AMP PEAK  5(7P22.1) MUTATED            5          5       40
  AMP PEAK  5(7P22.1) WILD-TYPE          1          0        6
D5V3, multiclass
            clus
vv           AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE
  STAGE I                             16                             3
  STAGE IA                            20                             5
  STAGE IB                            10                             1
  STAGE II                             5                             0
  STAGE IIA                            6                             0
  STAGE IIB                            1                             0
  STAGE IIC                            1                             0
  STAGE III                            2                             0
  STAGE IIIA                           0                             1
  STAGE IIIB                           5                             1
  STAGE IIIC                           5                             0
  STAGE IS                            40                             6
[1] 12  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
  AMP PEAK  5(7P22.1) MUTATED   64 45  5
  AMP PEAK  5(7P22.1) WILD-TYPE 11  6  1
D5V4, multiclass
    clus
vv   AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE
  T1                          64                            11
  T2                          45                             6
  T3                           5                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  AMP PEAK  5(7P22.1) MUTATED   38    12
  AMP PEAK  5(7P22.1) WILD-TYPE  8     1
D5V5, multiclass
       clus
vv      AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE
  N0                             38                             8
  N1+N2                          12                             1
[1] 2 2
[1] FALSE
D5V6, binary
                               cls
clus                              0   1
  AMP PEAK  5(7P22.1) MUTATED   100   3
  AMP PEAK  5(7P22.1) WILD-TYPE  14   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P22.1) MUTATED    100    3
  AMP PEAK  5(7P22.1) WILD-TYPE   14    1
   clus
vv  AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE
  0                         100                            14
  1                           3                             1
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(7P22.1) MUTATED       3                         5   103
  AMP PEAK  5(7P22.1) WILD-TYPE     1                         1    15
D5V7, multiclass
                           clus
vv                          AMP PEAK  5(7P22.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                             103
                           clus
vv                          AMP PEAK  5(7P22.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                15
[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"
D5V8, binary
                               cls
clus                             0  1
  AMP PEAK  5(7P22.1) MUTATED    8 99
  AMP PEAK  5(7P22.1) WILD-TYPE  3 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P22.1) MUTATED      8   99
  AMP PEAK  5(7P22.1) WILD-TYPE    3   12
                        clus
vv                       AMP PEAK  5(7P22.1) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                          99
                        clus
vv                       AMP PEAK  5(7P22.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            12
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(7Q11.22) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(7Q11.22) MUTATED   106   3
  AMP PEAK  6(7Q11.22) WILD-TYPE  23   1
  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE 
                           109                             24 
  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE 
                             3                              1 
$`AMP PEAK  6(7Q11.22) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE 
       20.32        30.35        38.30        59.70       102.35       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       72.20        61.71        63.22        63.32        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.38        79.76        67.96        92.09        75.09       108.16 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW 
      106.39       115.00       120.62       124.57       128.94        61.45 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      170.33        80.94        60.26        59.84        59.90       125.69 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       61.84        98.53        59.74        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
        6.08       122.50       161.72        95.67       229.22       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AAAL TCGA-S6-A8JW 
       70.59         2.73         0.13         3.52         4.83        20.68 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84Y 
       18.15         9.14        13.58         1.38        16.31        17.23 
TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
        3.52        36.79        37.68        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
       41.52        24.26         3.65         5.06         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AANR 
       28.14         6.87        18.38        40.01        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOD TCGA-XE-AAOL 
       53.03        93.93        12.07         7.89        67.66         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
        8.32        12.92        20.12        57.90        54.35        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 
       21.96         0.56         5.29         7.96        40.96        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

$`AMP PEAK  6(7Q11.22) WILD-TYPE`
TCGA-2G-AAF8 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAGM TCGA-2G-AAGS TCGA-2G-AAGZ 
      122.40        52.37        71.24        59.64        59.28        60.16 
TCGA-2G-AAHG TCGA-2G-AAKG TCGA-2G-AAL5 TCGA-4K-AA1H TCGA-4K-AA1I TCGA-SN-A84W 
       59.80       212.65       184.41         7.00         0.10         9.63 
TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8AB TCGA-W4-A7U3 TCGA-XE-AANI TCGA-XE-AAOB 
       10.26        37.18        24.99         4.90        34.22        16.87 
TCGA-XE-AAOC TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A9T9 TCGA-YU-A94D TCGA-YU-AA61 
        8.88        41.69        50.96         6.90        58.88         8.15 

  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE 
                          0.13                           0.10 
  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE 
                        229.22                         212.65 
  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE 
                        37.680                         39.435 
[1] "0.1 - 229.2 (37.7)" "0.1 - 212.7 (39.4)"
[1] "hr=" "2.4"
D6V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  6(7Q11.22) MUTATED        16       18       11        5         6
  AMP PEAK  6(7Q11.22) WILD-TYPE       3        7        0        0         0
                                vv
clus                             STAGE IIB STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  6(7Q11.22) MUTATED           1         1         2          0
  AMP PEAK  6(7Q11.22) WILD-TYPE         0         0         0          1
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IS
  AMP PEAK  6(7Q11.22) MUTATED            4          5       36
  AMP PEAK  6(7Q11.22) WILD-TYPE          2          0       10
D6V3, multiclass
            clus
vv           AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE
  STAGE I                              16                              3
  STAGE IA                             18                              7
  STAGE IB                             11                              0
  STAGE II                              5                              0
  STAGE IIA                             6                              0
  STAGE IIB                             1                              0
  STAGE IIC                             1                              0
  STAGE III                             2                              0
  STAGE IIIA                            0                              1
  STAGE IIIB                            4                              2
  STAGE IIIC                            5                              0
  STAGE IS                             36                             10
[1] 12  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
  AMP PEAK  6(7Q11.22) MUTATED   58 45  5
  AMP PEAK  6(7Q11.22) WILD-TYPE 17  6  1
D6V4, multiclass
    clus
vv   AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE
  T1                           58                             17
  T2                           45                              6
  T3                            5                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1+N2
  AMP PEAK  6(7Q11.22) MUTATED   36    11
  AMP PEAK  6(7Q11.22) WILD-TYPE 10     2
D6V5, multiclass
       clus
vv      AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE
  N0                              36                             10
  N1+N2                           11                              2
[1] 2 2
[1] FALSE
D6V6, binary
                                cls
clus                              0  1
  AMP PEAK  6(7Q11.22) MUTATED   94  3
  AMP PEAK  6(7Q11.22) WILD-TYPE 20  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(7Q11.22) MUTATED     94    3
  AMP PEAK  6(7Q11.22) WILD-TYPE   20    1
   clus
vv  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE
  0                           94                             20
  1                            3                              1
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(7Q11.22) MUTATED       3                         5    97
  AMP PEAK  6(7Q11.22) WILD-TYPE     1                         1    21
D6V7, multiclass
                           clus
vv                          AMP PEAK  6(7Q11.22) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               97
                           clus
vv                          AMP PEAK  6(7Q11.22) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 21
[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"
D6V8, binary
                                cls
clus                              0  1
  AMP PEAK  6(7Q11.22) MUTATED    7 94
  AMP PEAK  6(7Q11.22) WILD-TYPE  4 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(7Q11.22) MUTATED      7   94
  AMP PEAK  6(7Q11.22) WILD-TYPE    4   17
                        clus
vv                       AMP PEAK  6(7Q11.22) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           94
                        clus
vv                       AMP PEAK  6(7Q11.22) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             17
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(8Q11.23) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  7(8Q11.23) MUTATED   109   4
  AMP PEAK  7(8Q11.23) WILD-TYPE  20   0
  AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE 
                           113                             20 
  AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE 
                             4                              0 
$`AMP PEAK  7(8Q11.23) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFM 
      154.59       191.31        36.99        14.14        14.56         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 
       14.86        16.50        36.13        36.89        52.37        71.24 
TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       72.20        63.22        63.32        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       79.76        67.96        92.09        59.64       106.39       115.00 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      120.62        59.28       128.94        61.45       170.33        80.94 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       60.26        59.84        59.90        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2X-A9D5 
      212.65       161.72        95.67       229.22       131.21         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
        0.13         3.52         0.10         4.83        20.68        18.15 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X TCGA-SN-A84Y 
        9.14        13.58         1.38        16.31        10.26        17.23 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC 
        3.52        37.18        36.79        37.68        24.99        35.61 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       23.90        41.52        24.26         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       16.87        41.69        50.96         0.43         8.32        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y 
       20.12         6.90        57.90        54.35        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        5.29        58.88         8.15        37.02        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

$`AMP PEAK  7(8Q11.23) WILD-TYPE`
TCGA-2G-AAFL TCGA-2G-AAFV TCGA-2G-AAG0 TCGA-2G-AAG7 TCGA-2G-AAGJ TCGA-2G-AAGK 
       17.16        40.70        40.01        61.71        75.09       108.16 
TCGA-2G-AAGT TCGA-2G-AAGZ TCGA-2G-AAH4 TCGA-2G-AAL5 TCGA-2G-AALP TCGA-4K-AA1H 
      124.57        60.16       125.69       184.41        70.59         7.00 
TCGA-SN-A84W TCGA-VF-A8AD TCGA-W4-A7U3 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-YU-A90S 
        9.63        33.07         4.90         8.88        67.66        31.92 
TCGA-YU-A94I TCGA-YU-AA4L 
        7.96        40.96 

  AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE 
                           0.1                            4.9 
  AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE 
                        229.22                         184.41 
  AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE 
                         37.02                          40.83 
[1] "0.1 - 229.2 (37.0)" "4.9 - 184.4 (40.8)"
[1] "hr="     "8.7e+07"
D7V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  7(8Q11.23) MUTATED        18       20        8        4         6
  AMP PEAK  7(8Q11.23) WILD-TYPE       1        5        3        1         0
                                vv
clus                             STAGE IIB STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  7(8Q11.23) MUTATED           1         1         2          0
  AMP PEAK  7(8Q11.23) WILD-TYPE         0         0         0          1
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IS
  AMP PEAK  7(8Q11.23) MUTATED            5          4       40
  AMP PEAK  7(8Q11.23) WILD-TYPE          1          1        6
D7V3, multiclass
            clus
vv           AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE
  STAGE I                              18                              1
  STAGE IA                             20                              5
  STAGE IB                              8                              3
  STAGE II                              4                              1
  STAGE IIA                             6                              0
  STAGE IIB                             1                              0
  STAGE IIC                             1                              0
  STAGE III                             2                              0
  STAGE IIIA                            0                              1
  STAGE IIIB                            5                              1
  STAGE IIIC                            4                              1
  STAGE IS                             40                              6
[1] 12  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
  AMP PEAK  7(8Q11.23) MUTATED   64 42  6
  AMP PEAK  7(8Q11.23) WILD-TYPE 11  9  0
D7V4, multiclass
    clus
vv   AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE
  T1                           64                             11
  T2                           42                              9
  T3                            6                              0
[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"
                                vv
clus                             N0 N1+N2
  AMP PEAK  7(8Q11.23) MUTATED   38    12
  AMP PEAK  7(8Q11.23) WILD-TYPE  8     1
D7V5, multiclass
       clus
vv      AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE
  N0                              38                              8
  N1+N2                           12                              1
[1] 2 2
[1] FALSE
D7V6, binary
                                cls
clus                               0   1
  AMP PEAK  7(8Q11.23) MUTATED   100   2
  AMP PEAK  7(8Q11.23) WILD-TYPE  14   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q11.23) MUTATED    100    2
  AMP PEAK  7(8Q11.23) WILD-TYPE   14    2
   clus
vv  AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE
  0                          100                             14
  1                            2                              2
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(8Q11.23) MUTATED       4                         4   101
  AMP PEAK  7(8Q11.23) WILD-TYPE     0                         2    17
D7V7, multiclass
                           clus
vv                          AMP PEAK  7(8Q11.23) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                              101
                           clus
vv                          AMP PEAK  7(8Q11.23) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 17
[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"
D7V8, binary
                                cls
clus                              0  1
  AMP PEAK  7(8Q11.23) MUTATED    9 97
  AMP PEAK  7(8Q11.23) WILD-TYPE  2 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q11.23) MUTATED      9   97
  AMP PEAK  7(8Q11.23) WILD-TYPE    2   14
                        clus
vv                       AMP PEAK  7(8Q11.23) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                           97
                        clus
vv                       AMP PEAK  7(8Q11.23) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             14
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(8Q23.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  8(8Q23.3) MUTATED   96  4
  AMP PEAK  8(8Q23.3) WILD-TYPE 33  0
  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE 
                          100                            33 
  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE 
                            4                             0 
$`AMP PEAK  8(8Q23.3) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFI TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
      154.59       191.31        14.14         9.57        14.86        16.50 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 
       36.13        36.89        52.37        71.24        72.20        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       63.32        68.22        72.85        79.76        67.96        92.09 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH8 
      128.94        61.45       170.33        59.84        59.90        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
        6.08       122.50       212.65        95.67       229.22       131.21 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
        2.73         0.13         0.10         4.83        20.68        18.15 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
       13.58         1.38        16.31        10.26        17.23         3.52 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AE 
       37.18        36.79        37.68        24.99        35.61        23.90 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
        6.87        18.38        40.01         0.46        53.03        93.93 
TCGA-XE-AAO4 TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       12.07        16.87        41.69         0.43         8.32        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y 
       20.12         6.90        57.90        54.35        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
        5.29        58.88        37.02        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

$`AMP PEAK  8(8Q23.3) WILD-TYPE`
TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFV TCGA-2G-AAG0 TCGA-2G-AAG7 
       36.99        14.56        17.16        40.70        40.01        61.71 
TCGA-2G-AAGE TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
       68.38        75.09       108.16        80.94        60.16        60.26 
TCGA-2G-AAH4 TCGA-2G-AAKH TCGA-2G-AAL5 TCGA-2G-AALP TCGA-4K-AA1G TCGA-4K-AA1H 
      125.69       161.72       184.41        70.59         3.52         7.00 
TCGA-S6-A8JY TCGA-SN-A84W TCGA-VF-A8AD TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-XE-AANI 
        9.14         9.63        33.07        41.52         4.90        34.22 
TCGA-XE-AANJ TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-YU-A90S 
       65.98         7.89         8.88        67.66        50.96        31.92 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        7.96        40.96         8.15 

  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE 
                         0.10                          3.52 
  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE 
                       229.22                        184.41 
  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE 
                         37.1                          40.7 
[1] "0.1 - 229.2 (37.1)" "3.5 - 184.4 (40.7)"
[1] "hr="     "2.9e+08"
D8V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  8(8Q23.3) MUTATED        17       19        8        3         6
  AMP PEAK  8(8Q23.3) WILD-TYPE       2        6        3        2         0
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  8(8Q23.3) MUTATED           0         1         2          0
  AMP PEAK  8(8Q23.3) WILD-TYPE         1         0         0          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  AMP PEAK  8(8Q23.3) MUTATED            5          4       32
  AMP PEAK  8(8Q23.3) WILD-TYPE          1          1       14
D8V3, multiclass
            clus
vv           AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE
  STAGE I                             17                             2
  STAGE IA                            19                             6
  STAGE IB                             8                             3
  STAGE II                             3                             2
  STAGE IIA                            6                             0
  STAGE IIB                            0                             1
  STAGE IIC                            1                             0
  STAGE III                            2                             0
  STAGE IIIA                           0                             1
  STAGE IIIB                           5                             1
  STAGE IIIC                           4                             1
  STAGE IS                            32                            14
[1] 12  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
  AMP PEAK  8(8Q23.3) MUTATED   53 40  6
  AMP PEAK  8(8Q23.3) WILD-TYPE 22 11  0
D8V4, multiclass
    clus
vv   AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE
  T1                          53                            22
  T2                          40                            11
  T3                           6                             0
[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"
                               vv
clus                            N0 N1+N2
  AMP PEAK  8(8Q23.3) MUTATED   34    11
  AMP PEAK  8(8Q23.3) WILD-TYPE 12     2
D8V5, multiclass
       clus
vv      AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE
  N0                             34                            12
  N1+N2                          11                             2
[1] 2 2
[1] FALSE
D8V6, binary
                               cls
clus                             0  1
  AMP PEAK  8(8Q23.3) MUTATED   89  2
  AMP PEAK  8(8Q23.3) WILD-TYPE 25  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q23.3) MUTATED     89    2
  AMP PEAK  8(8Q23.3) WILD-TYPE   25    2
   clus
vv  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE
  0                          89                            25
  1                           2                             2
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(8Q23.3) MUTATED       3                         4    89
  AMP PEAK  8(8Q23.3) WILD-TYPE     1                         2    29
D8V7, multiclass
                           clus
vv                          AMP PEAK  8(8Q23.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              89
                           clus
vv                          AMP PEAK  8(8Q23.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                29
[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"
D8V8, binary
                               cls
clus                             0  1
  AMP PEAK  8(8Q23.3) MUTATED    7 87
  AMP PEAK  8(8Q23.3) WILD-TYPE  4 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q23.3) MUTATED      7   87
  AMP PEAK  8(8Q23.3) WILD-TYPE    4   24
                        clus
vv                       AMP PEAK  8(8Q23.3) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                          87
                        clus
vv                       AMP PEAK  8(8Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            24
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(12P13.33) MUTATION ANALYSIS
D9V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK  9(12P13.33) MUTATED   124   4
  AMP PEAK  9(12P13.33) WILD-TYPE   5   0
  AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE 
                            128                               5 
  AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE 
                              4                               0 
$`AMP PEAK  9(12P13.33) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE 
       20.32        30.35        38.30        59.70       102.35       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
        6.08       122.50       212.65       161.72        95.67       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      184.41       131.21        70.59         2.73         0.13         3.52 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C 
        0.10         4.83        20.68        18.15        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       16.31         9.63        10.26        17.23         3.52        37.18 
TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       36.79        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       41.52         4.90        24.26         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
       16.87         8.88        67.66        41.69        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
        8.32        12.92        20.12         6.90        57.90        54.35 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       21.96         0.56         5.29        58.88         7.96        40.96 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0E TCGA-ZM-AA0F 
        8.15        37.02        39.35        27.55        16.41        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

$`AMP PEAK  9(12P13.33) WILD-TYPE`
TCGA-2G-AAF8 TCGA-4K-AA1H TCGA-S6-A8JY TCGA-YU-A90S TCGA-ZM-AA0D 
      122.40         7.00         9.14        31.92        17.39 

  AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE 
                            0.1                             7.0 
  AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE 
                         229.22                          122.40 
  AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE 
                         38.825                          17.390 
[1] "0.1 - 229.2 (38.8)" "7.0 - 122.4 (17.4)"
[1] "hr="     "2.5e+07"
D9V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(12P13.33) MUTATED        19       21       11        5         6
  AMP PEAK  9(12P13.33) WILD-TYPE       0        4        0        0         0
                                 vv
clus                              STAGE IIB STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  9(12P13.33) MUTATED           1         1         2          1
  AMP PEAK  9(12P13.33) WILD-TYPE         0         0         0          0
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IS
  AMP PEAK  9(12P13.33) MUTATED            6          5       45
  AMP PEAK  9(12P13.33) WILD-TYPE          0          0        1
D9V3, multiclass
            clus
vv           AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE
  STAGE I                               19                               0
  STAGE IA                              21                               4
  STAGE IB                              11                               0
  STAGE II                               5                               0
  STAGE IIA                              6                               0
  STAGE IIB                              1                               0
  STAGE IIC                              1                               0
  STAGE III                              2                               0
  STAGE IIIA                             1                               0
  STAGE IIIB                             6                               0
  STAGE IIIC                             5                               0
  STAGE IS                              45                               1
[1] 12  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
  AMP PEAK  9(12P13.33) MUTATED   71 50  6
  AMP PEAK  9(12P13.33) WILD-TYPE  4  1  0
D9V4, multiclass
    clus
vv   AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE
  T1                            71                               4
  T2                            50                               1
  T3                             6                               0
[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"
                                 vv
clus                              N0 N1+N2
  AMP PEAK  9(12P13.33) MUTATED   44    13
  AMP PEAK  9(12P13.33) WILD-TYPE  2     0
D9V5, multiclass
[1] "Remove cluster labels:"          "AMP PEAK  9(12P13.33) WILD-TYPE"
clus
  AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE 
                             57                               2 
                   TCGA-2G-AAEW                    TCGA-2G-AAEX 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAF1                    TCGA-2G-AAF4 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAF6                    TCGA-2G-AAFE 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAFG                    TCGA-2G-AAFH 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAFI                    TCGA-2G-AAFJ 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAFL                    TCGA-2G-AAFM 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAFN                    TCGA-2G-AAFO 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAFV                    TCGA-2G-AAFY 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAG0                    TCGA-2G-AAG5 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAG6                    TCGA-2G-AAG7 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAG8                    TCGA-2G-AAG9 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAGA                    TCGA-2G-AAGC 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAGE                    TCGA-2G-AAGF 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAGG                    TCGA-2G-AAGI 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAGJ                    TCGA-2G-AAGK 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAGM                    TCGA-2G-AAGN 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAGO                    TCGA-2G-AAGP 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAGS                    TCGA-2G-AAGW 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAGX                    TCGA-2G-AAGY 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAGZ                    TCGA-2G-AAH2 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAHG                    TCGA-2G-AAHL 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAHN                    TCGA-2G-AAHP 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAHT                    TCGA-2G-AAKG 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-2G-AAL5                    TCGA-2G-AAL7 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-4K-AA1G                    TCGA-4K-AA1I 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-4K-AAAL                    TCGA-SO-A8JP 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-VF-A8A8                    TCGA-VF-A8A9 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-VF-A8AA                    TCGA-VF-A8AB 
"AMP PEAK  9(12P13.33) MUTATED" "AMP PEAK  9(12P13.33) MUTATED" 
                   TCGA-X3-A8G4 
"AMP PEAK  9(12P13.33) MUTATED" 
D9V6, binary
                                 cls
clus                                0   1
  AMP PEAK  9(12P13.33) MUTATED   110   4
  AMP PEAK  9(12P13.33) WILD-TYPE   4   0
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  9(12P13.33) MUTATED    110    4
  AMP PEAK  9(12P13.33) WILD-TYPE    4    0
   clus
vv  AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE
  0                           110                               4
  1                             4                               0
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(12P13.33) MUTATED       4                         6   113
  AMP PEAK  9(12P13.33) WILD-TYPE     0                         0     5
D9V7, multiclass
                           clus
vv                          AMP PEAK  9(12P13.33) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               113
                           clus
vv                          AMP PEAK  9(12P13.33) WILD-TYPE
  ASIAN                                                   0
  BLACK OR AFRICAN AMERICAN                               0
  WHITE                                                   5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                                 cls
clus                                0   1
  AMP PEAK  9(12P13.33) MUTATED    11 107
  AMP PEAK  9(12P13.33) WILD-TYPE   0   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  9(12P13.33) MUTATED     11  107
  AMP PEAK  9(12P13.33) WILD-TYPE    0    4
                        clus
vv                       AMP PEAK  9(12P13.33) MUTATED
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           107
                        clus
vv                       AMP PEAK  9(12P13.33) WILD-TYPE
  HISPANIC OR LATINO                                   0
  NOT HISPANIC OR LATINO                               4
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(12P12.1) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 10(12P12.1) MUTATED   126   4
  AMP PEAK 10(12P12.1) WILD-TYPE   3   0
  AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE 
                           130                              3 
  AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE 
                             4                              0 
$`AMP PEAK 10(12P12.1) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       40.01        52.37        71.24        72.20        61.71        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       63.32        68.22        72.85        68.38        79.76        67.96 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       92.09        75.09       108.16        59.64       106.39       115.00 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      120.62        59.28       124.57       128.94        61.45       170.33 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
       80.94        60.16        60.26        59.84        59.90       125.69 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       61.84        98.53        59.74        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
      176.15         6.08       122.50       212.65       161.72        95.67 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
      229.22       184.41       131.21        70.59         2.73         0.13 
TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
        3.52         0.10         4.83        20.68        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y 
       13.58         1.38        16.31         9.63        10.26        17.23 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC 
        3.52        37.18        36.79        37.68        24.99        35.61 
TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 
       33.07        23.90        41.52         4.90        24.26         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
        5.06         0.16         0.82        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        34.22        65.98         0.46        53.03        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF 
       12.07         7.89        16.87         8.88        67.66        41.69 
TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       50.96         0.43         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       57.90        54.35        21.96         0.56         5.29        58.88 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        7.96        40.96         8.15        37.02        39.35        27.55 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

$`AMP PEAK 10(12P12.1) WILD-TYPE`
TCGA-4K-AA1H TCGA-YU-A90S TCGA-ZM-AA0D 
        7.00        31.92        17.39 

  AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE 
                           0.1                            7.0 
  AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE 
                        229.22                          31.92 
  AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE 
                        38.825                         17.390 
[1] "0.1 - 229.2 (38.8)" "7.0 - 31.9 (17.4)" 
[1] "hr="     "9200000"
D10V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(12P12.1) MUTATED        19       22       11        5         6
  AMP PEAK 10(12P12.1) WILD-TYPE       0        3        0        0         0
                                vv
clus                             STAGE IIB STAGE IIC STAGE III STAGE IIIA
  AMP PEAK 10(12P12.1) MUTATED           1         1         2          1
  AMP PEAK 10(12P12.1) WILD-TYPE         0         0         0          0
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IS
  AMP PEAK 10(12P12.1) MUTATED            6          5       46
  AMP PEAK 10(12P12.1) WILD-TYPE          0          0        0
D10V3, multiclass
            clus
vv           AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE
  STAGE I                              19                              0
  STAGE IA                             22                              3
  STAGE IB                             11                              0
  STAGE II                              5                              0
  STAGE IIA                             6                              0
  STAGE IIB                             1                              0
  STAGE IIC                             1                              0
  STAGE III                             2                              0
  STAGE IIIA                            1                              0
  STAGE IIIB                            6                              0
  STAGE IIIC                            5                              0
  STAGE IS                             46                              0
[1] 12  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
  AMP PEAK 10(12P12.1) MUTATED   73 50  6
  AMP PEAK 10(12P12.1) WILD-TYPE  2  1  0
D10V4, multiclass
    clus
vv   AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE
  T1                           73                              2
  T2                           50                              1
  T3                            6                              0
[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"
                                vv
clus                             N0 N1+N2
  AMP PEAK 10(12P12.1) MUTATED   45    13
  AMP PEAK 10(12P12.1) WILD-TYPE  1     0
D10V5, multiclass
[1] "Remove cluster labels:"         "AMP PEAK 10(12P12.1) WILD-TYPE"
clus
  AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE 
                            58                              1 
                  TCGA-2G-AAEW                   TCGA-2G-AAEX 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAF1                   TCGA-2G-AAF4 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAF6                   TCGA-2G-AAF8 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAFE                   TCGA-2G-AAFG 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAFH                   TCGA-2G-AAFI 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAFJ                   TCGA-2G-AAFL 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAFM                   TCGA-2G-AAFN 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAFO                   TCGA-2G-AAFV 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAFY                   TCGA-2G-AAG0 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAG5                   TCGA-2G-AAG6 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAG7                   TCGA-2G-AAG8 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAG9                   TCGA-2G-AAGA 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAGC                   TCGA-2G-AAGE 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAGF                   TCGA-2G-AAGG 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAGI                   TCGA-2G-AAGJ 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAGK                   TCGA-2G-AAGM 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAGN                   TCGA-2G-AAGO 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAGP                   TCGA-2G-AAGS 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAGW                   TCGA-2G-AAGX 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAGY                   TCGA-2G-AAGZ 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAH2                   TCGA-2G-AAHG 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAHL                   TCGA-2G-AAHN 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAHP                   TCGA-2G-AAHT 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAKG                   TCGA-2G-AAL5 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAL7                   TCGA-4K-AA1G 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-4K-AA1I                   TCGA-4K-AAAL 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-SO-A8JP                   TCGA-VF-A8A8 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-VF-A8A9                   TCGA-VF-A8AA 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-VF-A8AB                   TCGA-X3-A8G4 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
D10V6, binary
                                cls
clus                               0   1
  AMP PEAK 10(12P12.1) MUTATED   112   4
  AMP PEAK 10(12P12.1) WILD-TYPE   2   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(12P12.1) MUTATED    112    4
  AMP PEAK 10(12P12.1) WILD-TYPE    2    0
   clus
vv  AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE
  0                          112                              2
  1                            4                              0
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(12P12.1) MUTATED       4                         6   115
  AMP PEAK 10(12P12.1) WILD-TYPE     0                         0     3
D10V7, multiclass
                           clus
vv                          AMP PEAK 10(12P12.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                              115
                           clus
vv                          AMP PEAK 10(12P12.1) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                                cls
clus                               0   1
  AMP PEAK 10(12P12.1) MUTATED    11 109
  AMP PEAK 10(12P12.1) WILD-TYPE   0   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(12P12.1) MUTATED     11  109
  AMP PEAK 10(12P12.1) WILD-TYPE    0    2
                        clus
vv                       AMP PEAK 10(12P12.1) MUTATED
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          109
                        clus
vv                       AMP PEAK 10(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                              2
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(12P11.21) MUTATION ANALYSIS
D11V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 11(12P11.21) MUTATED   123   4
  AMP PEAK 11(12P11.21) WILD-TYPE   6   0
  AMP PEAK 11(12P11.21) MUTATED AMP PEAK 11(12P11.21) WILD-TYPE 
                            127                               6 
  AMP PEAK 11(12P11.21) MUTATED AMP PEAK 11(12P11.21) WILD-TYPE 
                              4                               0 
$`AMP PEAK 11(12P11.21) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       40.01        52.37        71.24        72.20        61.71        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       63.32        68.22        72.85        68.38        79.76        67.96 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       92.09        75.09       108.16        59.64       106.39       115.00 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      120.62        59.28       124.57       128.94        61.45       170.33 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
       80.94        60.16        60.26        59.84        59.90       125.69 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       61.84        98.53        59.74        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
      176.15         6.08       122.50       212.65       161.72        95.67 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
      229.22       184.41       131.21        70.59         2.73         0.13 
TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 
        3.52         0.10         4.83        20.68        18.15        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23         3.52 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       37.18        36.79        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       23.90        41.52         4.90        24.26         3.65         5.06 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        53.03        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43         8.32 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W 
       12.92        20.12         6.90        57.90        54.35        21.96 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56         5.29        58.88         7.96        40.96         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        39.35        27.55        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

$`AMP PEAK 11(12P11.21) WILD-TYPE`
TCGA-4K-AA1H TCGA-S6-A8JY TCGA-WZ-A7V5 TCGA-XE-AANJ TCGA-YU-A90S TCGA-ZM-AA0D 
        7.00         9.14         0.16        65.98        31.92        17.39 

  AMP PEAK 11(12P11.21) MUTATED AMP PEAK 11(12P11.21) WILD-TYPE 
                           0.10                            0.16 
  AMP PEAK 11(12P11.21) MUTATED AMP PEAK 11(12P11.21) WILD-TYPE 
                         229.22                           65.98 
  AMP PEAK 11(12P11.21) MUTATED AMP PEAK 11(12P11.21) WILD-TYPE 
                         39.350                          13.265 
[1] "0.1 - 229.2 (39.4)" "0.2 - 66.0 (13.3)" 
[1] "hr="     "2.5e+07"
D11V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 11(12P11.21) MUTATED        18       22       11        5         6
  AMP PEAK 11(12P11.21) WILD-TYPE       1        3        0        0         0
                                 vv
clus                              STAGE IIB STAGE IIC STAGE III STAGE IIIA
  AMP PEAK 11(12P11.21) MUTATED           1         1         2          1
  AMP PEAK 11(12P11.21) WILD-TYPE         0         0         0          0
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IS
  AMP PEAK 11(12P11.21) MUTATED            6          5       44
  AMP PEAK 11(12P11.21) WILD-TYPE          0          0        2
D11V3, multiclass
            clus
vv           AMP PEAK 11(12P11.21) MUTATED AMP PEAK 11(12P11.21) WILD-TYPE
  STAGE I                               18                               1
  STAGE IA                              22                               3
  STAGE IB                              11                               0
  STAGE II                               5                               0
  STAGE IIA                              6                               0
  STAGE IIB                              1                               0
  STAGE IIC                              1                               0
  STAGE III                              2                               0
  STAGE IIIA                             1                               0
  STAGE IIIB                             6                               0
  STAGE IIIC                             5                               0
  STAGE IS                              44                               2
[1] 12  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
  AMP PEAK 11(12P11.21) MUTATED   72 48  6
  AMP PEAK 11(12P11.21) WILD-TYPE  3  3  0
D11V4, multiclass
    clus
vv   AMP PEAK 11(12P11.21) MUTATED AMP PEAK 11(12P11.21) WILD-TYPE
  T1                            72                               3
  T2                            48                               3
  T3                             6                               0
[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"
                                 vv
clus                              N0 N1+N2
  AMP PEAK 11(12P11.21) MUTATED   45    13
  AMP PEAK 11(12P11.21) WILD-TYPE  1     0
D11V5, multiclass
[1] "Remove cluster labels:"          "AMP PEAK 11(12P11.21) WILD-TYPE"
clus
  AMP PEAK 11(12P11.21) MUTATED AMP PEAK 11(12P11.21) WILD-TYPE 
                             58                               1 
                   TCGA-2G-AAEW                    TCGA-2G-AAEX 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAF1                    TCGA-2G-AAF4 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAF6                    TCGA-2G-AAF8 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAFE                    TCGA-2G-AAFG 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAFH                    TCGA-2G-AAFI 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAFJ                    TCGA-2G-AAFL 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAFM                    TCGA-2G-AAFN 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAFO                    TCGA-2G-AAFV 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAFY                    TCGA-2G-AAG0 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAG5                    TCGA-2G-AAG6 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAG7                    TCGA-2G-AAG8 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAG9                    TCGA-2G-AAGA 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAGC                    TCGA-2G-AAGE 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAGF                    TCGA-2G-AAGG 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAGI                    TCGA-2G-AAGJ 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAGK                    TCGA-2G-AAGM 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAGN                    TCGA-2G-AAGO 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAGP                    TCGA-2G-AAGS 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAGW                    TCGA-2G-AAGX 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAGY                    TCGA-2G-AAGZ 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAH2                    TCGA-2G-AAHG 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAHL                    TCGA-2G-AAHN 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAHP                    TCGA-2G-AAHT 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAKG                    TCGA-2G-AAL5 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-2G-AAL7                    TCGA-4K-AA1G 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-4K-AA1I                    TCGA-4K-AAAL 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-SO-A8JP                    TCGA-VF-A8A8 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-VF-A8A9                    TCGA-VF-A8AA 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
                   TCGA-VF-A8AB                    TCGA-X3-A8G4 
"AMP PEAK 11(12P11.21) MUTATED" "AMP PEAK 11(12P11.21) MUTATED" 
D11V6, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P11.21) MUTATED   110   4
  AMP PEAK 11(12P11.21) WILD-TYPE   4   0
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P11.21) MUTATED    110    4
  AMP PEAK 11(12P11.21) WILD-TYPE    4    0
   clus
vv  AMP PEAK 11(12P11.21) MUTATED AMP PEAK 11(12P11.21) WILD-TYPE
  0                           110                               4
  1                             4                               0
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(12P11.21) MUTATED       4                         6   112
  AMP PEAK 11(12P11.21) WILD-TYPE     0                         0     6
D11V7, multiclass
                           clus
vv                          AMP PEAK 11(12P11.21) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               112
                           clus
vv                          AMP PEAK 11(12P11.21) WILD-TYPE
  ASIAN                                                   0
  BLACK OR AFRICAN AMERICAN                               0
  WHITE                                                   6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P11.21) MUTATED    10 107
  AMP PEAK 11(12P11.21) WILD-TYPE   1   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P11.21) MUTATED     10  107
  AMP PEAK 11(12P11.21) WILD-TYPE    1    4
                        clus
vv                       AMP PEAK 11(12P11.21) MUTATED
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           107
                        clus
vv                       AMP PEAK 11(12P11.21) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                               4
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(12Q15) MUTATION ANALYSIS
D12V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 12(12Q15) MUTATED   87  2
  AMP PEAK 12(12Q15) WILD-TYPE 42  2
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                          89                           44 
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                           2                            2 
$`AMP PEAK 12(12Q15) MUTATED`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAFH 
       30.35        38.30        59.70       122.40       154.59        36.99 
TCGA-2G-AAFI TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
       14.14        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       40.01        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       68.22        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW 
       59.64       106.39       120.62        59.28       124.57        61.45 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      170.33        80.94        60.26        59.84        59.90       125.69 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKH 
       61.84        98.53        59.74        91.43       176.15       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
       95.67       229.22       131.21        70.59         2.73         0.13 
TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 
        3.52         0.10         4.83        20.68        18.15        13.58 
TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA 
       10.26        17.23         3.52        37.18        36.79        37.68 
TCGA-VF-A8AB TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
       24.99        33.07        23.90        41.52         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H5 TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       28.14         6.87        40.01        53.03        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOL TCGA-XY-A8S2 TCGA-YU-A90P 
        7.89         8.88        67.66         0.43        12.92        57.90 
TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I TCGA-ZM-AA05 
       54.35        21.96         0.56         5.29         7.96        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       39.35        27.55        11.34        46.88        10.85 

$`AMP PEAK 12(12Q15) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAF6 TCGA-2G-AAFG TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
       20.32       102.35       191.31        14.56        17.16         9.57 
TCGA-2G-AAG3 TCGA-2G-AAGC TCGA-2G-AAGK TCGA-2G-AAGO TCGA-2G-AAGV TCGA-2G-AAGZ 
       52.37        72.85       108.16       115.00       128.94        60.16 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAL5 
       59.80        59.80         6.08       122.50       212.65       184.41 
TCGA-4K-AA1H TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-VF-A8AC 
        7.00         9.14         1.38        16.31         9.63        35.61 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-XE-A8H4 TCGA-XE-AANI 
        4.90        24.26         3.65         5.06        18.38        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B 
       65.98         0.46        16.87        41.69        50.96         8.32 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90S TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 
       20.12         6.90        31.92        58.88        40.96         8.15 
TCGA-ZM-AA0D TCGA-ZM-AA0E 
       17.39        16.41 

  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                        0.10                         0.46 
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                      229.22                       212.65 
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                       40.01                        22.29 
[1] "0.1 - 229.2 (40.0)" "0.5 - 212.7 (22.3)"
[1] "hr=" "4.7"
D12V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(12Q15) MUTATED        11       17       10        4         5
  AMP PEAK 12(12Q15) WILD-TYPE       8        8        1        1         1
                              vv
clus                           STAGE IIB STAGE IIC STAGE III STAGE IIIA
  AMP PEAK 12(12Q15) MUTATED           1         1         1          0
  AMP PEAK 12(12Q15) WILD-TYPE         0         0         1          1
                              vv
clus                           STAGE IIIB STAGE IIIC STAGE IS
  AMP PEAK 12(12Q15) MUTATED            5          4       28
  AMP PEAK 12(12Q15) WILD-TYPE          1          1       18
D12V3, multiclass
            clus
vv           AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE
  STAGE I                            11                            8
  STAGE IA                           17                            8
  STAGE IB                           10                            1
  STAGE II                            4                            1
  STAGE IIA                           5                            1
  STAGE IIB                           1                            0
  STAGE IIC                           1                            0
  STAGE III                           1                            1
  STAGE IIIA                          0                            1
  STAGE IIIB                          5                            1
  STAGE IIIC                          4                            1
  STAGE IS                           28                           18
[1] 12  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
  AMP PEAK 12(12Q15) MUTATED   48 36  5
  AMP PEAK 12(12Q15) WILD-TYPE 27 15  1
D12V4, multiclass
    clus
vv   AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE
  T1                         48                           27
  T2                         36                           15
  T3                          5                            1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1+N2
  AMP PEAK 12(12Q15) MUTATED   32    11
  AMP PEAK 12(12Q15) WILD-TYPE 14     2
D12V5, multiclass
       clus
vv      AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE
  N0                            32                           14
  N1+N2                         11                            2
[1] 2 2
[1] FALSE
D12V6, binary
                              cls
clus                            0  1
  AMP PEAK 12(12Q15) MUTATED   78  3
  AMP PEAK 12(12Q15) WILD-TYPE 36  1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(12Q15) MUTATED     78    3
  AMP PEAK 12(12Q15) WILD-TYPE   36    1
   clus
vv  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE
  0                         78                           36
  1                          3                            1
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(12Q15) MUTATED       2                         5    78
  AMP PEAK 12(12Q15) WILD-TYPE     2                         1    40
D12V7, multiclass
                           clus
vv                          AMP PEAK 12(12Q15) MUTATED
  ASIAN                                              2
  BLACK OR AFRICAN AMERICAN                          5
  WHITE                                             78
                           clus
vv                          AMP PEAK 12(12Q15) WILD-TYPE
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               40
[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"
D12V8, binary
                              cls
clus                            0  1
  AMP PEAK 12(12Q15) MUTATED    6 77
  AMP PEAK 12(12Q15) WILD-TYPE  5 34
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(12Q15) MUTATED      6   77
  AMP PEAK 12(12Q15) WILD-TYPE    5   34
                        clus
vv                       AMP PEAK 12(12Q15) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                         77
                        clus
vv                       AMP PEAK 12(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           34
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(16Q21) MUTATION ANALYSIS
D13V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 13(16Q21) MUTATED    17   1
  AMP PEAK 13(16Q21) WILD-TYPE 112   3
  AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE 
                          18                          115 
  AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE 
                           1                            3 
$`AMP PEAK 13(16Q21) MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAGE 
       59.70        36.99        14.14        71.24        72.20        68.38 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAH2 TCGA-SN-A84X 
       67.96        92.09        59.64       124.57        59.84        10.26 
TCGA-SN-A84Y TCGA-X3-A8G4 TCGA-XE-AAOC TCGA-YU-A90P TCGA-YU-A90Y TCGA-ZM-AA06 
       17.23        28.14         8.88        57.90         0.56        39.35 

$`AMP PEAK 13(16Q21) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        38.30       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
      191.31        14.56        17.16         9.57        14.86        16.50 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG7 
       40.70        36.13        36.89        40.01        52.37        61.71 
TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGJ 
       63.22        63.32        68.22        72.85        79.76        75.09 
TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV 
      108.16       106.39       115.00       120.62        59.28       128.94 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH3 
       61.45       170.33        80.94        60.16        60.26        59.90 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL 
      125.69        61.84        98.53        59.74        59.80        59.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
       91.43       176.15         6.08       122.50       212.65       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
       95.67       229.22       184.41       131.21        70.59         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
        0.13         3.52         7.00         0.10         4.83        20.68 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
       18.15         9.14        13.58         1.38        16.31         9.63 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC 
        3.52        37.18        36.79        37.68        24.99        35.61 
TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 
       33.07        23.90        41.52         4.90        24.26         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        5.06         0.16         0.82         6.87        18.38        40.01 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
        7.89        16.87        67.66        41.69        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S 
        8.32        12.92        20.12         6.90        54.35        31.92 
TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       21.96         5.29        58.88         7.96        40.96         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE 
                        0.56                         0.10 
  AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE 
                      124.57                       229.22 
  AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE 
                       58.77                        37.02 
[1] "0.6 - 124.6 (58.8)" "0.1 - 229.2 (37.0)"
[1] "hr=" "2.9"
D13V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(16Q21) MUTATED         1        2        2        0         0
  AMP PEAK 13(16Q21) WILD-TYPE      18       23        9        5         6
                              vv
clus                           STAGE IIB STAGE IIC STAGE III STAGE IIIA
  AMP PEAK 13(16Q21) MUTATED           1         0         0          0
  AMP PEAK 13(16Q21) WILD-TYPE         0         1         2          1
                              vv
clus                           STAGE IIIB STAGE IIIC STAGE IS
  AMP PEAK 13(16Q21) MUTATED            0          2       10
  AMP PEAK 13(16Q21) WILD-TYPE          6          3       36
D13V3, multiclass
            clus
vv           AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE
  STAGE I                             1                           18
  STAGE IA                            2                           23
  STAGE IB                            2                            9
  STAGE II                            0                            5
  STAGE IIA                           0                            6
  STAGE IIB                           1                            0
  STAGE IIC                           0                            1
  STAGE III                           0                            2
  STAGE IIIA                          0                            1
  STAGE IIIB                          0                            6
  STAGE IIIC                          2                            3
  STAGE IS                           10                           36
[1] 12  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
  AMP PEAK 13(16Q21) MUTATED   10  6  2
  AMP PEAK 13(16Q21) WILD-TYPE 65 45  4
D13V4, multiclass
    clus
vv   AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE
  T1                         10                           65
  T2                          6                           45
  T3                          2                            4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1+N2
  AMP PEAK 13(16Q21) MUTATED    9     2
  AMP PEAK 13(16Q21) WILD-TYPE 37    11
D13V5, multiclass
       clus
vv      AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE
  N0                             9                           37
  N1+N2                          2                           11
[1] 2 2
[1] FALSE
D13V6, binary
                              cls
clus                            0  1
  AMP PEAK 13(16Q21) MUTATED   15  1
  AMP PEAK 13(16Q21) WILD-TYPE 99  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(16Q21) MUTATED     15    1
  AMP PEAK 13(16Q21) WILD-TYPE   99    3
   clus
vv  AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE
  0                         15                           99
  1                          1                            3
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(16Q21) MUTATED       0                         1    17
  AMP PEAK 13(16Q21) WILD-TYPE     4                         5   101
D13V7, multiclass
                           clus
vv                          AMP PEAK 13(16Q21) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             17
                           clus
vv                          AMP PEAK 13(16Q21) WILD-TYPE
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                              101
[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"
D13V8, binary
                              cls
clus                            0  1
  AMP PEAK 13(16Q21) MUTATED    3 13
  AMP PEAK 13(16Q21) WILD-TYPE  8 98
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(16Q21) MUTATED      3   13
  AMP PEAK 13(16Q21) WILD-TYPE    8   98
                        clus
vv                       AMP PEAK 13(16Q21) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         13
                        clus
vv                       AMP PEAK 13(16Q21) WILD-TYPE
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           98
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(20Q11.21) MUTATION ANALYSIS
D14V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 14(20Q11.21) MUTATED   39  2
  AMP PEAK 14(20Q11.21) WILD-TYPE 90  2
  AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE 
                             41                              92 
  AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE 
                              2                               2 
$`AMP PEAK 14(20Q11.21) MUTATED`
TCGA-2G-AAFI TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 
       14.14        36.89        52.37        71.24        72.20        63.22 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAH0 
       67.96        92.09        59.64       120.62       124.57        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHP TCGA-2G-AAKH TCGA-2G-AAKL 
       59.84        61.84        98.53       176.15       161.72        95.67 
TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-4K-AA1G TCGA-4K-AAAL TCGA-S6-A8JW TCGA-SB-A6J6 
      229.22       131.21         3.52         4.83        20.68        13.58 
TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-W4-A7U4 TCGA-WZ-A7V3 
       10.26        17.23         3.52        37.18        24.26         3.65 
TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-AAOC TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W 
        0.16        28.14         8.88        57.90        54.35        21.96 
TCGA-YU-A90Y TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA06 
        0.56         7.96        40.96        37.02        39.35 

$`AMP PEAK 14(20Q11.21) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        36.99        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG7 
       14.86        16.50        40.70        36.13        40.01        61.71 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGJ 
       63.32        68.22        72.85        68.38        79.76        75.09 
TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW 
      108.16       106.39       115.00        59.28       128.94        61.45 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC 
      170.33        80.94        60.16        59.90       125.69        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        59.80        91.43         6.08       122.50       212.65 
TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I 
      184.41        70.59         2.73         0.13         7.00         0.10 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-VF-A8A9 
       18.15         9.14         1.38        16.31         9.63        36.79 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U3 TCGA-WZ-A7V4 TCGA-WZ-A8D5 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        4.90         5.06         0.82         6.87        18.38        40.01 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
        7.89        16.87        67.66        41.69        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90S TCGA-YU-A912 
        8.32        12.92        20.12         6.90        31.92         5.29 
TCGA-YU-A94D TCGA-YU-AA61 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       58.88         8.15        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

  AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE 
                           0.16                            0.10 
  AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE 
                         229.22                          212.65 
  AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE 
                          40.96                           36.89 
[1] "0.2 - 229.2 (41.0)" "0.1 - 212.7 (36.9)"
[1] "hr=" "1"  
D14V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(20Q11.21) MUTATED         3        6        5        3         1
  AMP PEAK 14(20Q11.21) WILD-TYPE      16       19        6        2         5
                                 vv
clus                              STAGE IIB STAGE IIC STAGE III STAGE IIIA
  AMP PEAK 14(20Q11.21) MUTATED           0         1         1          0
  AMP PEAK 14(20Q11.21) WILD-TYPE         1         0         1          1
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IS
  AMP PEAK 14(20Q11.21) MUTATED            0          4       16
  AMP PEAK 14(20Q11.21) WILD-TYPE          6          1       30
D14V3, multiclass
            clus
vv           AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE
  STAGE I                                3                              16
  STAGE IA                               6                              19
  STAGE IB                               5                               6
  STAGE II                               3                               2
  STAGE IIA                              1                               5
  STAGE IIB                              0                               1
  STAGE IIC                              1                               0
  STAGE III                              1                               1
  STAGE IIIA                             0                               1
  STAGE IIIB                             0                               6
  STAGE IIIC                             4                               1
  STAGE IS                              16                              30
[1] 12  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
  AMP PEAK 14(20Q11.21) MUTATED   16 22  3
  AMP PEAK 14(20Q11.21) WILD-TYPE 59 29  3
D14V4, multiclass
    clus
vv   AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE
  T1                            16                              59
  T2                            22                              29
  T3                             3                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1+N2
  AMP PEAK 14(20Q11.21) MUTATED   14     2
  AMP PEAK 14(20Q11.21) WILD-TYPE 32    11
D14V5, multiclass
       clus
vv      AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE
  N0                               14                              32
  N1+N2                             2                              11
[1] 2 2
[1] FALSE
D14V6, binary
                                 cls
clus                               0  1
  AMP PEAK 14(20Q11.21) MUTATED   31  2
  AMP PEAK 14(20Q11.21) WILD-TYPE 83  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(20Q11.21) MUTATED     31    2
  AMP PEAK 14(20Q11.21) WILD-TYPE   83    2
   clus
vv  AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE
  0                            31                              83
  1                             2                               2
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(20Q11.21) MUTATED       0                         2    37
  AMP PEAK 14(20Q11.21) WILD-TYPE     4                         4    81
D14V7, multiclass
                           clus
vv                          AMP PEAK 14(20Q11.21) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                37
                           clus
vv                          AMP PEAK 14(20Q11.21) WILD-TYPE
  ASIAN                                                   4
  BLACK OR AFRICAN AMERICAN                               4
  WHITE                                                  81
[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"
D14V8, binary
                                 cls
clus                               0  1
  AMP PEAK 14(20Q11.21) MUTATED    3 32
  AMP PEAK 14(20Q11.21) WILD-TYPE  8 79
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(20Q11.21) MUTATED      3   32
  AMP PEAK 14(20Q11.21) WILD-TYPE    8   79
                        clus
vv                       AMP PEAK 14(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            32
                        clus
vv                       AMP PEAK 14(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                              79
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(22Q11.21) MUTATION ANALYSIS
D15V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 15(22Q11.21) MUTATED   52  1
  AMP PEAK 15(22Q11.21) WILD-TYPE 77  3
  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE 
                             53                              80 
  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE 
                              1                               3 
$`AMP PEAK 15(22Q11.21) MUTATED`
TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       30.35        59.70       102.35       191.31        36.99        14.14 
TCGA-2G-AAG3 TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGO TCGA-2G-AAH2 TCGA-2G-AAH8 
       52.37        92.09       108.16       115.00        59.84        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHN TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2X-A9D6 
       98.53        59.74        91.43       122.50       161.72         0.13 
TCGA-4K-AA1G TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        3.52         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A9 
        1.38        16.31        10.26        17.23         3.52        36.79 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 
       23.90        41.52         0.16         0.82        18.38        40.01 
TCGA-XE-AANJ TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOD TCGA-XE-AAOL 
       65.98        53.03        93.93         7.89        67.66         0.43 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-AA4L 
       20.12         6.90        57.90        21.96         0.56        40.96 
TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0H TCGA-ZM-AA0N 
        8.15        39.35        27.55        46.88        10.85 

$`AMP PEAK 15(22Q11.21) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAFJ TCGA-2G-AAFL 
       20.32        38.30       122.40       154.59        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       40.01        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGJ 
       68.22        72.85        68.38        79.76        67.96        75.09 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
       59.64       106.39       120.62        59.28       124.57       128.94 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH3 
       61.45       170.33        80.94        60.16        60.26        59.90 
TCGA-2G-AAH4 TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKG 
      125.69        59.80        59.80       176.15         6.08       212.65 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
       95.67       229.22       184.41       131.21        70.59         2.73 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-SN-A84W TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB 
        7.00         0.10         9.63        37.18        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       35.61        33.07         4.90        24.26         3.65         5.06 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AAO4 TCGA-XE-AAOB 
       28.14         6.87        34.22         0.46        12.07        16.87 
TCGA-XE-AAOC TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S2 TCGA-YU-A90Q 
        8.88        41.69        50.96         8.32        12.92        54.35 
TCGA-YU-A90S TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-ZM-AA05 TCGA-ZM-AA0D 
       31.92         5.29        58.88         7.96        37.02        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F 
       16.41        11.34 

  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE 
                           0.13                            0.10 
  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE 
                         191.31                          229.22 
  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE 
                         30.350                          40.355 
[1] "0.1 - 191.3 (30.4)" "0.1 - 229.2 (40.4)"
[1] "hr=" "1.2"
D15V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(22Q11.21) MUTATED         7        8        7        1         0
  AMP PEAK 15(22Q11.21) WILD-TYPE      12       17        4        4         6
                                 vv
clus                              STAGE IIB STAGE IIC STAGE III STAGE IIIA
  AMP PEAK 15(22Q11.21) MUTATED           1         0         1          0
  AMP PEAK 15(22Q11.21) WILD-TYPE         0         1         1          1
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IS
  AMP PEAK 15(22Q11.21) MUTATED            0          3       22
  AMP PEAK 15(22Q11.21) WILD-TYPE          6          2       24
D15V3, multiclass
            clus
vv           AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE
  STAGE I                                7                              12
  STAGE IA                               8                              17
  STAGE IB                               7                               4
  STAGE II                               1                               4
  STAGE IIA                              0                               6
  STAGE IIB                              1                               0
  STAGE IIC                              0                               1
  STAGE III                              1                               1
  STAGE IIIA                             0                               1
  STAGE IIIB                             0                               6
  STAGE IIIC                             3                               2
  STAGE IS                              22                              24
[1] 12  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
  AMP PEAK 15(22Q11.21) MUTATED   29 20  3
  AMP PEAK 15(22Q11.21) WILD-TYPE 46 31  3
D15V4, multiclass
    clus
vv   AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE
  T1                            29                              46
  T2                            20                              31
  T3                             3                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1+N2
  AMP PEAK 15(22Q11.21) MUTATED   14     1
  AMP PEAK 15(22Q11.21) WILD-TYPE 32    12
D15V5, multiclass
       clus
vv      AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE
  N0                               14                              32
  N1+N2                             1                              12
[1] 2 2
[1] FALSE
D15V6, binary
                                 cls
clus                               0  1
  AMP PEAK 15(22Q11.21) MUTATED   46  0
  AMP PEAK 15(22Q11.21) WILD-TYPE 68  4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(22Q11.21) MUTATED     46    0
  AMP PEAK 15(22Q11.21) WILD-TYPE   68    4
   clus
vv  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE
  0                            46                              68
  1                             0                               4
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(22Q11.21) MUTATED       1                         3    47
  AMP PEAK 15(22Q11.21) WILD-TYPE     3                         3    71
D15V7, multiclass
                           clus
vv                          AMP PEAK 15(22Q11.21) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                47
                           clus
vv                          AMP PEAK 15(22Q11.21) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               3
  WHITE                                                  71
[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"
D15V8, binary
                                 cls
clus                               0  1
  AMP PEAK 15(22Q11.21) MUTATED    5 43
  AMP PEAK 15(22Q11.21) WILD-TYPE  6 68
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(22Q11.21) MUTATED      5   43
  AMP PEAK 15(22Q11.21) WILD-TYPE    6   68
                        clus
vv                       AMP PEAK 15(22Q11.21) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            43
                        clus
vv                       AMP PEAK 15(22Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                              68
[1] 2 2
[1] FALSE

Clustering(16) Variable = DEL PEAK  1(1P36.31) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.31) MUTATED    27   2
  DEL PEAK  1(1P36.31) WILD-TYPE 102   2
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            29                            104 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                             2                              2 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAG6 TCGA-2G-AAGP 
       20.32        59.70       102.35       154.59        72.20       120.62 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAHC TCGA-2G-AAHP 
      128.94        61.45        60.26        59.84        59.74       176.15 
TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-SB-A76C TCGA-SN-A84W TCGA-SN-A84Y TCGA-VF-A8AE 
        2.73         3.52         1.38         9.63        17.23        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAO3 
       41.52         4.90        34.22        65.98         0.46        93.93 
TCGA-XE-AAOJ TCGA-YU-A90Y TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       50.96         0.56         7.96        40.96         8.15 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       30.35        38.30       122.40       191.31        36.99        14.14 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       14.56        17.16         9.57        14.86        16.50        40.70 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG7 
       36.13        36.89        40.01        52.37        71.24        61.71 
TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       63.22        63.32        68.22        72.85        68.38        79.76 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN 
       67.96        92.09        75.09       108.16        59.64       106.39 
TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      115.00        59.28       124.57       170.33        80.94        60.16 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHL 
       59.90       125.69        61.84        98.53        59.80        59.80 
TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
       91.43         6.08       122.50       212.65       161.72        95.67 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D6 TCGA-4K-AA1H 
      229.22       184.41       131.21        70.59         0.13         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SN-A6IS TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA 
       16.31        10.26         3.52        37.18        36.79        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       24.99        35.61        33.07        24.26         3.65         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        0.16         0.82        28.14         6.87        18.38        40.01 
TCGA-XE-AANV TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       53.03        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       41.69         0.43         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-A94D 
       57.90        54.35        31.92        21.96         5.29        58.88 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        39.35        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          0.46                           0.10 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        176.15                         229.22 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         41.52                          37.10 
[1] "0.5 - 176.2 (41.5)" "0.1 - 229.2 (37.1)"
[1] "hr=" "7.2"
D16V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  1(1P36.31) MUTATED         4        2        0        1         2
  DEL PEAK  1(1P36.31) WILD-TYPE      15       23       11        4         4
                                vv
clus                             STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  1(1P36.31) MUTATED           0         0         0          0
  DEL PEAK  1(1P36.31) WILD-TYPE         1         1         2          1
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK  1(1P36.31) MUTATED            0          2       15
  DEL PEAK  1(1P36.31) WILD-TYPE          6          3       31
D16V3, multiclass
            clus
vv           DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  STAGE I                               4                             15
  STAGE IA                              2                             23
  STAGE IB                              0                             11
  STAGE II                              1                              4
  STAGE IIA                             2                              4
  STAGE IIB                             0                              1
  STAGE IIC                             0                              1
  STAGE III                             0                              2
  STAGE IIIA                            0                              1
  STAGE IIIB                            0                              6
  STAGE IIIC                            2                              3
  STAGE IS                             15                             31
[1] 12  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
  DEL PEAK  1(1P36.31) MUTATED   18 10  1
  DEL PEAK  1(1P36.31) WILD-TYPE 57 41  5
D16V4, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T1                           18                             57
  T2                           10                             41
  T3                            1                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1+N2
  DEL PEAK  1(1P36.31) MUTATED    8     2
  DEL PEAK  1(1P36.31) WILD-TYPE 38    11
D16V5, multiclass
       clus
vv      DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  N0                               8                             38
  N1+N2                            2                             11
[1] 2 2
[1] FALSE
D16V6, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED   23  0
  DEL PEAK  1(1P36.31) WILD-TYPE 91  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     23    0
  DEL PEAK  1(1P36.31) WILD-TYPE   91    4
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                           23                             91
  1                            0                              4
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.31) MUTATED       1                         2    25
  DEL PEAK  1(1P36.31) WILD-TYPE     3                         4    93
D16V7, multiclass
                           clus
vv                          DEL PEAK  1(1P36.31) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               25
                           clus
vv                          DEL PEAK  1(1P36.31) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 93
[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"
D16V8, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED    5 19
  DEL PEAK  1(1P36.31) WILD-TYPE  6 92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      5   19
  DEL PEAK  1(1P36.31) WILD-TYPE    6   92
                        clus
vv                       DEL PEAK  1(1P36.31) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           19
                        clus
vv                       DEL PEAK  1(1P36.31) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             92
[1] 2 2
[1] FALSE

Clustering(17) Variable = DEL PEAK  2(1P31.1) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P31.1) MUTATED    24   2
  DEL PEAK  2(1P31.1) WILD-TYPE 105   2
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                           26                           107 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                            2                             2 
$`DEL PEAK  2(1P31.1) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAG6 TCGA-2G-AAGG 
       20.32        59.70       102.35       154.59        72.20        67.96 
TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGO TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAHC 
       75.09        59.64       115.00        60.26        59.84        59.74 
TCGA-2G-AAHP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-SB-A76C TCGA-SN-A84W TCGA-SO-A8JP 
      176.15         2.73         3.52         1.38         9.63         3.52 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A7V5 TCGA-XE-AANR TCGA-YU-A90Q TCGA-YU-A90Y 
       23.90        41.52         0.16         0.46        54.35         0.56 
TCGA-YU-A94I TCGA-YU-AA61 
        7.96         8.15 

$`DEL PEAK  2(1P31.1) WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       30.35        38.30       122.40       191.31        36.99        14.14 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       14.56        17.16         9.57        14.86        16.50        40.70 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG7 
       36.13        36.89        40.01        52.37        71.24        61.71 
TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       63.22        63.32        68.22        72.85        68.38        79.76 
TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       92.09       108.16       106.39       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH3 
      128.94        61.45       170.33        80.94        60.16        59.90 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
      125.69        61.84        98.53        59.80        59.80        91.43 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
        6.08       122.50       212.65       161.72        95.67       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I 
      184.41       131.21        70.59         0.13         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A6IS 
        4.83        20.68        18.15         9.14        13.58        16.31 
TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB 
       10.26        17.23        37.18        36.79        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       35.61        33.07         4.90        24.26         3.65         5.06 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
       65.98        53.03        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43         8.32 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90S TCGA-YU-A90W 
       12.92        20.12         6.90        57.90        31.92        21.96 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        5.29        58.88        40.96        37.02        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                         0.16                          0.10 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                       176.15                        229.22 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                       47.935                        37.180 
[1] "0.2 - 176.2 (47.9)" "0.1 - 229.2 (37.2)"
[1] "hr=" "9"  
D17V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  2(1P31.1) MUTATED         5        3        1        0         1
  DEL PEAK  2(1P31.1) WILD-TYPE      14       22       10        5         5
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  2(1P31.1) MUTATED           0         0         0          0
  DEL PEAK  2(1P31.1) WILD-TYPE         1         1         2          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK  2(1P31.1) MUTATED            0          2       12
  DEL PEAK  2(1P31.1) WILD-TYPE          6          3       34
D17V3, multiclass
            clus
vv           DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  STAGE I                              5                            14
  STAGE IA                             3                            22
  STAGE IB                             1                            10
  STAGE II                             0                             5
  STAGE IIA                            1                             5
  STAGE IIB                            0                             1
  STAGE IIC                            0                             1
  STAGE III                            0                             2
  STAGE IIIA                           0                             1
  STAGE IIIB                           0                             6
  STAGE IIIC                           2                             3
  STAGE IS                            12                            34
[1] 12  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
  DEL PEAK  2(1P31.1) MUTATED   14 10  2
  DEL PEAK  2(1P31.1) WILD-TYPE 61 41  4
D17V4, multiclass
    clus
vv   DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  T1                          14                            61
  T2                          10                            41
  T3                           2                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  DEL PEAK  2(1P31.1) MUTATED   11     2
  DEL PEAK  2(1P31.1) WILD-TYPE 35    11
D17V5, multiclass
       clus
vv      DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  N0                             11                            35
  N1+N2                           2                            11
[1] 2 2
[1] FALSE
D17V6, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P31.1) MUTATED   19  1
  DEL PEAK  2(1P31.1) WILD-TYPE 95  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED     19    1
  DEL PEAK  2(1P31.1) WILD-TYPE   95    3
   clus
vv  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  0                          19                            95
  1                           1                             3
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P31.1) MUTATED       0                         2    22
  DEL PEAK  2(1P31.1) WILD-TYPE     4                         4    96
D17V7, multiclass
                           clus
vv                          DEL PEAK  2(1P31.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              22
                           clus
vv                          DEL PEAK  2(1P31.1) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                96
[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"
D17V8, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P31.1) MUTATED    2 20
  DEL PEAK  2(1P31.1) WILD-TYPE  9 91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED      2   20
  DEL PEAK  2(1P31.1) WILD-TYPE    9   91
                        clus
vv                       DEL PEAK  2(1P31.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          20
                        clus
vv                       DEL PEAK  2(1P31.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                            91
[1] 2 2
[1] FALSE

Clustering(18) Variable = DEL PEAK  3(1Q42.12) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  3(1Q42.12) MUTATED     8   1
  DEL PEAK  3(1Q42.12) WILD-TYPE 121   3
  DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE 
                             9                            124 
  DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE 
                             1                              3 
$`DEL PEAK  3(1Q42.12) MUTATED`
TCGA-2G-AAG7 TCGA-2G-AAHP TCGA-S6-A8JX TCGA-SB-A76C TCGA-X3-A8G4 TCGA-XE-AANJ 
       61.71       176.15        18.15         1.38        28.14        65.98 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-ZM-AA0B 
        0.56         5.29        27.55 

$`DEL PEAK  3(1Q42.12) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAG9 
       40.01        52.37        71.24        72.20        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT 
       98.53        59.74        59.80        59.80        91.43         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A6IS 
        0.10         4.83        20.68         9.14        13.58        16.31 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 
        9.63        10.26        17.23         3.52        37.18        36.79 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
        4.90        24.26         3.65         5.06         0.16         0.82 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AANV 
        6.87        18.38        40.01        34.22         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       41.69        50.96         0.43         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A94D 
        6.90        57.90        54.35        31.92        21.96        58.88 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0D 
        7.96        40.96         8.15        37.02        39.35        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE 
                          0.56                           0.10 
  DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE 
                        176.15                         229.22 
  DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE 
                        27.550                         38.825 
[1] "0.6 - 176.2 (27.6)" "0.1 - 229.2 (38.8)"
[1] "hr=" "7.3"
D18V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  3(1Q42.12) MUTATED         0        1        1        0         0
  DEL PEAK  3(1Q42.12) WILD-TYPE      19       24       10        5         6
                                vv
clus                             STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  3(1Q42.12) MUTATED           0         0         0          0
  DEL PEAK  3(1Q42.12) WILD-TYPE         1         1         2          1
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK  3(1Q42.12) MUTATED            0          2        4
  DEL PEAK  3(1Q42.12) WILD-TYPE          6          3       42
D18V3, multiclass
            clus
vv           DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE
  STAGE I                               0                             19
  STAGE IA                              1                             24
  STAGE IB                              1                             10
  STAGE II                              0                              5
  STAGE IIA                             0                              6
  STAGE IIB                             0                              1
  STAGE IIC                             0                              1
  STAGE III                             0                              2
  STAGE IIIA                            0                              1
  STAGE IIIB                            0                              6
  STAGE IIIC                            2                              3
  STAGE IS                              4                             42
[1] 12  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
  DEL PEAK  3(1Q42.12) MUTATED    5  3  1
  DEL PEAK  3(1Q42.12) WILD-TYPE 70 48  5
D18V4, multiclass
    clus
vv   DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE
  T1                            5                             70
  T2                            3                             48
  T3                            1                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1+N2
  DEL PEAK  3(1Q42.12) MUTATED    3     0
  DEL PEAK  3(1Q42.12) WILD-TYPE 43    13
D18V5, multiclass
       clus
vv      DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE
  N0                               3                             43
  N1+N2                            0                             13
[1] 2 2
[1] FALSE
D18V6, binary
                                cls
clus                               0   1
  DEL PEAK  3(1Q42.12) MUTATED     7   0
  DEL PEAK  3(1Q42.12) WILD-TYPE 107   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  3(1Q42.12) MUTATED      7    0
  DEL PEAK  3(1Q42.12) WILD-TYPE  107    4
   clus
vv  DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE
  0                            7                            107
  1                            0                              4
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q42.12) MUTATED       0                         2     7
  DEL PEAK  3(1Q42.12) WILD-TYPE     4                         4   111
D18V7, multiclass
                           clus
vv                          DEL PEAK  3(1Q42.12) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                                7
                           clus
vv                          DEL PEAK  3(1Q42.12) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                                cls
clus                               0   1
  DEL PEAK  3(1Q42.12) MUTATED     1   6
  DEL PEAK  3(1Q42.12) WILD-TYPE  10 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  3(1Q42.12) MUTATED      1    6
  DEL PEAK  3(1Q42.12) WILD-TYPE   10  105
                        clus
vv                       DEL PEAK  3(1Q42.12) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       DEL PEAK  3(1Q42.12) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            105
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D19V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.3) MUTATED    12   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 117   3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           13                           120 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            1                             3 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-2G-AAFE TCGA-2G-AAG0 TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO 
      154.59        40.01        75.09       108.16       106.39       115.00 
TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-SN-A84Y TCGA-XE-A8H5 TCGA-XE-AAO4 TCGA-XE-AAOL 
       59.84       125.69        17.23        40.01        12.07         0.43 
TCGA-YU-A90Y 
        0.56 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 
       14.86        16.50        40.70        36.13        36.89        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM 
       72.85        68.38        79.76        67.96        92.09        59.64 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      120.62        59.28       124.57       128.94        61.45       170.33 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA 
       80.94        60.16        60.26        59.90        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 
        1.38        16.31         9.63        10.26         3.52        37.18 
TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       36.79        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       41.52         4.90        24.26         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-AANI TCGA-XE-AANJ 
        0.82        28.14         6.87        18.38        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
        0.46        53.03        93.93         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       67.66        41.69        50.96         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 
        6.90        57.90        54.35        31.92        21.96         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         0.43                          0.10 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       154.59                        229.22 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       59.840                        37.005 
[1] "0.4 - 154.6 (59.8)" "0.1 - 229.2 (37.0)"
[1] "hr=" "4.4"
D19V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  4(2Q37.3) MUTATED         1        2        0        1         1
  DEL PEAK  4(2Q37.3) WILD-TYPE      18       23       11        4         5
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  4(2Q37.3) MUTATED           0         0         0          0
  DEL PEAK  4(2Q37.3) WILD-TYPE         1         1         2          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK  4(2Q37.3) MUTATED            1          1        6
  DEL PEAK  4(2Q37.3) WILD-TYPE          5          4       40
D19V3, multiclass
            clus
vv           DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  STAGE I                              1                            18
  STAGE IA                             2                            23
  STAGE IB                             0                            11
  STAGE II                             1                             4
  STAGE IIA                            1                             5
  STAGE IIB                            0                             1
  STAGE IIC                            0                             1
  STAGE III                            0                             2
  STAGE IIIA                           0                             1
  STAGE IIIB                           1                             5
  STAGE IIIC                           1                             4
  STAGE IS                             6                            40
[1] 12  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
  DEL PEAK  4(2Q37.3) MUTATED    6  6  1
  DEL PEAK  4(2Q37.3) WILD-TYPE 69 45  5
D19V4, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  T1                           6                            69
  T2                           6                            45
  T3                           1                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  DEL PEAK  4(2Q37.3) MUTATED    5     2
  DEL PEAK  4(2Q37.3) WILD-TYPE 41    11
D19V5, multiclass
       clus
vv      DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  N0                              5                            41
  N1+N2                           2                            11
[1] 2 2
[1] FALSE
D19V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    12   0
  DEL PEAK  4(2Q37.3) WILD-TYPE 102   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     12    0
  DEL PEAK  4(2Q37.3) WILD-TYPE  102    4
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                          12                           102
  1                           0                             4
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED       0                         3     9
  DEL PEAK  4(2Q37.3) WILD-TYPE     4                         3   109
D19V7, multiclass
                           clus
vv                          DEL PEAK  4(2Q37.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                               9
                           clus
vv                          DEL PEAK  4(2Q37.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     3   9
  DEL PEAK  4(2Q37.3) WILD-TYPE   8 102
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      3    9
  DEL PEAK  4(2Q37.3) WILD-TYPE    8  102
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           102
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK  5(3P26.2) MUTATION ANALYSIS
D20V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(3P26.2) MUTATED   39  1
  DEL PEAK  5(3P26.2) WILD-TYPE 90  3
  DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE 
                           40                            93 
  DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE 
                            1                             3 
$`DEL PEAK  5(3P26.2) MUTATED`
TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAG0 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
      102.35       154.59        40.01        63.22        63.32        68.22 
TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAH2 
       68.38        67.96        75.09       106.39       115.00        59.84 
TCGA-2G-AAH3 TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAKD TCGA-2G-AAKL 
       59.90        59.74        59.80        91.43       122.50        95.67 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-4K-AA1G TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A9 
      131.21        70.59         3.52        17.23         3.52        36.79 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-XE-AANJ 
       35.61        33.07         3.65         5.06         0.16        65.98 
TCGA-XE-AANR TCGA-XE-AAO4 TCGA-XY-A89B TCGA-XY-A8S2 TCGA-YU-A90P TCGA-YU-A90Y 
        0.46        12.07         8.32        12.92        57.90         0.56 
TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0H 
        5.29        37.02        39.35        46.88 

$`DEL PEAK  5(3P26.2) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF8 TCGA-2G-AAFG 
       20.32        30.35        38.30        59.70       122.40       191.31 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
       36.99        14.14        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 
       16.50        40.70        36.13        36.89        52.37        71.24 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGI TCGA-2G-AAGK 
       72.20        61.71        72.85        79.76        92.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW 
       59.64       120.62        59.28       124.57       128.94        61.45 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH4 TCGA-2G-AAH8 
      170.33        80.94        60.16        60.26       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKG TCGA-2G-AAKH 
       98.53        59.80       176.15         6.08       212.65       161.72 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I 
      229.22       184.41         2.73         0.13         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB 
       16.31         9.63        10.26        37.18        37.68        24.99 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       23.90        41.52         4.90        24.26         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANV TCGA-XE-AAO3 
        6.87        18.38        40.01        34.22        53.03        93.93 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ 
        7.89        16.87         8.88        67.66        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
        0.43        20.12         6.90        54.35        31.92        21.96 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       58.88         7.96        40.96         8.15        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0N 
       16.41        11.34        10.85 

  DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE 
                         0.16                          0.10 
  DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE 
                       154.59                        229.22 
  DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE 
                        58.82                         36.13 
[1] "0.2 - 154.6 (58.8)" "0.1 - 229.2 (36.1)"
[1] "hr=" "1.1"
D20V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  5(3P26.2) MUTATED         9        6        3        1         2
  DEL PEAK  5(3P26.2) WILD-TYPE      10       19        8        4         4
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  5(3P26.2) MUTATED           0         1         1          0
  DEL PEAK  5(3P26.2) WILD-TYPE         1         0         1          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK  5(3P26.2) MUTATED            3          3       11
  DEL PEAK  5(3P26.2) WILD-TYPE          3          2       35
D20V3, multiclass
            clus
vv           DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE
  STAGE I                              9                            10
  STAGE IA                             6                            19
  STAGE IB                             3                             8
  STAGE II                             1                             4
  STAGE IIA                            2                             4
  STAGE IIB                            0                             1
  STAGE IIC                            1                             0
  STAGE III                            1                             1
  STAGE IIIA                           0                             1
  STAGE IIIB                           3                             3
  STAGE IIIC                           3                             2
  STAGE IS                            11                            35
[1] 12  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
  DEL PEAK  5(3P26.2) MUTATED   17 20  3
  DEL PEAK  5(3P26.2) WILD-TYPE 58 31  3
D20V4, multiclass
    clus
vv   DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE
  T1                          17                            58
  T2                          20                            31
  T3                           3                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  DEL PEAK  5(3P26.2) MUTATED   13     5
  DEL PEAK  5(3P26.2) WILD-TYPE 33     8
D20V5, multiclass
       clus
vv      DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE
  N0                             13                            33
  N1+N2                           5                             8
[1] 2 2
[1] FALSE
D20V6, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P26.2) MUTATED   32  2
  DEL PEAK  5(3P26.2) WILD-TYPE 82  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.2) MUTATED     32    2
  DEL PEAK  5(3P26.2) WILD-TYPE   82    2
   clus
vv  DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE
  0                          32                            82
  1                           2                             2
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P26.2) MUTATED       0                         3    37
  DEL PEAK  5(3P26.2) WILD-TYPE     4                         3    81
D20V7, multiclass
                           clus
vv                          DEL PEAK  5(3P26.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              37
                           clus
vv                          DEL PEAK  5(3P26.2) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                81
[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"
D20V8, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P26.2) MUTATED    4 33
  DEL PEAK  5(3P26.2) WILD-TYPE  7 78
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.2) MUTATED      4   33
  DEL PEAK  5(3P26.2) WILD-TYPE    7   78
                        clus
vv                       DEL PEAK  5(3P26.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          33
                        clus
vv                       DEL PEAK  5(3P26.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            78
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK  6(4Q22.2) MUTATION ANALYSIS
D21V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(4Q22.2) MUTATED   95  4
  DEL PEAK  6(4Q22.2) WILD-TYPE 34  0
  DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE 
                           99                            34 
  DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE 
                            4                             0 
$`DEL PEAK  6(4Q22.2) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        59.70       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
      191.31        36.99        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 
       16.50        36.13        40.01        72.20        61.71        63.32 
TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.22        68.38        79.76        67.96        75.09       108.16 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW 
      106.39       115.00       120.62        59.28       128.94        61.45 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.74        59.80        59.80       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      212.65       161.72        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
       70.59         2.73         3.52         4.83        20.68        18.15 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y 
        9.14        13.58         1.38        16.31         9.63        17.23 
TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
        3.52        36.79        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       41.52         4.90        24.26         3.65         5.06         0.16 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ 
       28.14         6.87        18.38        40.01        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB TCGA-XE-AAOJ 
        0.46        53.03        93.93        12.07        16.87        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P 
        0.43         8.32        12.92        20.12         6.90        57.90 
TCGA-YU-A90Y TCGA-YU-A94I TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
        0.56         7.96         8.15        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0N 
       16.41        11.34        10.85 

$`DEL PEAK  6(4Q22.2) WILD-TYPE`
TCGA-2G-AAF1 TCGA-2G-AAFI TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 
       38.30        14.14        40.70        36.89        52.37        71.24 
TCGA-2G-AAG8 TCGA-2G-AAGC TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAGX 
       63.22        72.85        92.09        59.64       124.57       170.33 
TCGA-2G-AAGY TCGA-2G-AAHA TCGA-2G-AAHN TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I 
       80.94        98.53        91.43         0.13         7.00         0.10 
TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-WZ-A8D5 TCGA-XE-AAO6 TCGA-XE-AAOC 
       10.26        37.18        37.68         0.82         7.89         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 
       67.66        41.69        54.35        31.92        21.96         5.29 
TCGA-YU-A94D TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA0H 
       58.88        40.96        37.02        46.88 

  DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE 
                         0.16                          0.10 
  DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE 
                       229.22                        170.33 
  DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE 
                        36.13                         40.83 
[1] "0.2 - 229.2 (36.1)" "0.1 - 170.3 (40.8)"
[1] "hr="   "3e+08"
D21V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(4Q22.2) MUTATED        16       16        6        5         6
  DEL PEAK  6(4Q22.2) WILD-TYPE       3        9        5        0         0
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  6(4Q22.2) MUTATED           1         0         1          1
  DEL PEAK  6(4Q22.2) WILD-TYPE         0         1         1          0
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK  6(4Q22.2) MUTATED            5          3       35
  DEL PEAK  6(4Q22.2) WILD-TYPE          1          2       11
D21V3, multiclass
            clus
vv           DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE
  STAGE I                             16                             3
  STAGE IA                            16                             9
  STAGE IB                             6                             5
  STAGE II                             5                             0
  STAGE IIA                            6                             0
  STAGE IIB                            1                             0
  STAGE IIC                            0                             1
  STAGE III                            1                             1
  STAGE IIIA                           1                             0
  STAGE IIIB                           5                             1
  STAGE IIIC                           3                             2
  STAGE IS                            35                            11
[1] 12  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
  DEL PEAK  6(4Q22.2) MUTATED   56 40  2
  DEL PEAK  6(4Q22.2) WILD-TYPE 19 11  4
D21V4, multiclass
    clus
vv   DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE
  T1                          56                            19
  T2                          40                            11
  T3                           2                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  DEL PEAK  6(4Q22.2) MUTATED   31    13
  DEL PEAK  6(4Q22.2) WILD-TYPE 15     0
D21V5, multiclass
       clus
vv      DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE
  N0                             31                            15
  N1+N2                          13                             0
[1] 2 2
[1] FALSE
D21V6, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q22.2) MUTATED   87  3
  DEL PEAK  6(4Q22.2) WILD-TYPE 27  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q22.2) MUTATED     87    3
  DEL PEAK  6(4Q22.2) WILD-TYPE   27    1
   clus
vv  DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE
  0                          87                            27
  1                           3                             1
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4Q22.2) MUTATED       2                         4    90
  DEL PEAK  6(4Q22.2) WILD-TYPE     2                         2    28
D21V7, multiclass
                           clus
vv                          DEL PEAK  6(4Q22.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              90
                           clus
vv                          DEL PEAK  6(4Q22.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                28
[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"
D21V8, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q22.2) MUTATED    9 85
  DEL PEAK  6(4Q22.2) WILD-TYPE  2 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q22.2) MUTATED      9   85
  DEL PEAK  6(4Q22.2) WILD-TYPE    2   26
                        clus
vv                       DEL PEAK  6(4Q22.2) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                          85
                        clus
vv                       DEL PEAK  6(4Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            26
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK  7(5P15.2) MUTATION ANALYSIS
D22V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(5P15.2) MUTATED   88  3
  DEL PEAK  7(5P15.2) WILD-TYPE 41  1
  DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE 
                           91                            42 
  DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE 
                            3                             1 
$`DEL PEAK  7(5P15.2) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAFG 
       20.32        59.70       102.35       122.40       154.59       191.31 
TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG3 
       36.99        14.56        16.50        36.13        40.01        52.37 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       72.20        61.71        63.32        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGV 
       79.76        75.09       108.16        59.64       120.62       128.94 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAHC TCGA-2G-AAHG 
       80.94        60.16        59.84        59.90        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        91.43       176.15         6.08       122.50       212.65 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
       95.67       229.22       184.41        70.59         2.73         0.13 
TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        3.52         0.10         4.83        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SO-A8JP TCGA-VF-A8AB TCGA-VF-A8AC 
        1.38        16.31         9.63         3.52        24.99        35.61 
TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       33.07        23.90        41.52         4.90         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD 
       65.98        93.93        12.07         7.89        16.87        67.66 
TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       50.96         0.43         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       57.90        54.35         5.29         7.96        40.96         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        39.35        27.55        17.39        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

$`DEL PEAK  7(5P15.2) WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
       30.35        38.30        14.14        17.16         9.57        14.86 
TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGG TCGA-2G-AAGI 
       40.70        36.89        71.24        63.22        67.96        92.09 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGX 
      106.39       115.00        59.28       124.57        61.45       170.33 
TCGA-2G-AAH0 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAKH TCGA-2G-AAL7 
       60.26       125.69        61.84        98.53       161.72       131.21 
TCGA-4K-AA1H TCGA-S6-A8JW TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 
        7.00        20.68        10.26        17.23        37.18        36.79 
TCGA-VF-A8AA TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAOC 
       37.68        24.26         3.65         0.46        53.03         8.88 
TCGA-XE-AAOF TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D TCGA-ZM-AA0E 
       41.69        31.92        21.96         0.56        58.88        16.41 

  DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE 
                         0.10                          0.46 
  DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE 
                       229.22                        170.33 
  DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE 
                        37.02                         37.99 
[1] "0.1 - 229.2 (37.0)" "0.5 - 170.3 (38.0)"
[1] "hr=" "1"  
D22V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  7(5P15.2) MUTATED        16       16        6        3         5
  DEL PEAK  7(5P15.2) WILD-TYPE       3        9        5        2         1
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  7(5P15.2) MUTATED           1         1         1          1
  DEL PEAK  7(5P15.2) WILD-TYPE         0         0         1          0
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK  7(5P15.2) MUTATED            2          2       33
  DEL PEAK  7(5P15.2) WILD-TYPE          4          3       13
D22V3, multiclass
            clus
vv           DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE
  STAGE I                             16                             3
  STAGE IA                            16                             9
  STAGE IB                             6                             5
  STAGE II                             3                             2
  STAGE IIA                            5                             1
  STAGE IIB                            1                             0
  STAGE IIC                            1                             0
  STAGE III                            1                             1
  STAGE IIIA                           1                             0
  STAGE IIIB                           2                             4
  STAGE IIIC                           2                             3
  STAGE IS                            33                            13
[1] 12  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
  DEL PEAK  7(5P15.2) MUTATED   55 33  2
  DEL PEAK  7(5P15.2) WILD-TYPE 20 18  4
D22V4, multiclass
    clus
vv   DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE
  T1                          55                            20
  T2                          33                            18
  T3                           2                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  DEL PEAK  7(5P15.2) MUTATED   30     8
  DEL PEAK  7(5P15.2) WILD-TYPE 16     5
D22V5, multiclass
       clus
vv      DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE
  N0                             30                            16
  N1+N2                           8                             5
[1] 2 2
[1] FALSE
D22V6, binary
                               cls
clus                             0  1
  DEL PEAK  7(5P15.2) MUTATED   79  2
  DEL PEAK  7(5P15.2) WILD-TYPE 35  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5P15.2) MUTATED     79    2
  DEL PEAK  7(5P15.2) WILD-TYPE   35    2
   clus
vv  DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE
  0                          79                            35
  1                           2                             2
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(5P15.2) MUTATED       2                         5    81
  DEL PEAK  7(5P15.2) WILD-TYPE     2                         1    37
D22V7, multiclass
                           clus
vv                          DEL PEAK  7(5P15.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              81
                           clus
vv                          DEL PEAK  7(5P15.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                37
[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"
D22V8, binary
                               cls
clus                             0  1
  DEL PEAK  7(5P15.2) MUTATED    7 77
  DEL PEAK  7(5P15.2) WILD-TYPE  4 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5P15.2) MUTATED      7   77
  DEL PEAK  7(5P15.2) WILD-TYPE    4   34
                        clus
vv                       DEL PEAK  7(5P15.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                          77
                        clus
vv                       DEL PEAK  7(5P15.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            34
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK  8(5P14.3) MUTATION ANALYSIS
D23V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(5P14.3) MUTATED   89  3
  DEL PEAK  8(5P14.3) WILD-TYPE 40  1
  DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE 
                           92                            41 
  DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE 
                            3                             1 
$`DEL PEAK  8(5P14.3) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAFG 
       20.32        59.70       102.35       122.40       154.59       191.31 
TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG3 TCGA-2G-AAG6 
       36.99        14.56        16.50        36.13        52.37        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       61.71        63.32        68.22        72.85        68.38        79.76 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGV TCGA-2G-AAGX 
       75.09       108.16        59.64       120.62       128.94       170.33 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC 
       80.94        60.16        59.84        59.90       125.69        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 
      212.65        95.67       229.22       184.41        70.59         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JX TCGA-S6-A8JY 
        0.13         3.52         0.10         4.83        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SO-A8JP TCGA-VF-A8AB 
       13.58         1.38        16.31         9.63         3.52        24.99 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-WZ-A7V4 
       35.61        33.07        23.90        41.52         4.90         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        0.16         0.82        28.14         6.87        18.38        40.01 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
       34.22        65.98        93.93        12.07         7.89        16.87 
TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       67.66        50.96         0.43         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L 
        6.90        57.90        54.35         5.29         7.96        40.96 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
        8.15        37.02        39.35        27.55        17.39        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

$`DEL PEAK  8(5P14.3) WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
       30.35        38.30        14.14        17.16         9.57        14.86 
TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGG 
       40.70        36.89        40.01        71.24        63.22        67.96 
TCGA-2G-AAGI TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW 
       92.09       106.39       115.00        59.28       124.57        61.45 
TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAKH TCGA-2G-AAL7 TCGA-4K-AA1H 
       60.26        61.84        98.53       161.72       131.21         7.00 
TCGA-S6-A8JW TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA 
       20.68        10.26        17.23        37.18        36.79        37.68 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAOC TCGA-XE-AAOF 
       24.26         3.65         0.46        53.03         8.88        41.69 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D TCGA-ZM-AA0E 
       31.92        21.96         0.56        58.88        16.41 

  DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE 
                         0.10                          0.46 
  DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE 
                       229.22                        161.72 
  DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE 
                       38.185                        37.680 
[1] "0.1 - 229.2 (38.2)" "0.5 - 161.7 (37.7)"
[1] "hr=" "1"  
D23V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(5P14.3) MUTATED        16       17        6        4         5
  DEL PEAK  8(5P14.3) WILD-TYPE       3        8        5        1         1
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  8(5P14.3) MUTATED           1         1         1          1
  DEL PEAK  8(5P14.3) WILD-TYPE         0         0         1          0
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK  8(5P14.3) MUTATED            2          2       32
  DEL PEAK  8(5P14.3) WILD-TYPE          4          3       14
D23V3, multiclass
            clus
vv           DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE
  STAGE I                             16                             3
  STAGE IA                            17                             8
  STAGE IB                             6                             5
  STAGE II                             4                             1
  STAGE IIA                            5                             1
  STAGE IIB                            1                             0
  STAGE IIC                            1                             0
  STAGE III                            1                             1
  STAGE IIIA                           1                             0
  STAGE IIIB                           2                             4
  STAGE IIIC                           2                             3
  STAGE IS                            32                            14
[1] 12  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
  DEL PEAK  8(5P14.3) MUTATED   57 32  2
  DEL PEAK  8(5P14.3) WILD-TYPE 18 19  4
D23V4, multiclass
    clus
vv   DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE
  T1                          57                            18
  T2                          32                            19
  T3                           2                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  DEL PEAK  8(5P14.3) MUTATED   30     8
  DEL PEAK  8(5P14.3) WILD-TYPE 16     5
D23V5, multiclass
       clus
vv      DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE
  N0                             30                            16
  N1+N2                           8                             5
[1] 2 2
[1] FALSE
D23V6, binary
                               cls
clus                             0  1
  DEL PEAK  8(5P14.3) MUTATED   80  2
  DEL PEAK  8(5P14.3) WILD-TYPE 34  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P14.3) MUTATED     80    2
  DEL PEAK  8(5P14.3) WILD-TYPE   34    2
   clus
vv  DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE
  0                          80                            34
  1                           2                             2
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(5P14.3) MUTATED       2                         5    82
  DEL PEAK  8(5P14.3) WILD-TYPE     2                         1    36
D23V7, multiclass
                           clus
vv                          DEL PEAK  8(5P14.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              82
                           clus
vv                          DEL PEAK  8(5P14.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                36
[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"
D23V8, binary
                               cls
clus                             0  1
  DEL PEAK  8(5P14.3) MUTATED    7 78
  DEL PEAK  8(5P14.3) WILD-TYPE  4 33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P14.3) MUTATED      7   78
  DEL PEAK  8(5P14.3) WILD-TYPE    4   33
                        clus
vv                       DEL PEAK  8(5P14.3) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                          78
                        clus
vv                       DEL PEAK  8(5P14.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            33
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK  9(5Q12.1) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(5Q12.1) MUTATED   91  3
  DEL PEAK  9(5Q12.1) WILD-TYPE 38  1
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           94                            39 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                            3                             1 
$`DEL PEAK  9(5Q12.1) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        59.70       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG3 
      191.31        36.99        14.56        16.50        36.13        52.37 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       72.20        61.71        63.32        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGV 
       79.76        75.09       108.16        59.64       120.62       128.94 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      170.33        80.94        60.16        59.84        59.90       125.69 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 
      212.65        95.67       229.22       184.41        70.59         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JX TCGA-S6-A8JY 
        0.13         3.52         0.10         4.83        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SO-A8JP TCGA-VF-A8A9 
       13.58         1.38        16.31         9.63         3.52        36.79 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 
       24.99        35.61        33.07        23.90        41.52         4.90 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
        5.06         0.16         0.82        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       40.01        34.22        65.98        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       16.87        67.66        50.96         0.43         8.32        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A912 
       20.12         6.90        57.90        54.35        21.96         5.29 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        7.96        40.96         8.15        37.02        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        11.34        46.88        10.85 

$`DEL PEAK  9(5Q12.1) WILD-TYPE`
TCGA-2G-AAF1 TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFV 
       38.30        14.14        17.16         9.57        14.86        40.70 
TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGG TCGA-2G-AAGI 
       36.89        40.01        71.24        63.22        67.96        92.09 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAH0 
      106.39       115.00        59.28       124.57        61.45        60.26 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2G-AAL7 TCGA-4K-AA1H 
       61.84        98.53       122.50       161.72       131.21         7.00 
TCGA-S6-A8JW TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-W4-A7U4 
       20.68        10.26        17.23        37.18        37.68        24.26 
TCGA-WZ-A7V3 TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAOC TCGA-XE-AAOF TCGA-YU-A90S 
        3.65         0.46        53.03         8.88        41.69        31.92 
TCGA-YU-A90Y TCGA-YU-A94D TCGA-ZM-AA0E 
        0.56        58.88        16.41 

  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                         0.10                          0.46 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                       229.22                        161.72 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                        36.89                         40.01 
[1] "0.1 - 229.2 (36.9)" "0.5 - 161.7 (40.0)"
[1] "hr=" "1.1"
D24V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  9(5Q12.1) MUTATED        16       19        6        4         5
  DEL PEAK  9(5Q12.1) WILD-TYPE       3        6        5        1         1
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  9(5Q12.1) MUTATED           1         1         0          1
  DEL PEAK  9(5Q12.1) WILD-TYPE         0         0         2          0
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK  9(5Q12.1) MUTATED            2          2       33
  DEL PEAK  9(5Q12.1) WILD-TYPE          4          3       13
D24V3, multiclass
            clus
vv           DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  STAGE I                             16                             3
  STAGE IA                            19                             6
  STAGE IB                             6                             5
  STAGE II                             4                             1
  STAGE IIA                            5                             1
  STAGE IIB                            1                             0
  STAGE IIC                            1                             0
  STAGE III                            0                             2
  STAGE IIIA                           1                             0
  STAGE IIIB                           2                             4
  STAGE IIIC                           2                             3
  STAGE IS                            33                            13
[1] 12  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
  DEL PEAK  9(5Q12.1) MUTATED   60 31  2
  DEL PEAK  9(5Q12.1) WILD-TYPE 15 20  4
D24V4, multiclass
    clus
vv   DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  T1                          60                            15
  T2                          31                            20
  T3                           2                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  DEL PEAK  9(5Q12.1) MUTATED   32     8
  DEL PEAK  9(5Q12.1) WILD-TYPE 14     5
D24V5, multiclass
       clus
vv      DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  N0                             32                            14
  N1+N2                           8                             5
[1] 2 2
[1] FALSE
D24V6, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED   81  2
  DEL PEAK  9(5Q12.1) WILD-TYPE 33  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     81    2
  DEL PEAK  9(5Q12.1) WILD-TYPE   33    2
   clus
vv  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  0                          81                            33
  1                           2                             2
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(5Q12.1) MUTATED       2                         5    84
  DEL PEAK  9(5Q12.1) WILD-TYPE     2                         1    34
D24V7, multiclass
                           clus
vv                          DEL PEAK  9(5Q12.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              84
                           clus
vv                          DEL PEAK  9(5Q12.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED    7 79
  DEL PEAK  9(5Q12.1) WILD-TYPE  4 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED      7   79
  DEL PEAK  9(5Q12.1) WILD-TYPE    4   32
                        clus
vv                       DEL PEAK  9(5Q12.1) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                          79
                        clus
vv                       DEL PEAK  9(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            32
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK 10(6P22.3) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(6P22.3) MUTATED    18   1
  DEL PEAK 10(6P22.3) WILD-TYPE 111   3
  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE 
                           19                           114 
  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE 
                            1                             3 
$`DEL PEAK 10(6P22.3) MUTATED`
TCGA-2G-AAFN TCGA-2G-AAG6 TCGA-2G-AAGE TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGT 
       14.86        72.20        68.38       108.16        59.64       124.57 
TCGA-2G-AAGW TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AALP TCGA-4K-AA1G TCGA-SB-A6J6 
       61.45       229.22       184.41        70.59         3.52        13.58 
TCGA-SN-A6IS TCGA-W4-A7U4 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-YU-A90P TCGA-YU-A94I 
       16.31        24.26        28.14         6.87        57.90         7.96 
TCGA-ZM-AA06 
       39.35 

$`DEL PEAK 10(6P22.3) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
        9.57        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       52.37        71.24        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGN 
       72.85        79.76        67.96        92.09        75.09       106.39 
TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY 
      115.00       120.62        59.28       128.94       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAL7 
        6.08       122.50       212.65       161.72        95.67       131.21 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
        2.73         0.13         7.00         0.10         4.83        20.68 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y 
       18.15         9.14         1.38         9.63        10.26        17.23 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC 
        3.52        37.18        36.79        37.68        24.99        35.61 
TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       33.07        23.90        41.52         4.90         3.65         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ 
        0.16         0.82        18.38        40.01        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        53.03        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43         8.32 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       12.92        20.12         6.90        54.35        31.92        21.96 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        0.56         5.29        58.88        40.96         8.15        37.02 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE 
                         3.52                          0.10 
  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE 
                       229.22                        212.65 
  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE 
                         57.9                          37.1 
[1] "3.5 - 229.2 (57.9)" "0.1 - 212.7 (37.1)"
[1] "hr="     "8.5e+07"
D25V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 10(6P22.3) MUTATED         1        3        1        1         0
  DEL PEAK 10(6P22.3) WILD-TYPE      18       22       10        4         6
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 10(6P22.3) MUTATED           0         0         0          0
  DEL PEAK 10(6P22.3) WILD-TYPE         1         1         2          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 10(6P22.3) MUTATED            2          0       10
  DEL PEAK 10(6P22.3) WILD-TYPE          4          5       36
D25V3, multiclass
            clus
vv           DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE
  STAGE I                              1                            18
  STAGE IA                             3                            22
  STAGE IB                             1                            10
  STAGE II                             1                             4
  STAGE IIA                            0                             6
  STAGE IIB                            0                             1
  STAGE IIC                            0                             1
  STAGE III                            0                             2
  STAGE IIIA                           0                             1
  STAGE IIIB                           2                             4
  STAGE IIIC                           0                             5
  STAGE IS                            10                            36
[1] 12  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
  DEL PEAK 10(6P22.3) MUTATED   10  9  0
  DEL PEAK 10(6P22.3) WILD-TYPE 65 42  6
D25V4, multiclass
    clus
vv   DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE
  T1                          10                            65
  T2                           9                            42
  T3                           0                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  DEL PEAK 10(6P22.3) MUTATED    8     1
  DEL PEAK 10(6P22.3) WILD-TYPE 38    12
D25V5, multiclass
       clus
vv      DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE
  N0                              8                            38
  N1+N2                           1                            12
[1] 2 2
[1] FALSE
D25V6, binary
                               cls
clus                             0  1
  DEL PEAK 10(6P22.3) MUTATED   16  1
  DEL PEAK 10(6P22.3) WILD-TYPE 98  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P22.3) MUTATED     16    1
  DEL PEAK 10(6P22.3) WILD-TYPE   98    3
   clus
vv  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE
  0                          16                            98
  1                           1                             3
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6P22.3) MUTATED       0                         0    18
  DEL PEAK 10(6P22.3) WILD-TYPE     4                         6   100
D25V7, multiclass
                           clus
vv                          DEL PEAK 10(6P22.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              18
                           clus
vv                          DEL PEAK 10(6P22.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               100
[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"
D25V8, binary
                               cls
clus                             0  1
  DEL PEAK 10(6P22.3) MUTATED    2 15
  DEL PEAK 10(6P22.3) WILD-TYPE  9 96
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P22.3) MUTATED      2   15
  DEL PEAK 10(6P22.3) WILD-TYPE    9   96
                        clus
vv                       DEL PEAK 10(6P22.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          15
                        clus
vv                       DEL PEAK 10(6P22.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                            96
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK 11(6Q26) MUTATION ANALYSIS
D26V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 11(6Q26) MUTATED    22   0
  DEL PEAK 11(6Q26) WILD-TYPE 107   4
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                         22                         111 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                          0                           4 
$`DEL PEAK 11(6Q26) MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAFV TCGA-2G-AAGE TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM 
       59.70        40.70        68.38        75.09       108.16        59.64 
TCGA-2G-AAGP TCGA-2G-AAGZ TCGA-2G-AAH4 TCGA-2G-AAHG TCGA-2G-AAKH TCGA-2G-AAKL 
      120.62        60.16       125.69        59.80       161.72        95.67 
TCGA-2G-AALP TCGA-4K-AA1G TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-VF-A8A8 TCGA-W4-A7U4 
       70.59         3.52         9.14        13.58        37.18        24.26 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-YU-A90P TCGA-YU-A94I 
       28.14         6.87        57.90         7.96 

$`DEL PEAK 11(6Q26) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        38.30       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       14.86        16.50        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGN TCGA-2G-AAGO 
       72.85        79.76        67.96        92.09       106.39       115.00 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       60.26        59.84        59.90        61.84        98.53        59.74 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        91.43       176.15         6.08       122.50       212.65 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H 
      229.22       184.41       131.21         2.73         0.13         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A76C TCGA-SN-A6IS 
        0.10         4.83        20.68        18.15         1.38        16.31 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AA 
        9.63        10.26        17.23         3.52        36.79        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 
       24.99        35.61        33.07        23.90        41.52         4.90 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 
        3.65         5.06         0.16         0.82        18.38        40.01 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ 
        7.89        16.87         8.88        67.66        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q 
        0.43         8.32        12.92        20.12         6.90        54.35 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L 
       31.92        21.96         0.56         5.29        58.88        40.96 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
        8.15        37.02        39.35        27.55        17.39        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       11.34        46.88        10.85 

  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                       3.52                        0.10 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                     161.72                      229.22 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                      59.67                       36.89 
[1] "3.5 - 161.7 (59.7)" "0.1 - 229.2 (36.9)"
[1] "hr="     "9.1e+07"
D26V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 11(6Q26) MUTATED         2        5        0        3         1
  DEL PEAK 11(6Q26) WILD-TYPE      17       20       11        2         5
                             vv
clus                          STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 11(6Q26) MUTATED           0         0         0          1
  DEL PEAK 11(6Q26) WILD-TYPE         1         1         2          0
                             vv
clus                          STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 11(6Q26) MUTATED            1          0        8
  DEL PEAK 11(6Q26) WILD-TYPE          5          5       38
D26V3, multiclass
            clus
vv           DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  STAGE I                            2                          17
  STAGE IA                           5                          20
  STAGE IB                           0                          11
  STAGE II                           3                           2
  STAGE IIA                          1                           5
  STAGE IIB                          0                           1
  STAGE IIC                          0                           1
  STAGE III                          0                           2
  STAGE IIIA                         1                           0
  STAGE IIIB                         1                           5
  STAGE IIIC                         0                           5
  STAGE IS                           8                          38
[1] 12  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
  DEL PEAK 11(6Q26) MUTATED   14  8  0
  DEL PEAK 11(6Q26) WILD-TYPE 61 43  6
D26V4, multiclass
    clus
vv   DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  T1                        14                          61
  T2                         8                          43
  T3                         0                           6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1+N2
  DEL PEAK 11(6Q26) MUTATED   10     2
  DEL PEAK 11(6Q26) WILD-TYPE 36    11
D26V5, multiclass
       clus
vv      DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  N0                           10                          36
  N1+N2                         2                          11
[1] 2 2
[1] FALSE
D26V6, binary
                             cls
clus                           0  1
  DEL PEAK 11(6Q26) MUTATED   18  2
  DEL PEAK 11(6Q26) WILD-TYPE 96  2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED     18    2
  DEL PEAK 11(6Q26) WILD-TYPE   96    2
   clus
vv  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  0                        18                          96
  1                         2                           2
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q26) MUTATED       0                         1    20
  DEL PEAK 11(6Q26) WILD-TYPE     4                         5    98
D26V7, multiclass
                           clus
vv                          DEL PEAK 11(6Q26) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            20
                           clus
vv                          DEL PEAK 11(6Q26) WILD-TYPE
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              98
[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"
D26V8, binary
                             cls
clus                           0  1
  DEL PEAK 11(6Q26) MUTATED    1 19
  DEL PEAK 11(6Q26) WILD-TYPE 10 92
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED      1   19
  DEL PEAK 11(6Q26) WILD-TYPE   10   92
                        clus
vv                       DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             1                          10
  NOT HISPANIC OR LATINO                        19                          92
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK 12(7Q11.22) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 12(7Q11.22) MUTATED     3   0
  DEL PEAK 12(7Q11.22) WILD-TYPE 126   4
  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE 
                             3                            130 
  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE 
                             0                              4 
$`DEL PEAK 12(7Q11.22) MUTATED`
TCGA-2G-AAGM TCGA-2G-AAGY TCGA-XE-AAOJ 
       59.64        80.94        50.96 

$`DEL PEAK 12(7Q11.22) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       40.01        52.37        71.24        72.20        61.71        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       63.32        68.22        72.85        68.38        79.76        67.96 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       92.09        75.09       108.16       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGZ 
       59.28       124.57       128.94        61.45       170.33        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23         3.52 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       37.18        36.79        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       23.90        41.52         4.90        24.26         3.65         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        0.16         0.82        28.14         6.87        18.38        40.01 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL 
        7.89        16.87         8.88        67.66        41.69         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
        8.32        12.92        20.12         6.90        57.90        54.35 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       31.92        21.96         0.56         5.29        58.88         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       40.96         8.15        37.02        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE 
                         50.96                           0.10 
  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE 
                         80.94                         229.22 
  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE 
                         59.64                          37.10 
[1] "51.0 - 80.9 (59.6)" "0.1 - 229.2 (37.1)"
[1] "hr="     "2.5e+07"
D27V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 12(7Q11.22) MUTATED         0        0        0        0         0
  DEL PEAK 12(7Q11.22) WILD-TYPE      19       25       11        5         6
                                vv
clus                             STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 12(7Q11.22) MUTATED           0         0         0          0
  DEL PEAK 12(7Q11.22) WILD-TYPE         1         1         2          1
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 12(7Q11.22) MUTATED            0          0        3
  DEL PEAK 12(7Q11.22) WILD-TYPE          6          5       43
D27V3, multiclass
            clus
vv           DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE
  STAGE I                               0                             19
  STAGE IA                              0                             25
  STAGE IB                              0                             11
  STAGE II                              0                              5
  STAGE IIA                             0                              6
  STAGE IIB                             0                              1
  STAGE IIC                             0                              1
  STAGE III                             0                              2
  STAGE IIIA                            0                              1
  STAGE IIIB                            0                              6
  STAGE IIIC                            0                              5
  STAGE IS                              3                             43
[1] 12  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
  DEL PEAK 12(7Q11.22) MUTATED    2  1  0
  DEL PEAK 12(7Q11.22) WILD-TYPE 73 50  6
D27V4, multiclass
    clus
vv   DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE
  T1                            2                             73
  T2                            1                             50
  T3                            0                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1+N2
  DEL PEAK 12(7Q11.22) MUTATED    2     0
  DEL PEAK 12(7Q11.22) WILD-TYPE 44    13
D27V5, multiclass
[1] "Remove cluster labels:"       "DEL PEAK 12(7Q11.22) MUTATED"
clus
  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE 
                             2                             57 
                    TCGA-2G-AAEW                     TCGA-2G-AAEX 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAF1                     TCGA-2G-AAF4 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAF6                     TCGA-2G-AAF8 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAFE                     TCGA-2G-AAFG 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAFH                     TCGA-2G-AAFI 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAFJ                     TCGA-2G-AAFL 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAFM                     TCGA-2G-AAFN 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAFO                     TCGA-2G-AAFV 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAFY                     TCGA-2G-AAG0 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAG5                     TCGA-2G-AAG6 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAG7                     TCGA-2G-AAG8 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAG9                     TCGA-2G-AAGA 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAGC                     TCGA-2G-AAGE 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAGF                     TCGA-2G-AAGG 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAGI                     TCGA-2G-AAGJ 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAGK                     TCGA-2G-AAGN 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAGO                     TCGA-2G-AAGP 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAGS                     TCGA-2G-AAGW 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAGX                     TCGA-2G-AAGZ 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAH2                     TCGA-2G-AAHG 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAHL                     TCGA-2G-AAHN 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAHP                     TCGA-2G-AAHT 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAKG                     TCGA-2G-AAL5 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-2G-AAL7                     TCGA-4K-AA1G 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-4K-AA1H                     TCGA-4K-AA1I 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-4K-AAAL                     TCGA-SO-A8JP 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-VF-A8A8                     TCGA-VF-A8A9 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-VF-A8AA                     TCGA-VF-A8AB 
"DEL PEAK 12(7Q11.22) WILD-TYPE" "DEL PEAK 12(7Q11.22) WILD-TYPE" 
                    TCGA-X3-A8G4 
"DEL PEAK 12(7Q11.22) WILD-TYPE" 
D27V6, binary
                                cls
clus                               0   1
  DEL PEAK 12(7Q11.22) MUTATED     3   0
  DEL PEAK 12(7Q11.22) WILD-TYPE 111   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(7Q11.22) MUTATED      3    0
  DEL PEAK 12(7Q11.22) WILD-TYPE  111    4
   clus
vv  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE
  0                            3                            111
  1                            0                              4
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(7Q11.22) MUTATED       0                         0     3
  DEL PEAK 12(7Q11.22) WILD-TYPE     4                         6   115
D27V7, multiclass
                           clus
vv                          DEL PEAK 12(7Q11.22) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                3
                           clus
vv                          DEL PEAK 12(7Q11.22) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                115
[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"
D27V8, binary
                                cls
clus                               0   1
  DEL PEAK 12(7Q11.22) MUTATED     1   2
  DEL PEAK 12(7Q11.22) WILD-TYPE  10 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(7Q11.22) MUTATED      1    2
  DEL PEAK 12(7Q11.22) WILD-TYPE   10  109
                        clus
vv                       DEL PEAK 12(7Q11.22) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            2
                        clus
vv                       DEL PEAK 12(7Q11.22) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            109
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK 13(7Q36.1) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(7Q36.1) MUTATED    14   0
  DEL PEAK 13(7Q36.1) WILD-TYPE 115   4
  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE 
                           14                           119 
  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE 
                            0                             4 
$`DEL PEAK 13(7Q36.1) MUTATED`
TCGA-2G-AAFH TCGA-2G-AAG3 TCGA-2G-AAGM TCGA-2G-AAGS TCGA-2G-AAGW TCGA-SN-A84X 
       36.99        52.37        59.64        59.28        61.45        10.26 
TCGA-SN-A84Y TCGA-WZ-A7V3 TCGA-X3-A8G4 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AAOJ 
       17.23         3.65        28.14        40.01        65.98        50.96 
TCGA-XY-A9T9 TCGA-ZM-AA0B 
        6.90        27.55 

$`DEL PEAK 13(7Q36.1) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV 
      108.16       106.39       115.00       120.62       124.57       128.94 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
      170.33        80.94        60.16        60.26        59.84        59.90 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL 
      125.69        61.84        98.53        59.74        59.80        59.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
       91.43       176.15         6.08       122.50       212.65       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
       95.67       229.22       184.41       131.21        70.59         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
        0.13         3.52         7.00         0.10         4.83        20.68 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
       18.15         9.14        13.58         1.38        16.31         9.63 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC 
        3.52        37.18        36.79        37.68        24.99        35.61 
TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V4 
       33.07        23.90        41.52         4.90        24.26         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-AANI TCGA-XE-AANR 
        0.16         0.82         6.87        18.38        34.22         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       53.03        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       67.66        41.69         0.43         8.32        12.92        20.12 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE 
                         3.65                          0.10 
  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE 
                        65.98                        229.22 
  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE 
                        38.50                         37.68 
[1] "3.6 - 66.0 (38.5)"  "0.1 - 229.2 (37.7)"
[1] "hr="   "8e+07"
D28V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 13(7Q36.1) MUTATED         1        1        0        0         0
  DEL PEAK 13(7Q36.1) WILD-TYPE      18       24       11        5         6
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 13(7Q36.1) MUTATED           1         0         0          0
  DEL PEAK 13(7Q36.1) WILD-TYPE         0         1         2          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 13(7Q36.1) MUTATED            1          0       10
  DEL PEAK 13(7Q36.1) WILD-TYPE          5          5       36
D28V3, multiclass
            clus
vv           DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE
  STAGE I                              1                            18
  STAGE IA                             1                            24
  STAGE IB                             0                            11
  STAGE II                             0                             5
  STAGE IIA                            0                             6
  STAGE IIB                            1                             0
  STAGE IIC                            0                             1
  STAGE III                            0                             2
  STAGE IIIA                           0                             1
  STAGE IIIB                           1                             5
  STAGE IIIC                           0                             5
  STAGE IS                            10                            36
[1] 12  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
  DEL PEAK 13(7Q36.1) MUTATED    9  5  0
  DEL PEAK 13(7Q36.1) WILD-TYPE 66 46  6
D28V4, multiclass
    clus
vv   DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE
  T1                           9                            66
  T2                           5                            46
  T3                           0                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  DEL PEAK 13(7Q36.1) MUTATED    3     2
  DEL PEAK 13(7Q36.1) WILD-TYPE 43    11
D28V5, multiclass
       clus
vv      DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE
  N0                              3                            43
  N1+N2                           2                            11
[1] 2 2
[1] FALSE
D28V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(7Q36.1) MUTATED    13   0
  DEL PEAK 13(7Q36.1) WILD-TYPE 101   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.1) MUTATED     13    0
  DEL PEAK 13(7Q36.1) WILD-TYPE  101    4
   clus
vv  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE
  0                          13                           101
  1                           0                             4
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(7Q36.1) MUTATED       0                         0    13
  DEL PEAK 13(7Q36.1) WILD-TYPE     4                         6   105
D28V7, multiclass
                           clus
vv                          DEL PEAK 13(7Q36.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              13
                           clus
vv                          DEL PEAK 13(7Q36.1) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               105
[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"
D28V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(7Q36.1) MUTATED     5   9
  DEL PEAK 13(7Q36.1) WILD-TYPE   6 102
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.1) MUTATED      5    9
  DEL PEAK 13(7Q36.1) WILD-TYPE    6  102
                        clus
vv                       DEL PEAK 13(7Q36.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       DEL PEAK 13(7Q36.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           102
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK 14(9P24.3) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 14(9P24.3) MUTATED   60  2
  DEL PEAK 14(9P24.3) WILD-TYPE 69  2
  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE 
                           62                            71 
  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE 
                            2                             2 
$`DEL PEAK 14(9P24.3) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFJ 
       20.32       102.35       122.40       154.59       191.31        14.56 
TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       40.01        72.20        61.71        63.32        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       68.38        67.96       108.16        59.64       106.39       115.00 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH3 
      120.62        59.28       128.94        80.94        60.16        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHG TCGA-2G-AAHT TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM 
       61.84        59.80         6.08       212.65       161.72       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JY 
      184.41       131.21        70.59         0.10         4.83         9.14 
TCGA-SB-A6J6 TCGA-SN-A84W TCGA-VF-A8AB TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V5 
       13.58         9.63        24.99        41.52        24.26         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANJ 
        0.82        28.14         6.87        18.38        40.01        65.98 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A912 
       41.69        50.96         0.43         6.90        57.90         5.29 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0E 
        7.96        40.96        37.02        39.35        27.55        16.41 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

$`DEL PEAK 14(9P24.3) WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL 
       30.35        38.30        59.70        36.99        14.14        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGF TCGA-2G-AAGI TCGA-2G-AAGJ 
       52.37        71.24        63.22        79.76        92.09        75.09 
TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH4 
      124.57        61.45       170.33        60.26        59.84       125.69 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKD 
       98.53        59.74        59.80        91.43       176.15       122.50 
TCGA-2G-AAKL TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW 
       95.67         2.73         0.13         3.52         7.00        20.68 
TCGA-S6-A8JX TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
       18.15         1.38        16.31        10.26        17.23         3.52 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       37.18        36.79        37.68        35.61        33.07        23.90 
TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AANV 
        4.90         3.65         5.06        34.22         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
        8.32        12.92        20.12        54.35        31.92        21.96 
TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-AA61 TCGA-ZM-AA0D TCGA-ZM-AA0F 
        0.56        58.88         8.15        17.39        11.34 

  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE 
                         0.10                          0.13 
  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE 
                       229.22                        176.15 
  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE 
                        54.43                         33.07 
[1] "0.1 - 229.2 (54.4)" "0.1 - 176.2 (33.1)"
[1] "hr=" "1.9"
D29V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(9P24.3) MUTATED         7       10        2        3         3
  DEL PEAK 14(9P24.3) WILD-TYPE      12       15        9        2         3
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 14(9P24.3) MUTATED           0         1         0          1
  DEL PEAK 14(9P24.3) WILD-TYPE         1         0         2          0
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 14(9P24.3) MUTATED            4          4       24
  DEL PEAK 14(9P24.3) WILD-TYPE          2          1       22
D29V3, multiclass
            clus
vv           DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE
  STAGE I                              7                            12
  STAGE IA                            10                            15
  STAGE IB                             2                             9
  STAGE II                             3                             2
  STAGE IIA                            3                             3
  STAGE IIB                            0                             1
  STAGE IIC                            1                             0
  STAGE III                            0                             2
  STAGE IIIA                           1                             0
  STAGE IIIB                           4                             2
  STAGE IIIC                           4                             1
  STAGE IS                            24                            22
[1] 12  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
  DEL PEAK 14(9P24.3) MUTATED   35 23  3
  DEL PEAK 14(9P24.3) WILD-TYPE 40 28  3
D29V4, multiclass
    clus
vv   DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE
  T1                          35                            40
  T2                          23                            28
  T3                           3                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  DEL PEAK 14(9P24.3) MUTATED   23     8
  DEL PEAK 14(9P24.3) WILD-TYPE 23     5
D29V5, multiclass
       clus
vv      DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE
  N0                             23                            23
  N1+N2                           8                             5
[1] 2 2
[1] FALSE
D29V6, binary
                               cls
clus                             0  1
  DEL PEAK 14(9P24.3) MUTATED   53  3
  DEL PEAK 14(9P24.3) WILD-TYPE 61  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P24.3) MUTATED     53    3
  DEL PEAK 14(9P24.3) WILD-TYPE   61    1
   clus
vv  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE
  0                          53                            61
  1                           3                             1
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(9P24.3) MUTATED       2                         4    54
  DEL PEAK 14(9P24.3) WILD-TYPE     2                         2    64
D29V7, multiclass
                           clus
vv                          DEL PEAK 14(9P24.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              54
                           clus
vv                          DEL PEAK 14(9P24.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                64
[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"
D29V8, binary
                               cls
clus                             0  1
  DEL PEAK 14(9P24.3) MUTATED    5 53
  DEL PEAK 14(9P24.3) WILD-TYPE  6 58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P24.3) MUTATED      5   53
  DEL PEAK 14(9P24.3) WILD-TYPE    6   58
                        clus
vv                       DEL PEAK 14(9P24.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          53
                        clus
vv                       DEL PEAK 14(9P24.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            58
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK 15(9P23) MUTATION ANALYSIS
D30V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 15(9P23) MUTATED   56  2
  DEL PEAK 15(9P23) WILD-TYPE 73  2
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                         58                          75 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                          2                           2 
$`DEL PEAK 15(9P23) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFJ 
       20.32       102.35       122.40       154.59       191.31        14.56 
TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE 
       40.01        72.20        61.71        63.32        72.85        68.38 
TCGA-2G-AAGG TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       67.96       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAHG TCGA-2G-AAHT 
       59.28       128.94        80.94        60.16        59.80         6.08 
TCGA-2G-AAKG TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-4K-AA1I 
      212.65       229.22       184.41       131.21        70.59         0.10 
TCGA-4K-AAAL TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A84W TCGA-VF-A8AB TCGA-W4-A7U2 
        4.83         9.14        13.58         9.63        24.99        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
       24.26         0.16         0.82        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A9T9 
       40.01        65.98        41.69        50.96         0.43         6.90 
TCGA-YU-A90P TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA06 
       57.90         5.29         7.96        40.96        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0E TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        16.41        46.88        10.85 

$`DEL PEAK 15(9P23) WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL 
       30.35        38.30        59.70        36.99        14.14        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
        9.57        14.86        16.50        40.70        36.13        36.89 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGF TCGA-2G-AAGI 
       52.37        71.24        63.22        68.22        79.76        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAH0 TCGA-2G-AAH2 
       75.09       124.57        61.45       170.33        60.26        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL 
       59.90       125.69        61.84        98.53        59.74        59.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2X-A9D5 
       91.43       176.15       122.50       161.72        95.67         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A76C 
        0.13         3.52         7.00        20.68        18.15         1.38 
TCGA-SN-A6IS TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 
       16.31        10.26        17.23         3.52        37.18        36.79 
TCGA-VF-A8AA TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U3 TCGA-WZ-A7V3 
       37.68        35.61        33.07        23.90         4.90         3.65 
TCGA-WZ-A7V4 TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
        5.06        34.22         0.46        53.03        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XY-A89B TCGA-XY-A8S2 
        7.89        16.87         8.88        67.66         8.32        12.92 
TCGA-XY-A8S3 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D 
       20.12        54.35        31.92        21.96         0.56        58.88 
TCGA-YU-AA61 TCGA-ZM-AA0D TCGA-ZM-AA0F 
        8.15        17.39        11.34 

  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                       0.10                        0.13 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                     229.22                      176.15 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                     44.285                      35.610 
[1] "0.1 - 229.2 (44.3)" "0.1 - 176.2 (35.6)"
[1] "hr=" "1.7"
D30V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(9P23) MUTATED         6       10        2        2         2
  DEL PEAK 15(9P23) WILD-TYPE      13       15        9        3         4
                             vv
clus                          STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 15(9P23) MUTATED           0         1         0          1
  DEL PEAK 15(9P23) WILD-TYPE         1         0         2          0
                             vv
clus                          STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 15(9P23) MUTATED            4          3       24
  DEL PEAK 15(9P23) WILD-TYPE          2          2       22
D30V3, multiclass
            clus
vv           DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  STAGE I                            6                          13
  STAGE IA                          10                          15
  STAGE IB                           2                           9
  STAGE II                           2                           3
  STAGE IIA                          2                           4
  STAGE IIB                          0                           1
  STAGE IIC                          1                           0
  STAGE III                          0                           2
  STAGE IIIA                         1                           0
  STAGE IIIB                         4                           2
  STAGE IIIC                         3                           2
  STAGE IS                          24                          22
[1] 12  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
  DEL PEAK 15(9P23) MUTATED   33 21  3
  DEL PEAK 15(9P23) WILD-TYPE 42 30  3
D30V4, multiclass
    clus
vv   DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  T1                        33                          42
  T2                        21                          30
  T3                         3                           3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1+N2
  DEL PEAK 15(9P23) MUTATED   23     7
  DEL PEAK 15(9P23) WILD-TYPE 23     6
D30V5, multiclass
       clus
vv      DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  N0                           23                          23
  N1+N2                         7                           6
[1] 2 2
[1] FALSE
D30V6, binary
                             cls
clus                           0  1
  DEL PEAK 15(9P23) MUTATED   49  3
  DEL PEAK 15(9P23) WILD-TYPE 65  1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED     49    3
  DEL PEAK 15(9P23) WILD-TYPE   65    1
   clus
vv  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  0                        49                          65
  1                         3                           1
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(9P23) MUTATED       2                         4    50
  DEL PEAK 15(9P23) WILD-TYPE     2                         2    68
D30V7, multiclass
                           clus
vv                          DEL PEAK 15(9P23) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         4
  WHITE                                            50
                           clus
vv                          DEL PEAK 15(9P23) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              68
[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"
D30V8, binary
                             cls
clus                           0  1
  DEL PEAK 15(9P23) MUTATED    5 49
  DEL PEAK 15(9P23) WILD-TYPE  6 62
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED      5   49
  DEL PEAK 15(9P23) WILD-TYPE    6   62
                        clus
vv                       DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  HISPANIC OR LATINO                             5                           6
  NOT HISPANIC OR LATINO                        49                          62
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK 16(9Q33.3) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 16(9Q33.3) MUTATED   49  3
  DEL PEAK 16(9Q33.3) WILD-TYPE 80  1
  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE 
                           52                            81 
  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE 
                            3                             1 
$`DEL PEAK 16(9Q33.3) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAG0 TCGA-2G-AAG6 
       20.32       102.35       122.40       154.59        40.01        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG 
       61.71        63.32        68.22        72.85        79.76        67.96 
TCGA-2G-AAGJ TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV 
       75.09       106.39       115.00       120.62        59.28       128.94 
TCGA-2G-AAGX TCGA-2G-AAHG TCGA-2G-AAHT TCGA-2G-AAKG TCGA-2G-AAKM TCGA-2G-AAL5 
      170.33        59.80         6.08       212.65       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JY 
      131.21        70.59         2.73         0.10         4.83         9.14 
TCGA-SB-A6J6 TCGA-SN-A84W TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8AB TCGA-W4-A7U4 
       13.58         9.63        17.23         3.52        24.99        24.26 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-AANI TCGA-XE-AAOF TCGA-XE-AAOJ 
        5.06         0.16        28.14        34.22        41.69        50.96 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Y TCGA-YU-A912 
       12.92        20.12         6.90        57.90         0.56         5.29 
TCGA-YU-A94I TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0H 
        7.96        39.35        27.55        46.88 

$`DEL PEAK 16(9Q33.3) WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       30.35        38.30        59.70       191.31        36.99        14.14 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       14.56        17.16         9.57        14.86        16.50        40.70 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGE 
       36.13        36.89        52.37        71.24        63.22        68.38 
TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGY 
       92.09       108.16        59.64       124.57        61.45        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKD 
       98.53        59.74        59.80        91.43       176.15       122.50 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW 
      161.72        95.67         0.13         3.52         7.00        20.68 
TCGA-S6-A8JX TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8A9 
       18.15         1.38        16.31        10.26        37.18        36.79 
TCGA-VF-A8AA TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 
       37.68        35.61        33.07        23.90        41.52         4.90 
TCGA-WZ-A7V3 TCGA-WZ-A8D5 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANJ 
        3.65         0.82         6.87        18.38        40.01        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        53.03        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOL TCGA-XY-A89B TCGA-YU-A90Q TCGA-YU-A90S 
        8.88        67.66         0.43         8.32        54.35        31.92 
TCGA-YU-A90W TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0D 
       21.96        58.88        40.96         8.15        37.02        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0N 
       16.41        11.34        10.85 

  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE 
                         0.10                          0.13 
  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE 
                       229.22                        191.31 
  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE 
                       44.285                        36.990 
[1] "0.1 - 229.2 (44.3)" "0.1 - 191.3 (37.0)"
[1] "hr=" "3"  
D31V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(9Q33.3) MUTATED         8       10        1        2         3
  DEL PEAK 16(9Q33.3) WILD-TYPE      11       15       10        3         3
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 16(9Q33.3) MUTATED           0         0         0          0
  DEL PEAK 16(9Q33.3) WILD-TYPE         1         1         2          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 16(9Q33.3) MUTATED            4          3       20
  DEL PEAK 16(9Q33.3) WILD-TYPE          2          2       26
D31V3, multiclass
            clus
vv           DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE
  STAGE I                              8                            11
  STAGE IA                            10                            15
  STAGE IB                             1                            10
  STAGE II                             2                             3
  STAGE IIA                            3                             3
  STAGE IIB                            0                             1
  STAGE IIC                            0                             1
  STAGE III                            0                             2
  STAGE IIIA                           0                             1
  STAGE IIIB                           4                             2
  STAGE IIIC                           3                             2
  STAGE IS                            20                            26
[1] 12  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
  DEL PEAK 16(9Q33.3) MUTATED   31 18  3
  DEL PEAK 16(9Q33.3) WILD-TYPE 44 33  3
D31V4, multiclass
    clus
vv   DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE
  T1                          31                            44
  T2                          18                            33
  T3                           3                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  DEL PEAK 16(9Q33.3) MUTATED   21     7
  DEL PEAK 16(9Q33.3) WILD-TYPE 25     6
D31V5, multiclass
       clus
vv      DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE
  N0                             21                            25
  N1+N2                           7                             6
[1] 2 2
[1] FALSE
D31V6, binary
                               cls
clus                             0  1
  DEL PEAK 16(9Q33.3) MUTATED   44  2
  DEL PEAK 16(9Q33.3) WILD-TYPE 70  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9Q33.3) MUTATED     44    2
  DEL PEAK 16(9Q33.3) WILD-TYPE   70    2
   clus
vv  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE
  0                          44                            70
  1                           2                             2
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(9Q33.3) MUTATED       1                         4    46
  DEL PEAK 16(9Q33.3) WILD-TYPE     3                         2    72
D31V7, multiclass
                           clus
vv                          DEL PEAK 16(9Q33.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              46
                           clus
vv                          DEL PEAK 16(9Q33.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                72
[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"
D31V8, binary
                               cls
clus                             0  1
  DEL PEAK 16(9Q33.3) MUTATED    3 45
  DEL PEAK 16(9Q33.3) WILD-TYPE  8 66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9Q33.3) MUTATED      3   45
  DEL PEAK 16(9Q33.3) WILD-TYPE    8   66
                        clus
vv                       DEL PEAK 16(9Q33.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          45
                        clus
vv                       DEL PEAK 16(9Q33.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                            66
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK 17(9Q34.2) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 17(9Q34.2) MUTATED   49  3
  DEL PEAK 17(9Q34.2) WILD-TYPE 80  1
  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE 
                           52                            81 
  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE 
                            3                             1 
$`DEL PEAK 17(9Q34.2) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAG0 TCGA-2G-AAG6 
       20.32       102.35       122.40       154.59        40.01        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG 
       61.71        63.32        68.22        72.85        79.76        67.96 
TCGA-2G-AAGJ TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV 
       75.09       106.39       115.00       120.62        59.28       128.94 
TCGA-2G-AAGX TCGA-2G-AAHG TCGA-2G-AAHT TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM 
      170.33        59.80         6.08       212.65        95.67       229.22 
TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JY 
      184.41        70.59         2.73         0.10         4.83         9.14 
TCGA-SB-A6J6 TCGA-SN-A84W TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AB 
       13.58         9.63        17.23         3.52        37.18        24.99 
TCGA-W4-A7U4 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-AANI TCGA-XE-AAOF 
       24.26         5.06         0.16        28.14        34.22        41.69 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Y TCGA-YU-A912 
       12.92        20.12         6.90        57.90         0.56         5.29 
TCGA-YU-A94I TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0H 
        7.96        39.35        27.55        46.88 

$`DEL PEAK 17(9Q34.2) WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       30.35        38.30        59.70       191.31        36.99        14.14 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       14.56        17.16         9.57        14.86        16.50        40.70 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGE 
       36.13        36.89        52.37        71.24        63.22        68.38 
TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGY 
       92.09       108.16        59.64       124.57        61.45        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKD 
       98.53        59.74        59.80        91.43       176.15       122.50 
TCGA-2G-AAKH TCGA-2G-AAL7 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW 
      161.72       131.21         0.13         3.52         7.00        20.68 
TCGA-S6-A8JX TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X TCGA-VF-A8A9 TCGA-VF-A8AA 
       18.15         1.38        16.31        10.26        36.79        37.68 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-WZ-A7V3 
       35.61        33.07        23.90        41.52         4.90         3.65 
TCGA-WZ-A8D5 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AANR 
        0.82         6.87        18.38        40.01        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       53.03        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-YU-A90Q TCGA-YU-A90S 
       67.66        50.96         0.43         8.32        54.35        31.92 
TCGA-YU-A90W TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0D 
       21.96        58.88        40.96         8.15        37.02        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0N 
       16.41        11.34        10.85 

  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE 
                         0.10                          0.13 
  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE 
                       229.22                        191.31 
  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE 
                        40.85                         36.99 
[1] "0.1 - 229.2 (40.8)" "0.1 - 191.3 (37.0)"
[1] "hr=" "3"  
D32V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 17(9Q34.2) MUTATED         8       11        1        3         3
  DEL PEAK 17(9Q34.2) WILD-TYPE      11       14       10        2         3
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 17(9Q34.2) MUTATED           0         0         0          0
  DEL PEAK 17(9Q34.2) WILD-TYPE         1         1         2          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 17(9Q34.2) MUTATED            4          3       18
  DEL PEAK 17(9Q34.2) WILD-TYPE          2          2       28
D32V3, multiclass
            clus
vv           DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE
  STAGE I                              8                            11
  STAGE IA                            11                            14
  STAGE IB                             1                            10
  STAGE II                             3                             2
  STAGE IIA                            3                             3
  STAGE IIB                            0                             1
  STAGE IIC                            0                             1
  STAGE III                            0                             2
  STAGE IIIA                           0                             1
  STAGE IIIB                           4                             2
  STAGE IIIC                           3                             2
  STAGE IS                            18                            28
[1] 12  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
  DEL PEAK 17(9Q34.2) MUTATED   31 18  3
  DEL PEAK 17(9Q34.2) WILD-TYPE 44 33  3
D32V4, multiclass
    clus
vv   DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE
  T1                          31                            44
  T2                          18                            33
  T3                           3                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  DEL PEAK 17(9Q34.2) MUTATED   21     7
  DEL PEAK 17(9Q34.2) WILD-TYPE 25     6
D32V5, multiclass
       clus
vv      DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE
  N0                             21                            25
  N1+N2                           7                             6
[1] 2 2
[1] FALSE
D32V6, binary
                               cls
clus                             0  1
  DEL PEAK 17(9Q34.2) MUTATED   44  2
  DEL PEAK 17(9Q34.2) WILD-TYPE 70  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9Q34.2) MUTATED     44    2
  DEL PEAK 17(9Q34.2) WILD-TYPE   70    2
   clus
vv  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE
  0                          44                            70
  1                           2                             2
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(9Q34.2) MUTATED       1                         4    46
  DEL PEAK 17(9Q34.2) WILD-TYPE     3                         2    72
D32V7, multiclass
                           clus
vv                          DEL PEAK 17(9Q34.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              46
                           clus
vv                          DEL PEAK 17(9Q34.2) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                72
[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"
D32V8, binary
                               cls
clus                             0  1
  DEL PEAK 17(9Q34.2) MUTATED    2 46
  DEL PEAK 17(9Q34.2) WILD-TYPE  9 65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9Q34.2) MUTATED      2   46
  DEL PEAK 17(9Q34.2) WILD-TYPE    9   65
                        clus
vv                       DEL PEAK 17(9Q34.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          46
                        clus
vv                       DEL PEAK 17(9Q34.2) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                            65
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK 18(10P15.3) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(10P15.3) MUTATED   68  3
  DEL PEAK 18(10P15.3) WILD-TYPE 61  1
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                            71                             62 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                             3                              1 
$`DEL PEAK 18(10P15.3) MUTATED`
TCGA-2G-AAEX TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
       30.35       102.35       154.59         9.57        14.86        16.50 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 
       40.70        36.13        36.89        40.01        72.20        61.71 
TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGK 
       63.22        63.32        68.38        79.76        67.96       108.16 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGY 
      106.39       115.00       120.62       128.94        61.45        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG 
       60.16        59.84        59.90       125.69        59.74        59.80 
TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      176.15       122.50       212.65        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW 
      131.21        70.59         2.73         3.52         7.00        20.68 
TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y 
       18.15        13.58         1.38        16.31         9.63        17.23 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AC TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 
        3.52        37.18        35.61        41.52         4.90        24.26 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-AANI TCGA-XE-AANJ 
        5.06         0.16        28.14         6.87        34.22        65.98 
TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Y 
       16.87        41.69        12.92        20.12        57.90         0.56 
TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
        8.15        39.35        27.55        17.39        11.34 

$`DEL PEAK 18(10P15.3) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH 
       20.32        38.30        59.70       122.40       191.31        36.99 
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAGA 
       14.14        14.56        17.16        52.37        71.24        68.22 
TCGA-2G-AAGC TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGS TCGA-2G-AAGT 
       72.85        92.09        75.09        59.64        59.28       124.57 
TCGA-2G-AAGX TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHL TCGA-2G-AAHN 
      170.33        60.26        61.84        98.53        59.80        91.43 
TCGA-2G-AAHT TCGA-2G-AAKH TCGA-2X-A9D6 TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JY 
        6.08       161.72         0.13         0.10         4.83         9.14 
TCGA-SN-A84X TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AD TCGA-VF-A8AE 
       10.26        36.79        37.68        24.99        33.07        23.90 
TCGA-WZ-A7V3 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANR TCGA-XE-AANV 
        3.65         0.82        18.38        40.01         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ 
       93.93        12.07         7.89         8.88        67.66        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
        0.43         8.32         6.90        54.35        31.92        21.96 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA0E 
        5.29        58.88         7.96        40.96        37.02        16.41 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                          0.16                           0.10 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                        229.22                         191.31 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                        40.010                         37.005 
[1] "0.2 - 229.2 (40.0)" "0.1 - 191.3 (37.0)"
[1] "hr=" "1.6"
D33V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(10P15.3) MUTATED         9        9        3        4         5
  DEL PEAK 18(10P15.3) WILD-TYPE      10       16        8        1         1
                                vv
clus                             STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 18(10P15.3) MUTATED           0         0         2          1
  DEL PEAK 18(10P15.3) WILD-TYPE         1         1         0          0
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 18(10P15.3) MUTATED            4          2       28
  DEL PEAK 18(10P15.3) WILD-TYPE          2          3       18
D33V3, multiclass
            clus
vv           DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  STAGE I                               9                             10
  STAGE IA                              9                             16
  STAGE IB                              3                              8
  STAGE II                              4                              1
  STAGE IIA                             5                              1
  STAGE IIB                             0                              1
  STAGE IIC                             0                              1
  STAGE III                             2                              0
  STAGE IIIA                            1                              0
  STAGE IIIB                            4                              2
  STAGE IIIC                            2                              3
  STAGE IS                             28                             18
[1] 12  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
  DEL PEAK 18(10P15.3) MUTATED   37 31  3
  DEL PEAK 18(10P15.3) WILD-TYPE 38 20  3
D33V4, multiclass
    clus
vv   DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  T1                           37                             38
  T2                           31                             20
  T3                            3                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1+N2
  DEL PEAK 18(10P15.3) MUTATED   24    10
  DEL PEAK 18(10P15.3) WILD-TYPE 22     3
D33V5, multiclass
       clus
vv      DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  N0                              24                             22
  N1+N2                           10                              3
[1] 2 2
[1] FALSE
D33V6, binary
                                cls
clus                              0  1
  DEL PEAK 18(10P15.3) MUTATED   60  4
  DEL PEAK 18(10P15.3) WILD-TYPE 54  0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED     60    4
  DEL PEAK 18(10P15.3) WILD-TYPE   54    0
   clus
vv  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  0                           60                             54
  1                            4                              0
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(10P15.3) MUTATED       1                         1    69
  DEL PEAK 18(10P15.3) WILD-TYPE     3                         5    49
D33V7, multiclass
                           clus
vv                          DEL PEAK 18(10P15.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               69
                           clus
vv                          DEL PEAK 18(10P15.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 49
[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"
D33V8, binary
                                cls
clus                              0  1
  DEL PEAK 18(10P15.3) MUTATED    5 62
  DEL PEAK 18(10P15.3) WILD-TYPE  6 49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED      5   62
  DEL PEAK 18(10P15.3) WILD-TYPE    6   49
                        clus
vv                       DEL PEAK 18(10P15.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           62
                        clus
vv                       DEL PEAK 18(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             49
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 19(10Q23.1) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(10Q23.1) MUTATED   59  3
  DEL PEAK 19(10Q23.1) WILD-TYPE 70  1
  DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE 
                            62                             71 
  DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE 
                             3                              1 
$`DEL PEAK 19(10Q23.1) MUTATED`
TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY 
      102.35       154.59         9.57        14.86        16.50        36.13 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE 
       72.20        61.71        63.22        63.32        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGP 
       79.76        67.96        75.09       108.16       106.39       120.62 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 
      128.94        61.45        80.94        60.16        59.84        59.90 
TCGA-2G-AAH4 TCGA-2G-AAHG TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
      125.69        59.80       176.15       122.50       212.65       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1H 
       95.67       229.22       131.21        70.59         2.73         7.00 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SN-A84W TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8AC 
       20.68        18.15         9.63        17.23         3.52        35.61 
TCGA-VF-A8AD TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       33.07        41.52         4.90        24.26         5.06         0.16 
TCGA-X3-A8G4 TCGA-XE-AANJ TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A8S2 
       28.14        65.98        16.87        41.69         0.43        12.92 
TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-AA61 TCGA-ZM-AA06 
       20.12        57.90         0.56         5.29         8.15        39.35 
TCGA-ZM-AA0D TCGA-ZM-AA0F 
       17.39        11.34 

$`DEL PEAK 19(10Q23.1) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF8 TCGA-2G-AAFG 
       20.32        30.35        38.30        59.70       122.40       191.31 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFV TCGA-2G-AAFZ 
       36.99        14.14        14.56        17.16        40.70        36.89 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAGA TCGA-2G-AAGI TCGA-2G-AAGM 
       40.01        52.37        71.24        68.22        92.09        59.64 
TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGX TCGA-2G-AAH0 TCGA-2G-AAH8 
      115.00        59.28       124.57       170.33        60.26        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAL5 
       98.53        59.74        59.80        91.43         6.08       184.41 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JY TCGA-SB-A6J6 
        0.13         3.52         0.10         4.83         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA 
        1.38        16.31        10.26        37.18        36.79        37.68 
TCGA-VF-A8AB TCGA-VF-A8AE TCGA-WZ-A7V3 TCGA-WZ-A8D5 TCGA-XE-A8H1 TCGA-XE-A8H4 
       24.99        23.90         3.65         0.82         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       40.01        34.22         0.46        53.03        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A9T9 
        7.89         8.88        67.66        50.96         8.32         6.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       54.35        31.92        21.96        58.88         7.96        40.96 
TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0E TCGA-ZM-AA0H TCGA-ZM-AA0N 
       37.02        27.55        16.41        46.88        10.85 

  DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE 
                          0.16                           0.10 
  DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE 
                        229.22                         191.31 
  DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE 
                         58.85                          36.89 
[1] "0.2 - 229.2 (58.8)" "0.1 - 191.3 (36.9)"
[1] "hr=" "2.2"
D34V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 19(10Q23.1) MUTATED         9        7        4        5         5
  DEL PEAK 19(10Q23.1) WILD-TYPE      10       18        7        0         1
                                vv
clus                             STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 19(10Q23.1) MUTATED           0         0         1          1
  DEL PEAK 19(10Q23.1) WILD-TYPE         1         1         1          0
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 19(10Q23.1) MUTATED            4          3       20
  DEL PEAK 19(10Q23.1) WILD-TYPE          2          2       26
D34V3, multiclass
            clus
vv           DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE
  STAGE I                               9                             10
  STAGE IA                              7                             18
  STAGE IB                              4                              7
  STAGE II                              5                              0
  STAGE IIA                             5                              1
  STAGE IIB                             0                              1
  STAGE IIC                             0                              1
  STAGE III                             1                              1
  STAGE IIIA                            1                              0
  STAGE IIIB                            4                              2
  STAGE IIIC                            3                              2
  STAGE IS                             20                             26
[1] 12  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
  DEL PEAK 19(10Q23.1) MUTATED   32 28  2
  DEL PEAK 19(10Q23.1) WILD-TYPE 43 23  4
D34V4, multiclass
    clus
vv   DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE
  T1                           32                             43
  T2                           28                             23
  T3                            2                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1+N2
  DEL PEAK 19(10Q23.1) MUTATED   19    10
  DEL PEAK 19(10Q23.1) WILD-TYPE 27     3
D34V5, multiclass
       clus
vv      DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE
  N0                              19                             27
  N1+N2                           10                              3
[1] 2 2
[1] FALSE
D34V6, binary
                                cls
clus                              0  1
  DEL PEAK 19(10Q23.1) MUTATED   51  3
  DEL PEAK 19(10Q23.1) WILD-TYPE 63  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q23.1) MUTATED     51    3
  DEL PEAK 19(10Q23.1) WILD-TYPE   63    1
   clus
vv  DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE
  0                           51                             63
  1                            3                              1
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(10Q23.1) MUTATED       1                         4    57
  DEL PEAK 19(10Q23.1) WILD-TYPE     3                         2    61
D34V7, multiclass
                           clus
vv                          DEL PEAK 19(10Q23.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               57
                           clus
vv                          DEL PEAK 19(10Q23.1) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 61
[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"
D34V8, binary
                                cls
clus                              0  1
  DEL PEAK 19(10Q23.1) MUTATED    3 54
  DEL PEAK 19(10Q23.1) WILD-TYPE  8 57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q23.1) MUTATED      3   54
  DEL PEAK 19(10Q23.1) WILD-TYPE    8   57
                        clus
vv                       DEL PEAK 19(10Q23.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           54
                        clus
vv                       DEL PEAK 19(10Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                             57
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 20(10Q26.3) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 20(10Q26.3) MUTATED   62  3
  DEL PEAK 20(10Q26.3) WILD-TYPE 67  1
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                            65                             68 
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                             3                              1 
$`DEL PEAK 20(10Q26.3) MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFM 
       59.70       102.35       154.59        14.14        14.56         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       14.86        16.50        36.13        72.20        61.71        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       63.32        68.22        72.85        68.38        79.76        67.96 
TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGY 
      108.16       106.39       120.62       128.94        61.45        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHG TCGA-2G-AAHP 
       60.16        59.84        59.90       125.69        59.80       176.15 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
      122.50       212.65       161.72        95.67       229.22       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW TCGA-S6-A8JX 
       70.59         2.73         3.52         7.00        20.68        18.15 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8AC 
        1.38        16.31         9.63        17.23         3.52        35.61 
TCGA-VF-A8AD TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-X3-A8G4 
       33.07         4.90        24.26         5.06         0.16        28.14 
TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Y 
       16.87        41.69        12.92        20.12        57.90         0.56 
TCGA-YU-A912 TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0D TCGA-ZM-AA0F 
        5.29         8.15        39.35        17.39        11.34 

$`DEL PEAK 20(10Q26.3) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH 
       20.32        30.35        38.30       122.40       191.31        36.99 
TCGA-2G-AAFL TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 
       17.16        40.70        36.89        40.01        52.37        71.24 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT 
       92.09        75.09        59.64       115.00        59.28       124.57 
TCGA-2G-AAGX TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL 
      170.33        60.26        61.84        98.53        59.74        59.80 
TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAL5 TCGA-2X-A9D6 TCGA-4K-AA1I TCGA-4K-AAAL 
       91.43         6.08       184.41         0.13         0.10         4.83 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA 
        9.14        13.58        10.26        37.18        36.79        37.68 
TCGA-VF-A8AB TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A7V3 TCGA-WZ-A8D5 TCGA-XE-A8H1 
       24.99        23.90        41.52         3.65         0.82         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ 
       93.93        12.07         7.89         8.88        67.66        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
        0.43         8.32         6.90        54.35        31.92        21.96 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0E 
       58.88         7.96        40.96        37.02        27.55        16.41 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                          0.16                           0.10 
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                        229.22                         191.31 
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                         41.69                          37.10 
[1] "0.2 - 229.2 (41.7)" "0.1 - 191.3 (37.1)"
[1] "hr=" "2.1"
D35V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(10Q26.3) MUTATED        10        6        5        5         6
  DEL PEAK 20(10Q26.3) WILD-TYPE       9       19        6        0         0
                                vv
clus                             STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 20(10Q26.3) MUTATED           0         0         1          1
  DEL PEAK 20(10Q26.3) WILD-TYPE         1         1         1          0
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 20(10Q26.3) MUTATED            4          3       21
  DEL PEAK 20(10Q26.3) WILD-TYPE          2          2       25
D35V3, multiclass
            clus
vv           DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE
  STAGE I                              10                              9
  STAGE IA                              6                             19
  STAGE IB                              5                              6
  STAGE II                              5                              0
  STAGE IIA                             6                              0
  STAGE IIB                             0                              1
  STAGE IIC                             0                              1
  STAGE III                             1                              1
  STAGE IIIA                            1                              0
  STAGE IIIB                            4                              2
  STAGE IIIC                            3                              2
  STAGE IS                             21                             25
[1] 12  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
  DEL PEAK 20(10Q26.3) MUTATED   34 29  2
  DEL PEAK 20(10Q26.3) WILD-TYPE 41 22  4
D35V4, multiclass
    clus
vv   DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE
  T1                           34                             41
  T2                           29                             22
  T3                            2                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1+N2
  DEL PEAK 20(10Q26.3) MUTATED   22    11
  DEL PEAK 20(10Q26.3) WILD-TYPE 24     2
D35V5, multiclass
       clus
vv      DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE
  N0                              22                             24
  N1+N2                           11                              2
[1] 2 2
[1] FALSE
D35V6, binary
                                cls
clus                              0  1
  DEL PEAK 20(10Q26.3) MUTATED   55  3
  DEL PEAK 20(10Q26.3) WILD-TYPE 59  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10Q26.3) MUTATED     55    3
  DEL PEAK 20(10Q26.3) WILD-TYPE   59    1
   clus
vv  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE
  0                           55                             59
  1                            3                              1
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(10Q26.3) MUTATED       2                         2    61
  DEL PEAK 20(10Q26.3) WILD-TYPE     2                         4    57
D35V7, multiclass
                           clus
vv                          DEL PEAK 20(10Q26.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               61
                           clus
vv                          DEL PEAK 20(10Q26.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 57
[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"
D35V8, binary
                                cls
clus                              0  1
  DEL PEAK 20(10Q26.3) MUTATED    3 57
  DEL PEAK 20(10Q26.3) WILD-TYPE  8 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10Q26.3) MUTATED      3   57
  DEL PEAK 20(10Q26.3) WILD-TYPE    8   54
                        clus
vv                       DEL PEAK 20(10Q26.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           57
                        clus
vv                       DEL PEAK 20(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                             54
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 21(11P15.5) MUTATION ANALYSIS
D36V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(11P15.5) MUTATED   82  2
  DEL PEAK 21(11P15.5) WILD-TYPE 47  2
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                            84                             49 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                             2                              2 
$`DEL PEAK 21(11P15.5) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAFG 
       20.32        59.70       102.35       122.40       154.59       191.31 
TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY 
       36.99        14.56         9.57        14.86        16.50        36.13 
TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE 
       40.01        72.20        61.71        63.32        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS 
       79.76        67.96       108.16       106.39       115.00        59.28 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 
      128.94        61.45       170.33        80.94        60.16        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       59.90       125.69        59.74        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAL7 TCGA-2G-AALP 
      176.15         6.08       122.50       212.65       131.21        70.59 
TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        2.73         3.52        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y TCGA-VF-A8A9 TCGA-VF-A8AB 
        1.38        16.31         9.63        17.23        36.79        24.99 
TCGA-VF-A8AC TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-XE-A8H1 
       35.61        24.26         3.65         5.06         0.16         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       18.38        40.01        65.98         0.46        53.03        93.93 
TCGA-XE-AAO4 TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A9T9 
       12.07        67.66        41.69         8.32        12.92         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90Y TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA06 
       57.90        54.35         0.56         5.29        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

$`DEL PEAK 21(11P15.5) WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFV TCGA-2G-AAFZ 
       30.35        38.30        14.14        17.16        40.70        36.89 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGI TCGA-2G-AAGJ 
       52.37        71.24        63.22        68.22        92.09        75.09 
TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA 
       59.64       120.62       124.57        60.26        61.84        98.53 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2X-A9D6 TCGA-4K-AA1H 
      161.72        95.67       229.22       184.41         0.13         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA 
        0.10         4.83        10.26         3.52        37.18        37.68 
TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       33.07        23.90        41.52         4.90         0.82        28.14 
TCGA-XE-AANI TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOJ TCGA-XE-AAOL 
       34.22         7.89        16.87         8.88        50.96         0.43 
TCGA-XY-A8S3 TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       20.12        31.92        21.96        58.88         7.96        40.96 
TCGA-YU-AA61 
        8.15 

  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                          0.16                           0.10 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                        212.65                         229.22 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                         40.01                          36.89 
[1] "0.2 - 212.7 (40.0)" "0.1 - 229.2 (36.9)"
[1] "hr=" "1.2"
D36V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(11P15.5) MUTATED        14       15        6        2         4
  DEL PEAK 21(11P15.5) WILD-TYPE       5       10        5        3         2
                                vv
clus                             STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 21(11P15.5) MUTATED           1         1         1          1
  DEL PEAK 21(11P15.5) WILD-TYPE         0         0         1          0
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 21(11P15.5) MUTATED            5          3       29
  DEL PEAK 21(11P15.5) WILD-TYPE          1          2       17
D36V3, multiclass
            clus
vv           DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  STAGE I                              14                              5
  STAGE IA                             15                             10
  STAGE IB                              6                              5
  STAGE II                              2                              3
  STAGE IIA                             4                              2
  STAGE IIB                             1                              0
  STAGE IIC                             1                              0
  STAGE III                             1                              1
  STAGE IIIA                            1                              0
  STAGE IIIB                            5                              1
  STAGE IIIC                            3                              2
  STAGE IS                             29                             17
[1] 12  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
  DEL PEAK 21(11P15.5) MUTATED   46 34  3
  DEL PEAK 21(11P15.5) WILD-TYPE 29 17  3
D36V4, multiclass
    clus
vv   DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  T1                           46                             29
  T2                           34                             17
  T3                            3                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1+N2
  DEL PEAK 21(11P15.5) MUTATED   28    11
  DEL PEAK 21(11P15.5) WILD-TYPE 18     2
D36V5, multiclass
       clus
vv      DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  N0                              28                             18
  N1+N2                           11                              2
[1] 2 2
[1] FALSE
D36V6, binary
                                cls
clus                              0  1
  DEL PEAK 21(11P15.5) MUTATED   74  3
  DEL PEAK 21(11P15.5) WILD-TYPE 40  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED     74    3
  DEL PEAK 21(11P15.5) WILD-TYPE   40    1
   clus
vv  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  0                           74                             40
  1                            3                              1
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(11P15.5) MUTATED       3                         3    75
  DEL PEAK 21(11P15.5) WILD-TYPE     1                         3    43
D36V7, multiclass
                           clus
vv                          DEL PEAK 21(11P15.5) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               75
                           clus
vv                          DEL PEAK 21(11P15.5) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              3
  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"
D36V8, binary
                                cls
clus                              0  1
  DEL PEAK 21(11P15.5) MUTATED    8 72
  DEL PEAK 21(11P15.5) WILD-TYPE  3 39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED      8   72
  DEL PEAK 21(11P15.5) WILD-TYPE    3   39
                        clus
vv                       DEL PEAK 21(11P15.5) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           72
                        clus
vv                       DEL PEAK 21(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             39
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 22(11P12) MUTATION ANALYSIS
D37V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 22(11P12) MUTATED   86  3
  DEL PEAK 22(11P12) WILD-TYPE 43  1
  DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE 
                          89                           44 
  DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE 
                           3                            1 
$`DEL PEAK 22(11P12) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        59.70       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
      191.31        36.99        14.56         9.57        14.86        16.50 
TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA 
       36.13        40.01        72.20        61.71        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGK TCGA-2G-AAGN 
       72.85        68.38        79.76        67.96       108.16       106.39 
TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      115.00        59.28       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG 
       60.16        59.84        59.90       125.69        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        91.43       176.15         6.08       122.50       212.65 
TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW 
      229.22       131.21        70.59         3.52         7.00        20.68 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
       18.15         9.14        13.58         1.38        16.31         9.63 
TCGA-SN-A84Y TCGA-VF-A8A9 TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U4 
       17.23        36.79        24.99        35.61        33.07        24.26 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        3.65         5.06         0.16         6.87        18.38        40.01 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A9T9 TCGA-YU-A90P 
       67.66        41.69         8.32        12.92         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       54.35         0.56         5.29         8.15        37.02        39.35 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

$`DEL PEAK 22(11P12) WILD-TYPE`
TCGA-2G-AAF1 TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 
       38.30        14.14        17.16        40.70        36.89        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGP 
       71.24        63.22        92.09        75.09        59.64       120.62 
TCGA-2G-AAGT TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAKH TCGA-2G-AAKL 
      124.57        60.26        61.84        98.53       161.72        95.67 
TCGA-2G-AAL5 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1I TCGA-4K-AAAL TCGA-SN-A84X 
      184.41         2.73         0.13         0.10         4.83        10.26 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 
        3.52        37.18        37.68        23.90        41.52         4.90 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-AANI TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOJ 
        0.82        28.14        34.22        16.87         8.88        50.96 
TCGA-XE-AAOL TCGA-XY-A8S3 TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A94D TCGA-YU-A94I 
        0.43        20.12        31.92        21.96        58.88         7.96 
TCGA-YU-AA4L TCGA-ZM-AA0B 
       40.96        27.55 

  DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE 
                        0.16                         0.10 
  DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE 
                      229.22                       184.41 
  DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE 
                      40.010                       37.035 
[1] "0.2 - 229.2 (40.0)" "0.1 - 184.4 (37.0)"
[1] "hr=" "1"  
D37V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(11P12) MUTATED        13       16        7        3         5
  DEL PEAK 22(11P12) WILD-TYPE       6        9        4        2         1
                              vv
clus                           STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 22(11P12) MUTATED           1         1         1          1
  DEL PEAK 22(11P12) WILD-TYPE         0         0         1          0
                              vv
clus                           STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 22(11P12) MUTATED            5          3       31
  DEL PEAK 22(11P12) WILD-TYPE          1          2       15
D37V3, multiclass
            clus
vv           DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE
  STAGE I                            13                            6
  STAGE IA                           16                            9
  STAGE IB                            7                            4
  STAGE II                            3                            2
  STAGE IIA                           5                            1
  STAGE IIB                           1                            0
  STAGE IIC                           1                            0
  STAGE III                           1                            1
  STAGE IIIA                          1                            0
  STAGE IIIB                          5                            1
  STAGE IIIC                          3                            2
  STAGE IS                           31                           15
[1] 12  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
  DEL PEAK 22(11P12) MUTATED   48 37  3
  DEL PEAK 22(11P12) WILD-TYPE 27 14  3
D37V4, multiclass
    clus
vv   DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE
  T1                         48                           27
  T2                         37                           14
  T3                          3                            3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1+N2
  DEL PEAK 22(11P12) MUTATED   30    12
  DEL PEAK 22(11P12) WILD-TYPE 16     1
D37V5, multiclass
       clus
vv      DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE
  N0                            30                           16
  N1+N2                         12                            1
[1] 2 2
[1] FALSE
D37V6, binary
                              cls
clus                            0  1
  DEL PEAK 22(11P12) MUTATED   78  3
  DEL PEAK 22(11P12) WILD-TYPE 36  1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(11P12) MUTATED     78    3
  DEL PEAK 22(11P12) WILD-TYPE   36    1
   clus
vv  DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE
  0                         78                           36
  1                          3                            1
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(11P12) MUTATED       3                         3    80
  DEL PEAK 22(11P12) WILD-TYPE     1                         3    38
D37V7, multiclass
                           clus
vv                          DEL PEAK 22(11P12) MUTATED
  ASIAN                                              3
  BLACK OR AFRICAN AMERICAN                          3
  WHITE                                             80
                           clus
vv                          DEL PEAK 22(11P12) WILD-TYPE
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               38
[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"
D37V8, binary
                              cls
clus                            0  1
  DEL PEAK 22(11P12) MUTATED    8 76
  DEL PEAK 22(11P12) WILD-TYPE  3 35
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(11P12) MUTATED      8   76
  DEL PEAK 22(11P12) WILD-TYPE    3   35
                        clus
vv                       DEL PEAK 22(11P12) MUTATED
  HISPANIC OR LATINO                              8
  NOT HISPANIC OR LATINO                         76
                        clus
vv                       DEL PEAK 22(11P12) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           35
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 23(11Q12.3) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(11Q12.3) MUTATED   100   3
  DEL PEAK 23(11Q12.3) WILD-TYPE  29   1
  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE 
                           103                             30 
  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE 
                             3                              1 
$`DEL PEAK 23(11Q12.3) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        59.70       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
      191.31        36.99        14.56         9.57        14.86        16.50 
TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       36.13        40.01        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGK TCGA-2G-AAGN 
       68.22        68.38        79.76        67.96       108.16       106.39 
TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      115.00        59.28       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP 
      122.50       212.65        95.67       229.22       131.21        70.59 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
        3.52         7.00         0.10         4.83        20.68        18.15 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y 
        9.14        13.58         1.38        16.31         9.63        17.23 
TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
        3.52        36.79        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOD TCGA-XE-AAOF 
       53.03        93.93        12.07         7.89        67.66        41.69 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P 
        0.43         8.32        12.92        20.12         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-AA61 TCGA-ZM-AA05 
       54.35        21.96         0.56         5.29         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

$`DEL PEAK 23(11Q12.3) WILD-TYPE`
TCGA-2G-AAF1 TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 
       38.30        14.14        17.16        40.70        36.89        52.37 
TCGA-2G-AAG5 TCGA-2G-AAGC TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGP 
       71.24        72.85        92.09        75.09        59.64       120.62 
TCGA-2G-AAGT TCGA-2G-AAHA TCGA-2G-AAKH TCGA-2G-AAL5 TCGA-2X-A9D5 TCGA-2X-A9D6 
      124.57        98.53       161.72       184.41         2.73         0.13 
TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-W4-A7U3 TCGA-XE-AAOB 
       10.26        37.18        37.68        24.99         4.90        16.87 
TCGA-XE-AAOC TCGA-XE-AAOJ TCGA-YU-A90S TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
        8.88        50.96        31.92        58.88         7.96        40.96 

  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE 
                          0.10                           0.13 
  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE 
                        229.22                         184.41 
  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE 
                         36.99                          39.50 
[1] "0.1 - 229.2 (37.0)" "0.1 - 184.4 (39.5)"
[1] "hr=" "1.6"
D38V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(11Q12.3) MUTATED        15       19        8        4         5
  DEL PEAK 23(11Q12.3) WILD-TYPE       4        6        3        1         1
                                vv
clus                             STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 23(11Q12.3) MUTATED           1         1         1          1
  DEL PEAK 23(11Q12.3) WILD-TYPE         0         0         1          0
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 23(11Q12.3) MUTATED            5          4       35
  DEL PEAK 23(11Q12.3) WILD-TYPE          1          1       11
D38V3, multiclass
            clus
vv           DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE
  STAGE I                              15                              4
  STAGE IA                             19                              6
  STAGE IB                              8                              3
  STAGE II                              4                              1
  STAGE IIA                             5                              1
  STAGE IIB                             1                              0
  STAGE IIC                             1                              0
  STAGE III                             1                              1
  STAGE IIIA                            1                              0
  STAGE IIIB                            5                              1
  STAGE IIIC                            4                              1
  STAGE IS                             35                             11
[1] 12  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
  DEL PEAK 23(11Q12.3) MUTATED   55 43  4
  DEL PEAK 23(11Q12.3) WILD-TYPE 20  8  2
D38V4, multiclass
    clus
vv   DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE
  T1                           55                             20
  T2                           43                              8
  T3                            4                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1+N2
  DEL PEAK 23(11Q12.3) MUTATED   33    12
  DEL PEAK 23(11Q12.3) WILD-TYPE 13     1
D38V5, multiclass
       clus
vv      DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE
  N0                              33                             13
  N1+N2                           12                              1
[1] 2 2
[1] FALSE
D38V6, binary
                                cls
clus                              0  1
  DEL PEAK 23(11Q12.3) MUTATED   90  3
  DEL PEAK 23(11Q12.3) WILD-TYPE 24  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q12.3) MUTATED     90    3
  DEL PEAK 23(11Q12.3) WILD-TYPE   24    1
   clus
vv  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE
  0                           90                             24
  1                            3                              1
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(11Q12.3) MUTATED       3                         3    94
  DEL PEAK 23(11Q12.3) WILD-TYPE     1                         3    24
D38V7, multiclass
                           clus
vv                          DEL PEAK 23(11Q12.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               94
                           clus
vv                          DEL PEAK 23(11Q12.3) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 24
[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"
D38V8, binary
                                cls
clus                              0  1
  DEL PEAK 23(11Q12.3) MUTATED    8 89
  DEL PEAK 23(11Q12.3) WILD-TYPE  3 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q12.3) MUTATED      8   89
  DEL PEAK 23(11Q12.3) WILD-TYPE    3   22
                        clus
vv                       DEL PEAK 23(11Q12.3) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           89
                        clus
vv                       DEL PEAK 23(11Q12.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             22
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 24(11Q24.2) MUTATION ANALYSIS
D39V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(11Q24.2) MUTATED   106   3
  DEL PEAK 24(11Q24.2) WILD-TYPE  23   1
  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE 
                           109                             24 
  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE 
                             3                              1 
$`DEL PEAK 24(11Q24.2) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        59.70       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
      191.31        36.99        14.56         9.57        14.86        16.50 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        36.89        40.01        72.20        61.71        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       63.32        68.22        72.85        68.38        79.76        67.96 
TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
       92.09       108.16       106.39       115.00       120.62        59.28 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHC TCGA-2G-AAHG 
       59.84        59.90       125.69        61.84        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        91.43       176.15         6.08       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      161.72        95.67       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
        2.73         3.52         0.10         4.83        20.68        18.15 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y 
        9.14        13.58         1.38        16.31         9.63        17.23 
TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
        3.52        36.79        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD 
       53.03        93.93        12.07         7.89        16.87        67.66 
TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       41.69         0.43         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-AA61 TCGA-ZM-AA05 
       57.90        54.35        21.96         5.29         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

$`DEL PEAK 24(11Q24.2) WILD-TYPE`
TCGA-2G-AAF1 TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFV TCGA-2G-AAG3 TCGA-2G-AAG5 
       38.30        14.14        17.16        40.70        52.37        71.24 
TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAHA TCGA-2X-A9D6 TCGA-4K-AA1H 
       75.09        59.64       124.57        98.53         0.13         7.00 
TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-W4-A7U3 TCGA-XE-AAOC 
       10.26        37.18        37.68        24.99         4.90         8.88 
TCGA-XE-AAOJ TCGA-YU-A90S TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       50.96        31.92         0.56        58.88         7.96        40.96 

  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE 
                          0.10                           0.13 
  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE 
                        229.22                         124.57 
  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE 
                         39.35                          37.43 
[1] "0.1 - 229.2 (39.4)" "0.1 - 124.6 (37.4)"
[1] "hr=" "2.4"
D39V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(11Q24.2) MUTATED        17       18        8        5         6
  DEL PEAK 24(11Q24.2) WILD-TYPE       2        7        3        0         0
                                vv
clus                             STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 24(11Q24.2) MUTATED           1         1         2          1
  DEL PEAK 24(11Q24.2) WILD-TYPE         0         0         0          0
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 24(11Q24.2) MUTATED            5          3       38
  DEL PEAK 24(11Q24.2) WILD-TYPE          1          2        8
D39V3, multiclass
            clus
vv           DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE
  STAGE I                              17                              2
  STAGE IA                             18                              7
  STAGE IB                              8                              3
  STAGE II                              5                              0
  STAGE IIA                             6                              0
  STAGE IIB                             1                              0
  STAGE IIC                             1                              0
  STAGE III                             2                              0
  STAGE IIIA                            1                              0
  STAGE IIIB                            5                              1
  STAGE IIIC                            3                              2
  STAGE IS                             38                              8
[1] 12  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
  DEL PEAK 24(11Q24.2) MUTATED   61 43  4
  DEL PEAK 24(11Q24.2) WILD-TYPE 14  8  2
D39V4, multiclass
    clus
vv   DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE
  T1                           61                             14
  T2                           43                              8
  T3                            4                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1+N2
  DEL PEAK 24(11Q24.2) MUTATED   35    13
  DEL PEAK 24(11Q24.2) WILD-TYPE 11     0
D39V5, multiclass
       clus
vv      DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE
  N0                              35                             11
  N1+N2                           13                              0
[1] 2 2
[1] FALSE
D39V6, binary
                                cls
clus                              0  1
  DEL PEAK 24(11Q24.2) MUTATED   96  4
  DEL PEAK 24(11Q24.2) WILD-TYPE 18  0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(11Q24.2) MUTATED     96    4
  DEL PEAK 24(11Q24.2) WILD-TYPE   18    0
   clus
vv  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE
  0                           96                             18
  1                            4                              0
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(11Q24.2) MUTATED       3                         2   101
  DEL PEAK 24(11Q24.2) WILD-TYPE     1                         4    17
D39V7, multiclass
                           clus
vv                          DEL PEAK 24(11Q24.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                              101
                           clus
vv                          DEL PEAK 24(11Q24.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 17
[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"
D39V8, binary
                                cls
clus                              0  1
  DEL PEAK 24(11Q24.2) MUTATED    8 96
  DEL PEAK 24(11Q24.2) WILD-TYPE  3 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(11Q24.2) MUTATED      8   96
  DEL PEAK 24(11Q24.2) WILD-TYPE    3   15
                        clus
vv                       DEL PEAK 24(11Q24.2) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           96
                        clus
vv                       DEL PEAK 24(11Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             15
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 25(13Q34) MUTATION ANALYSIS
D40V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 25(13Q34) MUTATED   97  4
  DEL PEAK 25(13Q34) WILD-TYPE 32  0
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                         101                           32 
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                           4                            0 
$`DEL PEAK 25(13Q34) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        36.99        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 
       14.86        36.13        40.01        72.20        61.71        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.22        72.85        79.76        67.96        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGX 
       59.64       106.39       120.62        59.28       128.94       170.33 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH8 TCGA-2G-AAHA 
       80.94        60.16        60.26        59.84        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JX TCGA-S6-A8JY 
       70.59         2.73         0.10         4.83        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y TCGA-SO-A8JP 
       13.58         1.38        16.31         9.63        17.23         3.52 
TCGA-VF-A8A9 TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       36.79        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U3 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
        4.90         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XE-AAOJ 
       93.93        12.07         7.89        16.87        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P 
        0.43         8.32        12.92        20.12         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L 
       54.35        21.96         0.56         5.29         7.96        40.96 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0N 
       39.35        27.55        17.39        16.41        10.85 

$`DEL PEAK 25(13Q34) WILD-TYPE`
TCGA-2G-AAFI TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 
       14.14        16.50        40.70        36.89        52.37        71.24 
TCGA-2G-AAG8 TCGA-2G-AAGE TCGA-2G-AAGI TCGA-2G-AAGO TCGA-2G-AAGT TCGA-2G-AAGW 
       63.22        68.38        92.09       115.00       124.57        61.45 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAL7 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
       59.90       125.69       131.21         0.13         3.52         7.00 
TCGA-S6-A8JW TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-W4-A7U4 TCGA-XE-AANV 
       20.68        10.26        37.18        37.68        24.26        53.03 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-YU-A90S TCGA-YU-A94D TCGA-YU-AA61 TCGA-ZM-AA05 
        8.88        67.66        31.92        58.88         8.15        37.02 
TCGA-ZM-AA0F TCGA-ZM-AA0H 
       11.34        46.88 

  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                        0.10                         0.13 
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                      229.22                       131.21 
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                       36.99                        39.19 
[1] "0.1 - 229.2 (37.0)" "0.1 - 131.2 (39.2)"
[1] "hr="     "2.9e+08"
D40V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(13Q34) MUTATED        16       20        7        4         5
  DEL PEAK 25(13Q34) WILD-TYPE       3        5        4        1         1
                              vv
clus                           STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 25(13Q34) MUTATED           1         0         1          1
  DEL PEAK 25(13Q34) WILD-TYPE         0         1         1          0
                              vv
clus                           STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 25(13Q34) MUTATED            5          5       32
  DEL PEAK 25(13Q34) WILD-TYPE          1          0       14
D40V3, multiclass
            clus
vv           DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE
  STAGE I                            16                            3
  STAGE IA                           20                            5
  STAGE IB                            7                            4
  STAGE II                            4                            1
  STAGE IIA                           5                            1
  STAGE IIB                           1                            0
  STAGE IIC                           0                            1
  STAGE III                           1                            1
  STAGE IIIA                          1                            0
  STAGE IIIB                          5                            1
  STAGE IIIC                          5                            0
  STAGE IS                           32                           14
[1] 12  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
  DEL PEAK 25(13Q34) MUTATED   60 37  3
  DEL PEAK 25(13Q34) WILD-TYPE 15 14  3
D40V4, multiclass
    clus
vv   DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE
  T1                         60                           15
  T2                         37                           14
  T3                          3                            3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1+N2
  DEL PEAK 25(13Q34) MUTATED   33    12
  DEL PEAK 25(13Q34) WILD-TYPE 13     1
D40V5, multiclass
       clus
vv      DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE
  N0                            33                           13
  N1+N2                         12                            1
[1] 2 2
[1] FALSE
D40V6, binary
                              cls
clus                            0  1
  DEL PEAK 25(13Q34) MUTATED   86  3
  DEL PEAK 25(13Q34) WILD-TYPE 28  1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(13Q34) MUTATED     86    3
  DEL PEAK 25(13Q34) WILD-TYPE   28    1
   clus
vv  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE
  0                         86                           28
  1                          3                            1
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(13Q34) MUTATED       4                         6    88
  DEL PEAK 25(13Q34) WILD-TYPE     0                         0    30
D40V7, multiclass
                           clus
vv                          DEL PEAK 25(13Q34) MUTATED
  ASIAN                                              4
  BLACK OR AFRICAN AMERICAN                          6
  WHITE                                             88
                           clus
vv                          DEL PEAK 25(13Q34) WILD-TYPE
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               30
[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"
D40V8, binary
                              cls
clus                            0  1
  DEL PEAK 25(13Q34) MUTATED    9 84
  DEL PEAK 25(13Q34) WILD-TYPE  2 27
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(13Q34) MUTATED      9   84
  DEL PEAK 25(13Q34) WILD-TYPE    2   27
                        clus
vv                       DEL PEAK 25(13Q34) MUTATED
  HISPANIC OR LATINO                              9
  NOT HISPANIC OR LATINO                         84
                        clus
vv                       DEL PEAK 25(13Q34) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           27
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 26(16Q23.1) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 26(16Q23.1) MUTATED   59  1
  DEL PEAK 26(16Q23.1) WILD-TYPE 70  3
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            60                             73 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                             1                              3 
$`DEL PEAK 26(16Q23.1) MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH 
       59.70       102.35       122.40       154.59       191.31        36.99 
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAG3 
       14.14        14.56        17.16        14.86        36.13        52.37 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGJ 
       61.71        63.32        68.22        72.85        79.76        75.09 
TCGA-2G-AAGP TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
      120.62        61.45        80.94        60.26        59.84        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       61.84        59.80        59.80       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      212.65       161.72        95.67       229.22       184.41       131.21 
TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-SB-A6J6 TCGA-SB-A76C TCGA-VF-A8AC TCGA-W4-A7U2 
        2.73         3.52        13.58         1.38        35.61        41.52 
TCGA-WZ-A7V3 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H5 
        3.65         0.16         0.82        28.14         6.87        40.01 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAO6 TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S2 
       65.98         0.46         7.89        50.96         8.32        12.92 
TCGA-XY-A9T9 TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA0D TCGA-ZM-AA0N 
        6.90         7.96        40.96         8.15        17.39        10.85 

$`DEL PEAK 26(16Q23.1) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAFM TCGA-2G-AAFO TCGA-2G-AAFV 
       20.32        30.35        38.30         9.57        16.50        40.70 
TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAGE 
       36.89        40.01        71.24        72.20        63.22        68.38 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       67.96        92.09       108.16        59.64       106.39       115.00 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAH4 
       59.28       124.57       128.94       170.33        60.16       125.69 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHN TCGA-2G-AALP TCGA-2X-A9D6 TCGA-4K-AA1H 
       98.53        59.74        91.43        70.59         0.13         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SN-A6IS 
        0.10         4.83        20.68        18.15         9.14        16.31 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 
        9.63        10.26        17.23         3.52        37.18        36.79 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U3 TCGA-W4-A7U4 
       37.68        24.99        33.07        23.90         4.90        24.26 
TCGA-WZ-A7V4 TCGA-XE-A8H4 TCGA-XE-AANI TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
        5.06        18.38        34.22        53.03        93.93        12.07 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A8S3 
       16.87         8.88        67.66        41.69         0.43        20.12 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0E TCGA-ZM-AA0F 
       58.88        37.02        39.35        27.55        16.41        11.34 
TCGA-ZM-AA0H 
       46.88 

  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                          0.16                           0.10 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                        229.22                         170.33 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                        51.665                         36.790 
[1] "0.2 - 229.2 (51.7)" "0.1 - 170.3 (36.8)"
[1] "hr="     "4.8e+08"
D41V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(16Q23.1) MUTATED        12        8        3        3         4
  DEL PEAK 26(16Q23.1) WILD-TYPE       7       17        8        2         2
                                vv
clus                             STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 26(16Q23.1) MUTATED           1         0         1          0
  DEL PEAK 26(16Q23.1) WILD-TYPE         0         1         1          1
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 26(16Q23.1) MUTATED            2          2       21
  DEL PEAK 26(16Q23.1) WILD-TYPE          4          3       25
D41V3, multiclass
            clus
vv           DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  STAGE I                              12                              7
  STAGE IA                              8                             17
  STAGE IB                              3                              8
  STAGE II                              3                              2
  STAGE IIA                             4                              2
  STAGE IIB                             1                              0
  STAGE IIC                             0                              1
  STAGE III                             1                              1
  STAGE IIIA                            0                              1
  STAGE IIIB                            2                              4
  STAGE IIIC                            2                              3
  STAGE IS                             21                             25
[1] 12  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
  DEL PEAK 26(16Q23.1) MUTATED   33 26  1
  DEL PEAK 26(16Q23.1) WILD-TYPE 42 25  5
D41V4, multiclass
    clus
vv   DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  T1                           33                             42
  T2                           26                             25
  T3                            1                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1+N2
  DEL PEAK 26(16Q23.1) MUTATED   23     7
  DEL PEAK 26(16Q23.1) WILD-TYPE 23     6
D41V5, multiclass
       clus
vv      DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  N0                              23                             23
  N1+N2                            7                              6
[1] 2 2
[1] FALSE
D41V6, binary
                                cls
clus                              0  1
  DEL PEAK 26(16Q23.1) MUTATED   54  0
  DEL PEAK 26(16Q23.1) WILD-TYPE 60  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED     54    0
  DEL PEAK 26(16Q23.1) WILD-TYPE   60    4
   clus
vv  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  0                           54                             60
  1                            0                              4
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(16Q23.1) MUTATED       1                         2    55
  DEL PEAK 26(16Q23.1) WILD-TYPE     3                         4    63
D41V7, multiclass
                           clus
vv                          DEL PEAK 26(16Q23.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               55
                           clus
vv                          DEL PEAK 26(16Q23.1) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 63
[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"
D41V8, binary
                                cls
clus                              0  1
  DEL PEAK 26(16Q23.1) MUTATED    5 52
  DEL PEAK 26(16Q23.1) WILD-TYPE  6 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED      5   52
  DEL PEAK 26(16Q23.1) WILD-TYPE    6   59
                        clus
vv                       DEL PEAK 26(16Q23.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           52
                        clus
vv                       DEL PEAK 26(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             59
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 27(18P11.32) MUTATION ANALYSIS
D42V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 27(18P11.32) MUTATED   101   4
  DEL PEAK 27(18P11.32) WILD-TYPE  28   0
  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE 
                            105                              28 
  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE 
                              4                               0 
$`DEL PEAK 27(18P11.32) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        38.30        59.70       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
      191.31        36.99        17.16         9.57        14.86        16.50 
TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        40.01        52.37        72.20        61.71        63.22 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       63.32        68.22        72.85        68.38        79.76        67.96 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS 
       75.09       108.16        59.64       106.39       115.00        59.28 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL 
       59.84        59.90       125.69        59.74        59.80        59.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL 
       91.43       176.15         6.08       122.50       212.65        95.67 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1I 
      229.22       184.41       131.21        70.59         2.73         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
        4.83        20.68        18.15         1.38        16.31         9.63 
TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       17.23         3.52        37.68        24.99        35.61        33.07 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       41.52         4.90        24.26         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB TCGA-XE-AAOD 
       65.98         0.46        93.93        12.07        16.87        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       41.69        50.96         0.43         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
        6.90        57.90        54.35        21.96         0.56         5.29 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
        7.96        40.96         8.15        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0N 
       16.41        11.34        10.85 

$`DEL PEAK 27(18P11.32) WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG5 
       30.35        14.14        14.56        40.70        36.89        71.24 
TCGA-2G-AAGI TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAKH 
       92.09       120.62       124.57        61.84        98.53       161.72 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A84X 
        0.13         3.52         7.00         9.14        13.58        10.26 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AE TCGA-XE-AANV TCGA-XE-AAO6 TCGA-XE-AAOC 
       37.18        36.79        23.90        53.03         7.89         8.88 
TCGA-YU-A90S TCGA-YU-A94D TCGA-ZM-AA05 TCGA-ZM-AA0H 
       31.92        58.88        37.02        46.88 

  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE 
                           0.10                            0.13 
  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE 
                         229.22                          161.72 
  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE 
                          40.01                           36.84 
[1] "0.1 - 229.2 (40.0)" "0.1 - 161.7 (36.8)"
[1] "hr="     "2.6e+08"
D42V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(18P11.32) MUTATED        17       17        8        4         5
  DEL PEAK 27(18P11.32) WILD-TYPE       2        8        3        1         1
                                 vv
clus                              STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 27(18P11.32) MUTATED           1         0         1          1
  DEL PEAK 27(18P11.32) WILD-TYPE         0         1         1          0
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 27(18P11.32) MUTATED            5          4       37
  DEL PEAK 27(18P11.32) WILD-TYPE          1          1        9
D42V3, multiclass
            clus
vv           DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE
  STAGE I                               17                               2
  STAGE IA                              17                               8
  STAGE IB                               8                               3
  STAGE II                               4                               1
  STAGE IIA                              5                               1
  STAGE IIB                              1                               0
  STAGE IIC                              0                               1
  STAGE III                              1                               1
  STAGE IIIA                             1                               0
  STAGE IIIB                             5                               1
  STAGE IIIC                             4                               1
  STAGE IS                              37                               9
[1] 12  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
  DEL PEAK 27(18P11.32) MUTATED   60 41  3
  DEL PEAK 27(18P11.32) WILD-TYPE 15 10  3
D42V4, multiclass
    clus
vv   DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE
  T1                            60                              15
  T2                            41                              10
  T3                             3                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1+N2
  DEL PEAK 27(18P11.32) MUTATED   36    12
  DEL PEAK 27(18P11.32) WILD-TYPE 10     1
D42V5, multiclass
       clus
vv      DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE
  N0                               36                              10
  N1+N2                            12                               1
[1] 2 2
[1] FALSE
D42V6, binary
                                 cls
clus                               0  1
  DEL PEAK 27(18P11.32) MUTATED   89  3
  DEL PEAK 27(18P11.32) WILD-TYPE 25  1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(18P11.32) MUTATED     89    3
  DEL PEAK 27(18P11.32) WILD-TYPE   25    1
   clus
vv  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE
  0                            89                              25
  1                             3                               1
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(18P11.32) MUTATED       3                         6    93
  DEL PEAK 27(18P11.32) WILD-TYPE     1                         0    25
D42V7, multiclass
                           clus
vv                          DEL PEAK 27(18P11.32) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                93
                           clus
vv                          DEL PEAK 27(18P11.32) WILD-TYPE
  ASIAN                                                   1
  BLACK OR AFRICAN AMERICAN                               0
  WHITE                                                  25
[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"
D42V8, binary
                                 cls
clus                               0  1
  DEL PEAK 27(18P11.32) MUTATED    9 87
  DEL PEAK 27(18P11.32) WILD-TYPE  2 24
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(18P11.32) MUTATED      9   87
  DEL PEAK 27(18P11.32) WILD-TYPE    2   24
                        clus
vv                       DEL PEAK 27(18P11.32) MUTATED
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                            87
                        clus
vv                       DEL PEAK 27(18P11.32) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                              24
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 28(18Q22.2) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(18Q22.2) MUTATED   108   4
  DEL PEAK 28(18Q22.2) WILD-TYPE  21   0
  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE 
                           112                             21 
  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE 
                             4                              0 
$`DEL PEAK 28(18Q22.2) MUTATED`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       191.31        36.99        14.14        14.56        17.16 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG3 
        9.57        14.86        16.50        36.13        40.01        52.37 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       72.20        61.71        63.22        63.32        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.38        79.76        67.96        92.09        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
       59.64       106.39       115.00        59.28       124.57       128.94 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
       61.45       170.33        80.94        60.16        60.26        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP 
       59.90       125.69        59.74        59.80        59.80       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
        6.08       122.50       212.65        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
      131.21        70.59         2.73         0.10         4.83        20.68 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
       18.15         9.14        13.58         1.38        16.31         9.63 
TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       17.23         3.52        37.68        24.99        35.61        33.07 
TCGA-W4-A7U2 TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       41.52         4.90        24.26         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
       65.98         0.46        93.93        12.07         7.89        16.87 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43         8.32        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y 
       20.12         6.90        57.90        54.35        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        5.29         7.96        40.96         8.15        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0N 
       17.39        16.41        11.34        10.85 

$`DEL PEAK 28(18Q22.2) WILD-TYPE`
TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAGP TCGA-2G-AAH8 TCGA-2G-AAHA 
       40.70        36.89        71.24       120.62        61.84        98.53 
TCGA-2G-AAHN TCGA-2G-AAKH TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-SN-A84X 
       91.43       161.72         0.13         3.52         7.00        10.26 
TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AE TCGA-XE-AANV TCGA-XE-AAOC TCGA-YU-A90S 
       37.18        36.79        23.90        53.03         8.88        31.92 
TCGA-YU-A94D TCGA-ZM-AA05 TCGA-ZM-AA0H 
       58.88        37.02        46.88 

  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE 
                          0.10                           0.13 
  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE 
                        229.22                         161.72 
  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE 
                         37.99                          37.18 
[1] "0.1 - 229.2 (38.0)" "0.1 - 161.7 (37.2)"
[1] "hr="     "8.9e+07"
D43V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(18Q22.2) MUTATED        17       19        9        4         5
  DEL PEAK 28(18Q22.2) WILD-TYPE       2        6        2        1         1
                                vv
clus                             STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 28(18Q22.2) MUTATED           1         0         1          1
  DEL PEAK 28(18Q22.2) WILD-TYPE         0         1         1          0
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 28(18Q22.2) MUTATED            5          4       41
  DEL PEAK 28(18Q22.2) WILD-TYPE          1          1        5
D43V3, multiclass
            clus
vv           DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE
  STAGE I                              17                              2
  STAGE IA                             19                              6
  STAGE IB                              9                              2
  STAGE II                              4                              1
  STAGE IIA                             5                              1
  STAGE IIB                             1                              0
  STAGE IIC                             0                              1
  STAGE III                             1                              1
  STAGE IIIA                            1                              0
  STAGE IIIB                            5                              1
  STAGE IIIC                            4                              1
  STAGE IS                             41                              5
[1] 12  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
  DEL PEAK 28(18Q22.2) MUTATED   65 43  3
  DEL PEAK 28(18Q22.2) WILD-TYPE 10  8  3
D43V4, multiclass
    clus
vv   DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE
  T1                           65                             10
  T2                           43                              8
  T3                            3                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1+N2
  DEL PEAK 28(18Q22.2) MUTATED   39    12
  DEL PEAK 28(18Q22.2) WILD-TYPE  7     1
D43V5, multiclass
       clus
vv      DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE
  N0                              39                              7
  N1+N2                           12                              1
[1] 2 2
[1] FALSE
D43V6, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q22.2) MUTATED   96  3
  DEL PEAK 28(18Q22.2) WILD-TYPE 18  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q22.2) MUTATED     96    3
  DEL PEAK 28(18Q22.2) WILD-TYPE   18    1
   clus
vv  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE
  0                           96                             18
  1                            3                              1
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(18Q22.2) MUTATED       4                         6    99
  DEL PEAK 28(18Q22.2) WILD-TYPE     0                         0    19
D43V7, multiclass
                           clus
vv                          DEL PEAK 28(18Q22.2) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               99
                           clus
vv                          DEL PEAK 28(18Q22.2) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 19
[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"
D43V8, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q22.2) MUTATED    9 94
  DEL PEAK 28(18Q22.2) WILD-TYPE  2 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q22.2) MUTATED      9   94
  DEL PEAK 28(18Q22.2) WILD-TYPE    2   17
                        clus
vv                       DEL PEAK 28(18Q22.2) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                           94
                        clus
vv                       DEL PEAK 28(18Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             17
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 29(19Q13.41) MUTATION ANALYSIS
D44V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 29(19Q13.41) MUTATED   44  3
  DEL PEAK 29(19Q13.41) WILD-TYPE 85  1
  DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE 
                             47                              86 
  DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE 
                              3                               1 
$`DEL PEAK 29(19Q13.41) MUTATED`
TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG6 
       14.56         9.57        14.86        36.13        40.01        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGG 
       61.71        63.22        68.22        72.85        68.38        67.96 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH4 
       59.28       128.94        61.45       170.33        80.94       125.69 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
      122.50       212.65       161.72        95.67       229.22       131.21 
TCGA-2G-AALP TCGA-S6-A8JX TCGA-SN-A84W TCGA-SN-A84Y TCGA-VF-A8AD TCGA-W4-A7U3 
       70.59        18.15         9.63        17.23        33.07         4.90 
TCGA-W4-A7U4 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-AANI TCGA-XE-AAOB TCGA-XE-AAOJ 
       24.26        28.14         6.87        34.22        16.87        50.96 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Y TCGA-YU-AA4L 
       12.92        20.12        57.90         0.56        40.96 

$`DEL PEAK 29(19Q13.41) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFO 
      154.59       191.31        36.99        14.14        17.16        16.50 
TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG9 TCGA-2G-AAGF 
       40.70        36.89        52.37        71.24        63.32        79.76 
TCGA-2G-AAGI TCGA-2G-AAGT TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
       92.09       124.57        60.16        60.26        59.84        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       61.84        98.53        59.74        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAL5 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      176.15         6.08       184.41         2.73         0.13         3.52 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JY TCGA-SB-A6J6 
        7.00         0.10         4.83        20.68         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 
        1.38        16.31        10.26         3.52        37.18        36.79 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A7V3 
       37.68        24.99        35.61        23.90        41.52         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANJ 
        5.06         0.16         0.82        18.38        40.01        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOC 
        0.46        53.03        93.93        12.07         7.89         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90Q 
       67.66        41.69         0.43         8.32         6.90        54.35 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA61 
       31.92        21.96         5.29        58.88         7.96         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        39.35        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

  DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE 
                           0.56                            0.10 
  DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE 
                         229.22                          191.31 
  DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE 
                         61.450                          33.765 
[1] "0.6 - 229.2 (61.5)" "0.1 - 191.3 (33.8)"
[1] "hr=" "3"  
D44V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 29(19Q13.41) MUTATED         3        3        3        5         4
  DEL PEAK 29(19Q13.41) WILD-TYPE      16       22        8        0         2
                                 vv
clus                              STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 29(19Q13.41) MUTATED           0         0         1          0
  DEL PEAK 29(19Q13.41) WILD-TYPE         1         1         1          1
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 29(19Q13.41) MUTATED            4          3       19
  DEL PEAK 29(19Q13.41) WILD-TYPE          2          2       27
D44V3, multiclass
            clus
vv           DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE
  STAGE I                                3                              16
  STAGE IA                               3                              22
  STAGE IB                               3                               8
  STAGE II                               5                               0
  STAGE IIA                              4                               2
  STAGE IIB                              0                               1
  STAGE IIC                              0                               1
  STAGE III                              1                               1
  STAGE IIIA                             0                               1
  STAGE IIIB                             4                               2
  STAGE IIIC                             3                               2
  STAGE IS                              19                              27
[1] 12  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
  DEL PEAK 29(19Q13.41) MUTATED   23 22  2
  DEL PEAK 29(19Q13.41) WILD-TYPE 52 29  4
D44V4, multiclass
    clus
vv   DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE
  T1                            23                              52
  T2                            22                              29
  T3                             2                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1+N2
  DEL PEAK 29(19Q13.41) MUTATED   17     8
  DEL PEAK 29(19Q13.41) WILD-TYPE 29     5
D44V5, multiclass
       clus
vv      DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE
  N0                               17                              29
  N1+N2                             8                               5
[1] 2 2
[1] FALSE
D44V6, binary
                                 cls
clus                               0  1
  DEL PEAK 29(19Q13.41) MUTATED   41  2
  DEL PEAK 29(19Q13.41) WILD-TYPE 73  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.41) MUTATED     41    2
  DEL PEAK 29(19Q13.41) WILD-TYPE   73    2
   clus
vv  DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE
  0                            41                              73
  1                             2                               2
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(19Q13.41) MUTATED       1                         3    43
  DEL PEAK 29(19Q13.41) WILD-TYPE     3                         3    75
D44V7, multiclass
                           clus
vv                          DEL PEAK 29(19Q13.41) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                43
                           clus
vv                          DEL PEAK 29(19Q13.41) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               3
  WHITE                                                  75
[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"
D44V8, binary
                                 cls
clus                               0  1
  DEL PEAK 29(19Q13.41) MUTATED    4 39
  DEL PEAK 29(19Q13.41) WILD-TYPE  7 72
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.41) MUTATED      4   39
  DEL PEAK 29(19Q13.41) WILD-TYPE    7   72
                        clus
vv                       DEL PEAK 29(19Q13.41) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            39
                        clus
vv                       DEL PEAK 29(19Q13.41) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                              72
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 30(20P12.1) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(20P12.1) MUTATED    27   0
  DEL PEAK 30(20P12.1) WILD-TYPE 102   4
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            27                            106 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                             0                              4 
$`DEL PEAK 30(20P12.1) MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAFN TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGJ 
       59.70        14.86        72.20        61.71        63.32        75.09 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAH4 
      120.62        59.28        61.45       170.33        60.16       125.69 
TCGA-2G-AAL5 TCGA-2G-AALP TCGA-S6-A8JY TCGA-SN-A84Y TCGA-VF-A8AC TCGA-WZ-A7V3 
      184.41        70.59         9.14        17.23        35.61         3.65 
TCGA-XE-A8H1 TCGA-XE-AANJ TCGA-XE-AAO6 TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
        6.87        65.98         7.89        12.92        20.12         6.90 
TCGA-YU-A912 TCGA-ZM-AA0B TCGA-ZM-AA0N 
        5.29        27.55        10.85 

$`DEL PEAK 30(20P12.1) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFE 
       20.32        30.35        38.30       102.35       122.40       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       71.24        63.22        68.22        72.85        68.38        79.76 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       67.96        92.09       108.16        59.64       106.39       115.00 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
      124.57       128.94        80.94        60.26        59.84        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       61.84        98.53        59.74        59.80        59.80        91.43 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
      176.15         6.08       122.50       212.65       161.72        95.67 
TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      229.22       131.21         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C 
        0.10         4.83        20.68        18.15        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 
       16.31         9.63        10.26         3.52        37.18        36.79 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 
       37.68        24.99        33.07        23.90        41.52         4.90 
TCGA-W4-A7U4 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H4 
       24.26         5.06         0.16         0.82        28.14        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       40.01        34.22         0.46        53.03        93.93        12.07 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
       16.87         8.88        67.66        41.69        50.96         0.43 
TCGA-XY-A89B TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        8.32        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       17.39        16.41        11.34        46.88 

  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                          3.65                           0.10 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                        184.41                         229.22 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                         59.28                          37.43 
[1] "3.6 - 184.4 (59.3)" "0.1 - 229.2 (37.4)"
[1] "hr="     "2.5e+08"
D45V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(20P12.1) MUTATED         4        5        1        1         1
  DEL PEAK 30(20P12.1) WILD-TYPE      15       20       10        4         5
                                vv
clus                             STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 30(20P12.1) MUTATED           0         0         0          1
  DEL PEAK 30(20P12.1) WILD-TYPE         1         1         2          0
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 30(20P12.1) MUTATED            4          1        9
  DEL PEAK 30(20P12.1) WILD-TYPE          2          4       37
D45V3, multiclass
            clus
vv           DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  STAGE I                               4                             15
  STAGE IA                              5                             20
  STAGE IB                              1                             10
  STAGE II                              1                              4
  STAGE IIA                             1                              5
  STAGE IIB                             0                              1
  STAGE IIC                             0                              1
  STAGE III                             0                              2
  STAGE IIIA                            1                              0
  STAGE IIIB                            4                              2
  STAGE IIIC                            1                              4
  STAGE IS                              9                             37
[1] 12  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
  DEL PEAK 30(20P12.1) MUTATED   17 10  0
  DEL PEAK 30(20P12.1) WILD-TYPE 58 41  6
D45V4, multiclass
    clus
vv   DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  T1                           17                             58
  T2                           10                             41
  T3                            0                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1+N2
  DEL PEAK 30(20P12.1) MUTATED    7     5
  DEL PEAK 30(20P12.1) WILD-TYPE 39     8
D45V5, multiclass
       clus
vv      DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  N0                               7                             39
  N1+N2                            5                              8
[1] 2 2
[1] FALSE
D45V6, binary
                                cls
clus                              0  1
  DEL PEAK 30(20P12.1) MUTATED   23  2
  DEL PEAK 30(20P12.1) WILD-TYPE 91  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED     23    2
  DEL PEAK 30(20P12.1) WILD-TYPE   91    2
   clus
vv  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  0                           23                             91
  1                            2                              2
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(20P12.1) MUTATED       0                         2    25
  DEL PEAK 30(20P12.1) WILD-TYPE     4                         4    93
D45V7, multiclass
                           clus
vv                          DEL PEAK 30(20P12.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               25
                           clus
vv                          DEL PEAK 30(20P12.1) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 93
[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"
D45V8, binary
                                cls
clus                              0  1
  DEL PEAK 30(20P12.1) MUTATED    3 23
  DEL PEAK 30(20P12.1) WILD-TYPE  8 88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED      3   23
  DEL PEAK 30(20P12.1) WILD-TYPE    8   88
                        clus
vv                       DEL PEAK 30(20P12.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           23
                        clus
vv                       DEL PEAK 30(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                             88
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 31(XP21.1) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 31(XP21.1) MUTATED    23   0
  DEL PEAK 31(XP21.1) WILD-TYPE 106   4
  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE 
                           23                           110 
  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE 
                            0                             4 
$`DEL PEAK 31(XP21.1) MUTATED`
TCGA-2G-AAFJ TCGA-2G-AAG5 TCGA-2G-AAG7 TCGA-2G-AAGJ TCGA-2G-AAGO TCGA-2G-AAGV 
       14.56        71.24        61.71        75.09       115.00       128.94 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHG TCGA-2G-AAHP TCGA-2G-AAL5 TCGA-2X-A9D5 
       59.90       125.69        59.80       176.15       184.41         2.73 
TCGA-S6-A8JY TCGA-SN-A84W TCGA-SO-A8JP TCGA-W4-A7U2 TCGA-XE-AANI TCGA-XE-AANJ 
        9.14         9.63         3.52        41.52        34.22        65.98 
TCGA-XE-AAOJ TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA0N 
       50.96         5.29         7.96        40.96        10.85 

$`DEL PEAK 31(XP21.1) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       191.31        36.99        14.14        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       52.37        72.20        63.22        63.32        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM 
       68.38        79.76        67.96        92.09       108.16        59.64 
TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGX 
      106.39       120.62        59.28       124.57        61.45       170.33 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH8 TCGA-2G-AAHA 
       80.94        60.16        60.26        59.84        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.74        59.80        91.43         6.08       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D6 
      161.72        95.67       229.22       131.21        70.59         0.13 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
        3.52         7.00         0.10         4.83        20.68        18.15 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 
       13.58         1.38        16.31        10.26        17.23        37.18 
TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       36.79        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U3 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
        4.90        24.26         3.65         5.06         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANR TCGA-XE-AANV 
       28.14         6.87        18.38        40.01         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       41.69         0.43         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D 
       57.90        54.35        31.92        21.96         0.56        58.88 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
        8.15        37.02        39.35        27.55        17.39        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0H 
       11.34        46.88 

  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE 
                         2.73                          0.10 
  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE 
                       184.41                        229.22 
  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE 
                       50.960                        37.005 
[1] "2.7 - 184.4 (51.0)" "0.1 - 229.2 (37.0)"
[1] "hr="     "8.9e+07"
D46V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 31(XP21.1) MUTATED         6        2        1        2         0
  DEL PEAK 31(XP21.1) WILD-TYPE      13       23       10        3         6
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 31(XP21.1) MUTATED           0         0         0          0
  DEL PEAK 31(XP21.1) WILD-TYPE         1         1         2          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 31(XP21.1) MUTATED            0          2        9
  DEL PEAK 31(XP21.1) WILD-TYPE          6          3       37
D46V3, multiclass
            clus
vv           DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE
  STAGE I                              6                            13
  STAGE IA                             2                            23
  STAGE IB                             1                            10
  STAGE II                             2                             3
  STAGE IIA                            0                             6
  STAGE IIB                            0                             1
  STAGE IIC                            0                             1
  STAGE III                            0                             2
  STAGE IIIA                           0                             1
  STAGE IIIB                           0                             6
  STAGE IIIC                           2                             3
  STAGE IS                             9                            37
[1] 12  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
  DEL PEAK 31(XP21.1) MUTATED   17  6  0
  DEL PEAK 31(XP21.1) WILD-TYPE 58 45  6
D46V4, multiclass
    clus
vv   DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE
  T1                          17                            58
  T2                           6                            45
  T3                           0                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  DEL PEAK 31(XP21.1) MUTATED    9     0
  DEL PEAK 31(XP21.1) WILD-TYPE 37    13
D46V5, multiclass
       clus
vv      DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE
  N0                              9                            37
  N1+N2                           0                            13
[1] 2 2
[1] FALSE
D46V6, binary
                               cls
clus                             0  1
  DEL PEAK 31(XP21.1) MUTATED   19  0
  DEL PEAK 31(XP21.1) WILD-TYPE 95  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 31(XP21.1) MUTATED     19    0
  DEL PEAK 31(XP21.1) WILD-TYPE   95    4
   clus
vv  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE
  0                          19                            95
  1                           0                             4
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(XP21.1) MUTATED       1                         3    18
  DEL PEAK 31(XP21.1) WILD-TYPE     3                         3   100
D46V7, multiclass
                           clus
vv                          DEL PEAK 31(XP21.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              18
                           clus
vv                          DEL PEAK 31(XP21.1) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                               100
[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"
D46V8, binary
                               cls
clus                             0  1
  DEL PEAK 31(XP21.1) MUTATED    3 17
  DEL PEAK 31(XP21.1) WILD-TYPE  8 94
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 31(XP21.1) MUTATED      3   17
  DEL PEAK 31(XP21.1) WILD-TYPE    8   94
                        clus
vv                       DEL PEAK 31(XP21.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          17
                        clus
vv                       DEL PEAK 31(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                            94
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 32(XQ27.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 32(XQ27.3) MUTATED    25   0
  DEL PEAK 32(XQ27.3) WILD-TYPE 104   4
  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE 
                           25                           108 
  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE 
                            0                             4 
$`DEL PEAK 32(XQ27.3) MUTATED`
TCGA-2G-AAF6 TCGA-2G-AAFE TCGA-2G-AAFJ TCGA-2G-AAG5 TCGA-2G-AAG7 TCGA-2G-AAGK 
      102.35       154.59        14.56        71.24        61.71       108.16 
TCGA-2G-AAGV TCGA-2G-AAGY TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHG TCGA-2G-AAHP 
      128.94        80.94        59.90       125.69        59.80       176.15 
TCGA-2G-AAHT TCGA-2G-AAL5 TCGA-2G-AALP TCGA-S6-A8JY TCGA-SN-A84W TCGA-W4-A7U2 
        6.08       184.41        70.59         9.14         9.63        41.52 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AAOJ TCGA-XY-A8S3 TCGA-YU-A912 
       40.01        34.22        65.98        50.96        20.12         5.29 
TCGA-YU-AA61 
        8.15 

$`DEL PEAK 32(XQ27.3) WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF8 TCGA-2G-AAFG 
       20.32        30.35        38.30        59.70       122.40       191.31 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
       36.99        14.14        17.16         9.57        14.86        16.50 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG6 
       40.70        36.13        36.89        40.01        52.37        72.20 
TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       63.22        63.32        68.22        72.85        68.38        79.76 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       67.96        92.09        75.09        59.64       106.39       115.00 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGZ 
      120.62        59.28       124.57        61.45       170.33        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL 
       60.26        59.84        61.84        98.53        59.74        59.80 
TCGA-2G-AAHN TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       91.43       122.50       212.65       161.72        95.67       229.22 
TCGA-2G-AAL7 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
      131.21         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
        4.83        20.68        18.15        13.58         1.38        16.31 
TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA 
       10.26        17.23         3.52        37.18        36.79        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U3 TCGA-W4-A7U4 
       24.99        35.61        33.07        23.90         4.90        24.26 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       18.38         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B 
       16.87         8.88        67.66        41.69         0.43         8.32 
TCGA-XY-A8S2 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       12.92         6.90        57.90        54.35        31.92        21.96 
TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA06 
        0.56        58.88         7.96        40.96        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE 
                         5.29                          0.10 
  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE 
                       184.41                        229.22 
  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE 
                        59.90                         36.84 
[1] "5.3 - 184.4 (59.9)" "0.1 - 229.2 (36.8)"
[1] "hr="     "2.6e+08"
D47V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(XQ27.3) MUTATED         4        0        0        2         1
  DEL PEAK 32(XQ27.3) WILD-TYPE      15       25       11        3         5
                               vv
clus                            STAGE IIB STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 32(XQ27.3) MUTATED           0         0         0          0
  DEL PEAK 32(XQ27.3) WILD-TYPE         1         1         2          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IS
  DEL PEAK 32(XQ27.3) MUTATED            1          1       15
  DEL PEAK 32(XQ27.3) WILD-TYPE          5          4       31
D47V3, multiclass
            clus
vv           DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE
  STAGE I                              4                            15
  STAGE IA                             0                            25
  STAGE IB                             0                            11
  STAGE II                             2                             3
  STAGE IIA                            1                             5
  STAGE IIB                            0                             1
  STAGE IIC                            0                             1
  STAGE III                            0                             2
  STAGE IIIA                           0                             1
  STAGE IIIB                           1                             5
  STAGE IIIC                           1                             4
  STAGE IS                            15                            31
[1] 12  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
  DEL PEAK 32(XQ27.3) MUTATED   17  8  0
  DEL PEAK 32(XQ27.3) WILD-TYPE 58 43  6
D47V4, multiclass
    clus
vv   DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE
  T1                          17                            58
  T2                           8                            43
  T3                           0                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1+N2
  DEL PEAK 32(XQ27.3) MUTATED   10     1
  DEL PEAK 32(XQ27.3) WILD-TYPE 36    12
D47V5, multiclass
       clus
vv      DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE
  N0                             10                            36
  N1+N2                           1                            12
[1] 2 2
[1] FALSE
D47V6, binary
                               cls
clus                             0  1
  DEL PEAK 32(XQ27.3) MUTATED   21  1
  DEL PEAK 32(XQ27.3) WILD-TYPE 93  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 32(XQ27.3) MUTATED     21    1
  DEL PEAK 32(XQ27.3) WILD-TYPE   93    3
   clus
vv  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE
  0                          21                            93
  1                           1                             3
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(XQ27.3) MUTATED       1                         1    22
  DEL PEAK 32(XQ27.3) WILD-TYPE     3                         5    96
D47V7, multiclass
                           clus
vv                          DEL PEAK 32(XQ27.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              22
                           clus
vv                          DEL PEAK 32(XQ27.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                96
[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"
D47V8, binary
                               cls
clus                             0  1
  DEL PEAK 32(XQ27.3) MUTATED    4 19
  DEL PEAK 32(XQ27.3) WILD-TYPE  7 92
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 32(XQ27.3) MUTATED      4   19
  DEL PEAK 32(XQ27.3) WILD-TYPE    7   92
                        clus
vv                       DEL PEAK 32(XQ27.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          19
                        clus
vv                       DEL PEAK 32(XQ27.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            92
[1] 2 2
[1] FALSE
