[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/19775566/TGCT-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/TGCT-TP/19781845/transformed.cor.cli.txt"

nPatients in clinical file=134, in cluster file=150, common to both=134
[1]  47 134
[1] "AMP PEAK  1(1Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                           63                            71 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                           63                            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                            81 
  AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE 
                           53                            81 
[1] "AMP PEAK  3(3Q27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                           41                            93 
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                           41                            93 
[1] "AMP PEAK  4(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                         19                         115 
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                         19                         115 
[1] "AMP PEAK  5(7P22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE 
                          116                            18 
  AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE 
                          116                            18 
[1] "AMP PEAK  6(7Q11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE 
                           110                             24 
  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE 
                           110                             24 
[1] "AMP PEAK  7(8Q11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE 
                           114                             20 
  AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE 
                           114                             20 
[1] "AMP PEAK  8(8Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE 
                          101                            33 
  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE 
                          101                            33 
[1] "AMP PEAK  9(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE 
                            129                               5 
  AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE 
                            129                               5 
[1] "AMP PEAK 10(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE 
                           131                              3 
  AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE 
                           131                              3 
[1] "AMP PEAK 11(12P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(12P11.21) MUTATED AMP PEAK 11(12P11.21) WILD-TYPE 
                            128                               6 
  AMP PEAK 11(12P11.21) MUTATED AMP PEAK 11(12P11.21) WILD-TYPE 
                            128                               6 
[1] "AMP PEAK 12(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                          90                           44 
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                          90                           44 
[1] "AMP PEAK 13(16Q21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE 
                          19                          115 
  AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE 
                          19                          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                              93 
  AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE 
                             41                              93 
[1] "AMP PEAK 15(22Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE 
                             54                              80 
  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE 
                             54                              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                            105 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            29                            105 
[1] "DEL PEAK  2(1P31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                           26                           108 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                           26                           108 
[1] "DEL PEAK  3(1Q42.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE 
                             9                            125 
  DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE 
                             9                            125 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           13                           121 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           13                           121 
[1] "DEL PEAK  5(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE 
                           40                            94 
  DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE 
                           40                            94 
[1] "DEL PEAK  6(4Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE 
                          100                            34 
  DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE 
                          100                            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                            43 
  DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE 
                           91                            43 
[1] "DEL PEAK  8(5P14.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE 
                           93                            41 
  DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE 
                           93                            41 
[1] "DEL PEAK  9(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           95                            39 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           95                            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                           115 
  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE 
                           19                           115 
[1] "DEL PEAK 11(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                         22                         112 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                         22                         112 
[1] "DEL PEAK 12(7Q11.22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE 
                             3                            131 
  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE 
                             3                            131 
[1] "DEL PEAK 13(7Q36.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE 
                           14                           120 
  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE 
                           14                           120 
[1] "DEL PEAK 14(9P24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE 
                           63                            71 
  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE 
                           63                            71 
[1] "DEL PEAK 15(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                         59                          75 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                         59                          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                            82 
  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE 
                           52                            82 
[1] "DEL PEAK 17(9Q34.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE 
                           52                            82 
  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE 
                           52                            82 
[1] "DEL PEAK 18(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                            72                             62 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                            72                             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                             72 
  DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE 
                            62                             72 
[1] "DEL PEAK 20(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                            66                             68 
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                            66                             68 
[1] "DEL PEAK 21(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                            85                             49 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                            85                             49 
[1] "DEL PEAK 22(11P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE 
                          90                           44 
  DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE 
                          90                           44 
[1] "DEL PEAK 23(11Q12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE 
                           104                             30 
  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE 
                           104                             30 
[1] "DEL PEAK 24(11Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE 
                           110                             24 
  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE 
                           110                             24 
[1] "DEL PEAK 25(13Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                         102                           32 
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                         102                           32 
[1] "DEL PEAK 26(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            61                             73 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            61                             73 
[1] "DEL PEAK 27(18P11.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE 
                            106                              28 
  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE 
                            106                              28 
[1] "DEL PEAK 28(18Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE 
                           113                             21 
  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE 
                           113                             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                              87 
  DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE 
                             47                              87 
[1] "DEL PEAK 30(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            27                            107 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            27                            107 
[1] "DEL PEAK 31(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE 
                           23                           111 
  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE 
                           23                           111 
[1] "DEL PEAK 32(XQ27.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE 
                           25                           109 
  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE 
                           25                           109 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "KARNOFSKY_PERFORMANCE_SCORE"         
[14] "RACE"                                
[15] "ETHNICITY"                           

Input Data has 15 rows and 134 columns.

[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=131,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=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:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 134 columns, 1 survival variables, and 9 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
[3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
[5] "PATHOLOGY_M_STAGE"           "RADIATION_THERAPY"          
[7] "KARNOFSKY_PERFORMANCE_SCORE" "RACE"                       
[9] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=38, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 
76 51  6 
[1] "table(vv)"
vv
T1 T2 T3 
76 51  6 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 
76 51  6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T1 T2 T3 
76 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
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=3, 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   61  2
  AMP PEAK  1(1Q21.2) WILD-TYPE 69  2
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                           63                            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        41.39        76.11       128.58        45.21        22.19 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAG0 
       16.54        14.86        22.52        45.67        36.13        50.27 
TCGA-2G-AAG3 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGI 
       52.37        73.35        81.37        81.47        85.84        92.09 
TCGA-2G-AAGK TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAH2 
      119.05       132.10       158.33       161.06       175.20       199.23 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHT TCGA-2G-AAKM TCGA-2G-AAL5 
       73.91       110.10        59.80        17.82       229.22       244.50 
TCGA-2G-AAL7 TCGA-4K-AA1G TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X 
      131.21        14.33         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-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AAO3 
        6.87        40.01        23.28        34.22        65.98        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOL TCGA-XY-A9T9 
       12.07         7.89         8.88        67.66         0.43         9.24 
TCGA-YU-A90P TCGA-YU-A90W TCGA-YU-A94D TCGA-YU-A94I TCGA-ZM-AA05 TCGA-ZM-AA06 
       68.02        36.59        71.24        17.62        37.02        49.25 
TCGA-ZM-AA0B TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        57.07        20.84 

$`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 
       46.13       114.77       154.59       203.28        14.56        24.66 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       44.48        75.58        75.25        73.45        80.19        84.99 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGT 
       89.88        96.59       127.92       120.20       132.36       144.85 
TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH4 
      148.83       181.28       172.04       180.07        59.90       204.16 
TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKG 
      182.10       232.80       211.89       186.31       208.44       216.92 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H 
      225.60       230.89        86.96        14.30        19.96        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SN-A84W 
        0.10        15.88        22.95        18.15        13.58         9.63 
TCGA-SO-A8JP TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U2 
       17.75        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        24.76         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        55.92        16.87        41.69        50.96        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90Y TCGA-YU-A912 
       22.09        27.72        64.57        31.92         0.56        28.47 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       51.72        28.41        27.88        26.66        22.39 

  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 
                        244.5                         232.8 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                        40.01                         41.69 
[1] "0.2 - 244.5 (40.0)" "0.1 - 232.8 (41.7)"
[1] "hr=" "1.1"
D1V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  1(1Q21.2) MUTATED         6       12        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                            12                            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   35 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                          35                            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   57  1
  AMP PEAK  1(1Q21.2) WILD-TYPE 58  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED     57    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                          57                            58
  1                           1                             3
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q21.2) MUTATED   50 11
  AMP PEAK  1(1Q21.2) WILD-TYPE 60  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED     50   11
  AMP PEAK  1(1Q21.2) WILD-TYPE   60    8
     clus
vv    AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  NO                           50                            60
  YES                          11                             8
[1] 2 2
[1] FALSE
D1V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q21.2) MUTATED       1                         1    58
  AMP PEAK  1(1Q21.2) WILD-TYPE     3                         5    61
D1V9, multiclass
                           clus
vv                          AMP PEAK  1(1Q21.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              58
                           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"
D1V10, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q21.2) MUTATED    9 50
  AMP PEAK  1(1Q21.2) WILD-TYPE  3 61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED      9   50
  AMP PEAK  1(1Q21.2) WILD-TYPE    3   61
                        clus
vv                       AMP PEAK  1(1Q21.2) MUTATED
  HISPANIC OR LATINO                               9
  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 78  3
  AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE 
                           53                            81 
  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 
       76.11       114.77       128.58        45.21        22.19        14.56 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG7 TCGA-2G-AAG8 
       22.52        45.67        44.48        52.37        81.37        75.25 
TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM 
       81.47        85.84        92.09        96.59       119.05       127.92 
TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAHC 
      132.10       144.85       161.06       175.20       199.23       182.10 
TCGA-2G-AAHP TCGA-2G-AAKL TCGA-4K-AA1G TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
      186.31       230.89        14.33        15.88        22.95        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        17.75        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        22.09        27.72        68.02 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-A94I TCGA-ZM-AA06 
       36.59         0.56        71.24        17.62        49.25 

$`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        41.39        46.13       154.59       203.28        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 
       16.54        14.86        36.13        50.27        75.58        73.35 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGN TCGA-2G-AAGO 
       73.45        80.19        84.99        89.88       120.20       132.36 
TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH3 
      158.33       148.83       181.28       172.04       180.07        59.90 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
      204.16        73.91       110.10        59.80       232.80       211.89 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM TCGA-2G-AAL5 
       17.82       208.44       216.92       225.60       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I 
      131.21        86.96        14.30        19.96        17.03         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-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
       24.76         0.82         6.87        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB TCGA-XE-AAOD 
        0.46        55.92        93.93        12.07        16.87        67.66 
TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A912 
       50.96        15.48         9.24        64.57        31.92        28.47 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
       51.72        28.41        37.02        27.55        27.88        26.66 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       22.39        57.07        20.84 

  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 
                       230.89                        244.50 
  AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE 
                        41.69                         41.39 
[1] "0.2 - 230.9 (41.7)" "0.1 - 244.5 (41.4)"
[1] "hr=" "1.6"
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       15        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                            15
  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 45 34  2
D2V4, multiclass
    clus
vv   AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE
  T1                          31                            45
  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 71  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P24.1) MUTATED     44    2
  AMP PEAK  2(2P24.1) WILD-TYPE   71    2
   clus
vv  AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE
  0                          44                            71
  1                           2                             2
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                             0  1
  AMP PEAK  2(2P24.1) MUTATED   41  9
  AMP PEAK  2(2P24.1) WILD-TYPE 69 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P24.1) MUTATED     41    9
  AMP PEAK  2(2P24.1) WILD-TYPE   69   10
     clus
vv    AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE
  NO                           41                            69
  YES                           9                            10
[1] 2 2
[1] FALSE
D2V8, continuous
                               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    74
D2V9, 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                                                74
[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"
D2V10, binary
                               cls
clus                             0  1
  AMP PEAK  2(2P24.1) MUTATED    3 45
  AMP PEAK  2(2P24.1) WILD-TYPE  9 66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P24.1) MUTATED      3   45
  AMP PEAK  2(2P24.1) WILD-TYPE    9   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                                 9
  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   40  1
  AMP PEAK  3(3Q27.3) WILD-TYPE 90  3
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                           41                            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 
       76.11        22.19        14.86        22.52        45.67        44.48 
TCGA-2G-AAG0 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       50.27        75.25        80.19        89.88        85.84        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGW TCGA-2G-AAGY 
       96.59       119.05       127.92       132.10       161.06       175.20 
TCGA-2G-AAHC TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-4K-AAAL TCGA-SB-A6J6 
      182.10       208.44       216.92       230.89        15.88        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        24.76         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A9SE TCGA-XE-AANJ TCGA-XE-AANV TCGA-XE-AAO6 TCGA-XE-AAOC 
        6.87        23.28        65.98        55.92         7.89         8.88 
TCGA-XY-A8S2 TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94I TCGA-ZM-AA0N 
       22.09        36.59         0.56        17.62        20.84 

$`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        41.39        46.13       114.77       128.58       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFY 
      203.28        45.21        14.56        24.66        16.54        36.13 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGC 
       52.37        75.58        73.35        81.37        73.45        84.99 
TCGA-2G-AAGE TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
       81.47       120.20       132.36       158.33       144.85       148.83 
TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      181.28       172.04       180.07       199.23        59.90       204.16 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       73.91       110.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKH TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
       17.82       225.60       229.22       244.50       131.21        86.96 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-S6-A8JW 
       14.30        19.96        14.33        17.03         0.10        22.95 
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 
       17.75        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        15.48        27.72 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A912 TCGA-YU-A94D 
        9.24        68.02        64.57        31.92        28.47        71.24 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       51.72        28.41        37.02        49.25        27.55        27.88 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       26.66        22.39        57.07 

  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 
                       230.89                        244.50 
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                        44.48                         41.39 
[1] "0.6 - 230.9 (44.5)" "0.1 - 244.5 (41.4)"
[1] "hr=" "1.2"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  3(3Q27.3) MUTATED         4        8        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                             8                            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   20 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                          20                            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   34  2
  AMP PEAK  3(3Q27.3) WILD-TYPE 81  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q27.3) MUTATED     34    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                          34                            81
  1                           2                             2
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                             0  1
  AMP PEAK  3(3Q27.3) MUTATED   36  4
  AMP PEAK  3(3Q27.3) WILD-TYPE 74 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q27.3) MUTATED     36    4
  AMP PEAK  3(3Q27.3) WILD-TYPE   74   15
     clus
vv    AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  NO                           36                            74
  YES                           4                            15
[1] 2 2
[1] FALSE
D3V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(3Q27.3) MUTATED       0                         2    37
  AMP PEAK  3(3Q27.3) WILD-TYPE     4                         4    82
D3V9, multiclass
                           clus
vv                          AMP PEAK  3(3Q27.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              37
                           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"
D3V10, binary
                               cls
clus                             0  1
  AMP PEAK  3(3Q27.3) MUTATED    5 32
  AMP PEAK  3(3Q27.3) WILD-TYPE  7 79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q27.3) MUTATED      5   32
  AMP PEAK  3(3Q27.3) WILD-TYPE    7   79
                        clus
vv                       AMP PEAK  3(3Q27.3) MUTATED
  HISPANIC OR LATINO                               5
  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 111   4
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                         19                         115 
  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 
      128.58       154.59       203.28        22.52        52.37        73.35 
TCGA-2G-AAGO TCGA-2G-AAGW TCGA-2G-AAHL TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2X-A9D5 
      132.36       161.06       232.80        17.82       208.44        14.30 
TCGA-4K-AAAL TCGA-S6-A8JY TCGA-SN-A6IS TCGA-XE-AAOL TCGA-XY-A9T9 TCGA-YU-A90P 
       15.88         9.14        16.31         0.43         9.24        68.02 
TCGA-ZM-AA0N 
       20.84 

$`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        41.39        46.13        76.11       114.77        45.21 
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFV 
       22.19        14.56        24.66        16.54        14.86        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        50.27        75.58        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGP 
       92.09        96.59       119.05       127.92       120.20       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      158.33       144.85       148.83       181.28       175.20       172.04 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
      180.07       199.23        59.90       204.16        73.91       110.10 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKG TCGA-2G-AAKH 
      182.10        59.80       211.89       186.31       216.92       225.60 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D6 
      230.89       229.22       244.50       131.21        86.96        19.96 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 
       14.33        17.03         0.10        22.95        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        17.75        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        24.76         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE 
        0.82        28.14         6.87        18.38        40.01        23.28 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        55.92        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-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       15.48        22.09        27.72        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        49.25        27.55        27.88        26.66        22.39 
TCGA-ZM-AA0H 
       57.07 

  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 
                      232.8                       244.5 
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                      52.37                       41.39 
[1] "0.4 - 232.8 (52.4)" "0.1 - 244.5 (41.4)"
[1] "hr="   "9e+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       24       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                          24
  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 65 43  6
D4V4, multiclass
    clus
vv   AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  T1                        11                          65
  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 97  4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(4Q12) MUTATED     18    0
  AMP PEAK  4(4Q12) WILD-TYPE   97    4
   clus
vv  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  0                        18                          97
  1                         0                           4
[1] 2 2
[1] FALSE
D4V7, binary
                             cls
clus                           0  1
  AMP PEAK  4(4Q12) MUTATED   13  5
  AMP PEAK  4(4Q12) WILD-TYPE 97 14
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(4Q12) MUTATED     13    5
  AMP PEAK  4(4Q12) WILD-TYPE   97   14
     clus
vv    AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  NO                         13                          97
  YES                         5                          14
[1] 2 2
[1] FALSE
D4V8, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(4Q12) MUTATED       0                         1    18
  AMP PEAK  4(4Q12) WILD-TYPE     4                         5   101
D4V9, 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                                             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"
D4V10, binary
                             cls
clus                           0  1
  AMP PEAK  4(4Q12) MUTATED    1 17
  AMP PEAK  4(4Q12) WILD-TYPE 11 94
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(4Q12) MUTATED      1   17
  AMP PEAK  4(4Q12) WILD-TYPE   11   94
                        clus
vv                       AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             1                          11
  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   113   3
  AMP PEAK  5(7P22.1) WILD-TYPE  17   1
  AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE 
                          116                            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        41.39        46.13        76.11       114.77       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
      203.28        45.21        14.56        24.66        16.54        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       22.52        45.67        36.13        44.48        50.27        52.37 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       73.35        81.37        75.25        73.45        80.19        84.99 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       81.47        89.88        85.84        92.09        96.59       119.05 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
      127.92       120.20       132.36       132.10       158.33       144.85 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH2 
      148.83       161.06       181.28       175.20       180.07       199.23 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL 
       59.90       204.16        73.91       110.10       182.10       232.80 
TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
      211.89        17.82       208.44       216.92       225.60       230.89 
TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I 
      229.22       131.21        86.96        19.96        14.33         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
       15.88        22.95        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        17.75        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 
       24.76         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        23.28        34.22         0.46        55.92 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XE-AAOL 
       93.93        12.07         7.89        67.66        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
       15.48        22.09        27.72         9.24        68.02        64.57 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L 
       31.92        36.59         0.56        28.47        17.62        51.72 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        49.25        27.55        27.88        26.66        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

$`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 
      128.58        22.19        75.58       172.04        59.80       186.31 
TCGA-2G-AAL5 TCGA-2X-A9D5 TCGA-4K-AA1H TCGA-SN-A84W TCGA-VF-A8AB TCGA-W4-A7U3 
      244.50        14.30        17.03         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        71.24        28.41 

  AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE 
                          0.1                           4.9 
  AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE 
                        232.8                         244.5 
  AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE 
                       41.455                        35.050 
[1] "0.1 - 232.8 (41.5)" "4.9 - 244.5 (35.0)"
[1] "hr=" "1.8"
D5V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  5(7P22.1) MUTATED        16       21       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                            21                             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   65 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                          65                            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   101   3
  AMP PEAK  5(7P22.1) WILD-TYPE  14   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P22.1) MUTATED    101    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                         101                            14
  1                           3                             1
[1] 2 2
[1] FALSE
D5V7, binary
                               cls
clus                             0  1
  AMP PEAK  5(7P22.1) MUTATED   96 15
  AMP PEAK  5(7P22.1) WILD-TYPE 14  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P22.1) MUTATED     96   15
  AMP PEAK  5(7P22.1) WILD-TYPE   14    4
     clus
vv    AMP PEAK  5(7P22.1) MUTATED AMP PEAK  5(7P22.1) WILD-TYPE
  NO                           96                            14
  YES                          15                             4
[1] 2 2
[1] FALSE
D5V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(7P22.1) MUTATED       3                         5   104
  AMP PEAK  5(7P22.1) WILD-TYPE     1                         1    15
D5V9, multiclass
                           clus
vv                          AMP PEAK  5(7P22.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                             104
                           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"
D5V10, binary
                               cls
clus                             0  1
  AMP PEAK  5(7P22.1) MUTATED    9 99
  AMP PEAK  5(7P22.1) WILD-TYPE  3 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P22.1) MUTATED      9   99
  AMP PEAK  5(7P22.1) WILD-TYPE    3   12
                        clus
vv                       AMP PEAK  5(7P22.1) MUTATED
  HISPANIC OR LATINO                               9
  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   107   3
  AMP PEAK  6(7Q11.22) WILD-TYPE  23   1
  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE 
                           110                             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        41.39        46.13        76.11       114.77       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      203.28        45.21        22.19        14.56        24.66        16.54 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        22.52        45.67        36.13        44.48        50.27 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       73.35        81.37        75.25        73.45        80.19        84.99 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       81.47        89.88        85.84        92.09        96.59       119.05 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW 
      120.20       132.36       132.10       144.85       148.83       161.06 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      181.28       175.20       180.07       199.23        59.90       204.16 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       73.91       110.10       182.10       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
       17.82       208.44       225.60       230.89       229.22       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AAAL TCGA-S6-A8JW 
       86.96        14.30        19.96        14.33        15.88        22.95 
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 
       17.75        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        24.76         5.06         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANJ 
       28.14         6.87        18.38        40.01        23.28        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOD 
        0.46        55.92        93.93        12.07         7.89        67.66 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Q 
        0.43        15.48        22.09        27.72        68.02        64.57 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L 
       31.92        36.59         0.56        28.47        17.62        51.72 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        49.25        27.55        27.88        26.66        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

$`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 
      128.58        52.37        75.58       127.92       158.33       172.04 
TCGA-2G-AAHG TCGA-2G-AAKG TCGA-2G-AAL5 TCGA-4K-AA1H TCGA-4K-AA1I TCGA-SN-A84W 
       59.80       216.92       244.50        17.03         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         9.24        71.24        28.41 

  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE 
                          0.16                           0.10 
  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE 
                         232.8                          244.5 
  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE 
                        41.455                         39.435 
[1] "0.2 - 232.8 (41.5)" "0.1 - 244.5 (39.4)"
[1] "hr=" "1.4"
D6V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  6(7Q11.22) MUTATED        16       19       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                             19                              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   59 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                           59                             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   95  3
  AMP PEAK  6(7Q11.22) WILD-TYPE 20  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(7Q11.22) MUTATED     95    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                           95                             20
  1                            3                              1
[1] 2 2
[1] FALSE
D6V7, binary
                                cls
clus                              0  1
  AMP PEAK  6(7Q11.22) MUTATED   90 15
  AMP PEAK  6(7Q11.22) WILD-TYPE 20  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(7Q11.22) MUTATED     90   15
  AMP PEAK  6(7Q11.22) WILD-TYPE   20    4
     clus
vv    AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE
  NO                            90                             20
  YES                           15                              4
[1] 2 2
[1] FALSE
D6V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(7Q11.22) MUTATED       3                         5    98
  AMP PEAK  6(7Q11.22) WILD-TYPE     1                         1    21
D6V9, multiclass
                           clus
vv                          AMP PEAK  6(7Q11.22) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               98
                           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"
D6V10, binary
                                cls
clus                              0  1
  AMP PEAK  6(7Q11.22) MUTATED    8 94
  AMP PEAK  6(7Q11.22) WILD-TYPE  4 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(7Q11.22) MUTATED      8   94
  AMP PEAK  6(7Q11.22) WILD-TYPE    4   17
                        clus
vv                       AMP PEAK  6(7Q11.22) MUTATED
  HISPANIC OR LATINO                                8
  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   110   4
  AMP PEAK  7(8Q11.23) WILD-TYPE  20   0
  AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE 
                           114                             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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFM 
      154.59       203.28        45.21        22.19        14.56        16.54 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 
       14.86        22.52        36.13        44.48        52.37        75.58 
TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       73.35        75.25        73.45        80.19        84.99        81.47 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       89.88        85.84        92.09       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      132.10       158.33       148.83       161.06       181.28       175.20 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
      180.07       199.23        59.90        73.91       110.10       182.10 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80       232.80       211.89       186.31        17.82       208.44 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2X-A9D5 
      216.92       225.60       230.89       229.22       131.21        14.30 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
       19.96        14.33         0.10        15.88        22.95        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 
       17.75        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        24.76         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE 
        0.82        28.14         6.87        18.38        40.01        23.28 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        55.92        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        7.89        16.87        41.69        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W 
       22.09        27.72         9.24        68.02        64.57        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
        0.56        28.47        71.24        28.41        37.02        49.25 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        27.88        26.66        22.39        57.07        20.84 

$`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 
       24.66        45.67        50.27        81.37        96.59       119.05 
TCGA-2G-AAGT TCGA-2G-AAGZ TCGA-2G-AAH4 TCGA-2G-AAL5 TCGA-2G-AALP TCGA-4K-AA1H 
      144.85       172.04       204.16       244.50        86.96        17.03 
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 
       17.62        51.72 

  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 
                         232.8                          244.5 
  AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE 
                        38.845                         50.995 
[1] "0.1 - 232.8 (38.8)" "4.9 - 244.5 (51.0)"
[1] "hr="     "2.5e+08"
D7V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  7(8Q11.23) MUTATED        18       21        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                             21                              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   65 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                           65                             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   101   2
  AMP PEAK  7(8Q11.23) WILD-TYPE  14   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q11.23) MUTATED    101    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                          101                             14
  1                            2                              2
[1] 2 2
[1] FALSE
D7V7, binary
                                cls
clus                              0  1
  AMP PEAK  7(8Q11.23) MUTATED   91 18
  AMP PEAK  7(8Q11.23) WILD-TYPE 19  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q11.23) MUTATED     91   18
  AMP PEAK  7(8Q11.23) WILD-TYPE   19    1
     clus
vv    AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE
  NO                            91                             19
  YES                           18                              1
[1] 2 2
[1] FALSE
D7V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(8Q11.23) MUTATED       4                         4   102
  AMP PEAK  7(8Q11.23) WILD-TYPE     0                         2    17
D7V9, multiclass
                           clus
vv                          AMP PEAK  7(8Q11.23) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                              102
                           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"
D7V10, binary
                                cls
clus                              0  1
  AMP PEAK  7(8Q11.23) MUTATED   10 97
  AMP PEAK  7(8Q11.23) WILD-TYPE  2 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q11.23) MUTATED     10   97
  AMP PEAK  7(8Q11.23) WILD-TYPE    2   14
                        clus
vv                       AMP PEAK  7(8Q11.23) MUTATED
  HISPANIC OR LATINO                               10
  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   97  4
  AMP PEAK  8(8Q23.3) WILD-TYPE 33  0
  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE 
                          101                            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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFI TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
      154.59       203.28        22.19        16.54        14.86        22.52 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 
       36.13        44.48        52.37        75.58        73.35        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       73.45        80.19        84.99        89.88        85.84        92.09 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
      127.92       120.20       132.36       132.10       158.33       144.85 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH8 
      148.83       161.06       181.28       199.23        59.90        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
       17.82       208.44       216.92       230.89       229.22       131.21 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
       14.30        19.96         0.10        15.88        22.95        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        17.75 
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        24.76         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANR TCGA-XE-AANV 
        6.87        18.38        40.01        23.28         0.46        55.92 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B 
       93.93        12.07        16.87        41.69         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W 
       22.09        27.72         9.24        68.02        64.57        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        0.56        28.47        71.24        37.02        49.25        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.88        26.66        22.39        57.07        20.84 

$`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 
       45.21        14.56        24.66        45.67        50.27        81.37 
TCGA-2G-AAGE TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
       81.47        96.59       119.05       175.20       172.04       180.07 
TCGA-2G-AAH4 TCGA-2G-AAKH TCGA-2G-AAL5 TCGA-2G-AALP TCGA-4K-AA1G TCGA-4K-AA1H 
      204.16       225.60       244.50        86.96        14.33        17.03 
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 
       17.62        51.72        28.41 

  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE 
                          0.1                           4.9 
  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE 
                        232.8                         244.5 
  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE 
                        37.68                         45.67 
[1] "0.1 - 232.8 (37.7)" "4.9 - 244.5 (45.7)"
[1] "hr="     "2.8e+08"
D8V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  8(8Q23.3) MUTATED        17       20        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                            20                             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   54 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                          54                            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   90  2
  AMP PEAK  8(8Q23.3) WILD-TYPE 25  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q23.3) MUTATED     90    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                          90                            25
  1                           2                             2
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                             0  1
  AMP PEAK  8(8Q23.3) MUTATED   79 17
  AMP PEAK  8(8Q23.3) WILD-TYPE 31  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q23.3) MUTATED     79   17
  AMP PEAK  8(8Q23.3) WILD-TYPE   31    2
     clus
vv    AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE
  NO                           79                            31
  YES                          17                             2
[1] 2 2
[1] FALSE
D8V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(8Q23.3) MUTATED       3                         4    90
  AMP PEAK  8(8Q23.3) WILD-TYPE     1                         2    29
D8V9, multiclass
                           clus
vv                          AMP PEAK  8(8Q23.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              90
                           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"
D8V10, binary
                               cls
clus                             0  1
  AMP PEAK  8(8Q23.3) MUTATED    8 87
  AMP PEAK  8(8Q23.3) WILD-TYPE  4 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q23.3) MUTATED      8   87
  AMP PEAK  8(8Q23.3) WILD-TYPE    4   24
                        clus
vv                       AMP PEAK  8(8Q23.3) MUTATED
  HISPANIC OR LATINO                               8
  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   125   4
  AMP PEAK  9(12P13.33) WILD-TYPE   5   0
  AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE 
                            129                               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        41.39        46.13        76.11       114.77       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      203.28        45.21        22.19        14.56        24.66        16.54 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        22.52        45.67        36.13        44.48        50.27 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C 
        0.10        15.88        22.95        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        17.75        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        24.76         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE 
        0.82        28.14         6.87        18.38        40.01        23.28 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        55.92        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-A90P 
        0.43        15.48        22.09        27.72         9.24        68.02 
TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       64.57        36.59         0.56        28.47        71.24        17.62 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0E 
       51.72        28.41        37.02        49.25        27.55        26.66 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       22.39        57.07        20.84 

$`AMP PEAK  9(12P13.33) WILD-TYPE`
TCGA-2G-AAF8 TCGA-4K-AA1H TCGA-S6-A8JY TCGA-YU-A90S TCGA-ZM-AA0D 
      128.58        17.03         9.14        31.92        27.88 

  AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE 
                           0.10                            9.14 
  AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE 
                         244.50                          128.58 
  AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE 
                          41.69                           27.88 
[1] "0.1 - 244.5 (41.7)" "9.1 - 128.6 (27.9)"
[1] "hr="     "2.6e+07"
D9V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(12P13.33) MUTATED        19       22       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                              22                               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   72 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                            72                               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   111   4
  AMP PEAK  9(12P13.33) WILD-TYPE   4   0
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  9(12P13.33) MUTATED    111    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                           111                               4
  1                             4                               0
[1] 2 2
[1] FALSE
D9V7, binary
                                 cls
clus                                0   1
  AMP PEAK  9(12P13.33) MUTATED   107  17
  AMP PEAK  9(12P13.33) WILD-TYPE   3   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  9(12P13.33) MUTATED    107   17
  AMP PEAK  9(12P13.33) WILD-TYPE    3    2
     clus
vv    AMP PEAK  9(12P13.33) MUTATED AMP PEAK  9(12P13.33) WILD-TYPE
  NO                            107                               3
  YES                            17                               2
[1] 2 2
[1] FALSE
D9V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(12P13.33) MUTATED       4                         6   114
  AMP PEAK  9(12P13.33) WILD-TYPE     0                         0     5
D9V9, multiclass
                           clus
vv                          AMP PEAK  9(12P13.33) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               114
                           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"
D9V10, binary
                                 cls
clus                                0   1
  AMP PEAK  9(12P13.33) MUTATED    12 107
  AMP PEAK  9(12P13.33) WILD-TYPE   0   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  9(12P13.33) MUTATED     12  107
  AMP PEAK  9(12P13.33) WILD-TYPE    0    4
                        clus
vv                       AMP PEAK  9(12P13.33) MUTATED
  HISPANIC OR LATINO                                12
  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   127   4
  AMP PEAK 10(12P12.1) WILD-TYPE   3   0
  AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE 
                           131                              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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       203.28        45.21        22.19        14.56        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
       16.54        14.86        22.52        45.67        36.13        44.48 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       50.27        52.37        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       92.09        96.59       119.05       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      132.10       158.33       144.85       148.83       161.06       181.28 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      175.20       172.04       180.07       199.23        59.90       204.16 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       73.91       110.10       182.10        59.80       232.80       211.89 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
      186.31        17.82       208.44       216.92       225.60       230.89 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
      229.22       244.50       131.21        86.96        14.30        19.96 
TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       14.33         0.10        15.88        22.95        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 
       17.75        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        24.76 
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-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       40.01        23.28        34.22        65.98         0.46        55.92 
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        15.48        22.09        27.72 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
        9.24        68.02        64.57        36.59         0.56        28.47 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       71.24        17.62        51.72        28.41        37.02        49.25 
TCGA-ZM-AA0B TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        26.66        22.39        57.07        20.84 

$`AMP PEAK 10(12P12.1) WILD-TYPE`
TCGA-4K-AA1H TCGA-YU-A90S TCGA-ZM-AA0D 
       17.03        31.92        27.88 

  AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE 
                          0.10                          17.03 
  AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE 
                        244.50                          31.92 
  AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE 
                         41.69                          27.88 
[1] "0.1 - 244.5 (41.7)" "17.0 - 31.9 (27.9)"
[1] "hr="     "9200000"
D10V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(12P12.1) MUTATED        19       23       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                             23                              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   74 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                           74                              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   113   4
  AMP PEAK 10(12P12.1) WILD-TYPE   2   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(12P12.1) MUTATED    113    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                          113                              2
  1                            4                              0
[1] 2 2
[1] FALSE
D10V7, binary
                                cls
clus                               0   1
  AMP PEAK 10(12P12.1) MUTATED   108  18
  AMP PEAK 10(12P12.1) WILD-TYPE   2   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(12P12.1) MUTATED    108   18
  AMP PEAK 10(12P12.1) WILD-TYPE    2    1
     clus
vv    AMP PEAK 10(12P12.1) MUTATED AMP PEAK 10(12P12.1) WILD-TYPE
  NO                           108                              2
  YES                           18                              1
[1] 2 2
[1] FALSE
D10V8, continuous
[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 
                            96                              2 
                  TCGA-2G-AAEX                   TCGA-2G-AAF1 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAF4                   TCGA-2G-AAF6 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAF8                   TCGA-2G-AAFE 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAFG                   TCGA-2G-AAFH 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAFI                   TCGA-2G-AAFJ 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAFL                   TCGA-2G-AAFM 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAFN                   TCGA-2G-AAFO 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAFV                   TCGA-2G-AAFY 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAFZ                   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-AAGT                   TCGA-2G-AAGV 
"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-AAH0                   TCGA-2G-AAH2 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAH3                   TCGA-2G-AAH4 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAH8                   TCGA-2G-AAHA 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAHC                   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-AAKD                   TCGA-2G-AAKG 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAKH                   TCGA-2G-AAKL 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAKM                   TCGA-2G-AAL5 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2G-AAL7                   TCGA-2G-AALP 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-2X-A9D5                   TCGA-2X-A9D6 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-4K-AA1G                   TCGA-4K-AAAL 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-S6-A8JW                   TCGA-S6-A8JX 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-SB-A6J6                   TCGA-SB-A76C 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-SN-A84Y                   TCGA-SO-A8JP 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-WZ-A7V3                   TCGA-XE-A8H1 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-XE-A8H4                   TCGA-XE-A8H5 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-XE-A9SE                   TCGA-XE-AANI 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-XE-AANJ                   TCGA-XE-AANR 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-XE-AANV                   TCGA-XE-AAO3 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-XE-AAO4                   TCGA-XE-AAO6 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-XE-AAOC                   TCGA-XE-AAOD 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-XE-AAOF                   TCGA-XE-AAOJ 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-XE-AAOL                   TCGA-ZM-AA05 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-ZM-AA06                   TCGA-ZM-AA0B 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-ZM-AA0E                   TCGA-ZM-AA0F 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                  TCGA-ZM-AA0H                   TCGA-ZM-AA0N 
"AMP PEAK 10(12P12.1) MUTATED" "AMP PEAK 10(12P12.1) MUTATED" 
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(12P12.1) MUTATED       4                         6   116
  AMP PEAK 10(12P12.1) WILD-TYPE     0                         0     3
D10V9, multiclass
                           clus
vv                          AMP PEAK 10(12P12.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                              116
                           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"
D10V10, binary
                                cls
clus                               0   1
  AMP PEAK 10(12P12.1) MUTATED    12 109
  AMP PEAK 10(12P12.1) WILD-TYPE   0   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(12P12.1) MUTATED     12  109
  AMP PEAK 10(12P12.1) WILD-TYPE    0    2
                        clus
vv                       AMP PEAK 10(12P12.1) MUTATED
  HISPANIC OR LATINO                               12
  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   124   4
  AMP PEAK 11(12P11.21) WILD-TYPE   6   0
  AMP PEAK 11(12P11.21) MUTATED AMP PEAK 11(12P11.21) WILD-TYPE 
                            128                               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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       203.28        45.21        22.19        14.56        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
       16.54        14.86        22.52        45.67        36.13        44.48 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       50.27        52.37        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       92.09        96.59       119.05       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      132.10       158.33       144.85       148.83       161.06       181.28 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      175.20       172.04       180.07       199.23        59.90       204.16 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       73.91       110.10       182.10        59.80       232.80       211.89 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
      186.31        17.82       208.44       216.92       225.60       230.89 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
      229.22       244.50       131.21        86.96        14.30        19.96 
TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 
       14.33         0.10        15.88        22.95        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        17.75 
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        24.76         5.06 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE 
        0.82        28.14         6.87        18.38        40.01        23.28 
TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       34.22         0.46        55.92        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 
       15.48        22.09        27.72         9.24        68.02        64.57 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       36.59         0.56        28.47        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0E TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        26.66        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

$`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 
       17.03         9.14         0.16        65.98        31.92        27.88 

  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 
                         244.50                           65.98 
  AMP PEAK 11(12P11.21) MUTATED AMP PEAK 11(12P11.21) WILD-TYPE 
                         43.085                          22.455 
[1] "0.1 - 244.5 (43.1)" "0.2 - 66.0 (22.5)" 
[1] "hr="     "2.6e+07"
D11V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 11(12P11.21) MUTATED        18       23       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                              23                               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   73 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                            73                               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   111   4
  AMP PEAK 11(12P11.21) WILD-TYPE   4   0
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P11.21) MUTATED    111    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                           111                               4
  1                             4                               0
[1] 2 2
[1] FALSE
D11V7, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P11.21) MUTATED   106  18
  AMP PEAK 11(12P11.21) WILD-TYPE   4   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P11.21) MUTATED    106   18
  AMP PEAK 11(12P11.21) WILD-TYPE    4    1
     clus
vv    AMP PEAK 11(12P11.21) MUTATED AMP PEAK 11(12P11.21) WILD-TYPE
  NO                            106                               4
  YES                            18                               1
[1] 2 2
[1] FALSE
D11V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(12P11.21) MUTATED       4                         6   113
  AMP PEAK 11(12P11.21) WILD-TYPE     0                         0     6
D11V9, multiclass
                           clus
vv                          AMP PEAK 11(12P11.21) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               113
                           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"
D11V10, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P11.21) MUTATED    11 107
  AMP PEAK 11(12P11.21) WILD-TYPE   1   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P11.21) MUTATED     11  107
  AMP PEAK 11(12P11.21) WILD-TYPE    1    4
                        clus
vv                       AMP PEAK 11(12P11.21) MUTATED
  HISPANIC OR LATINO                                11
  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   88  2
  AMP PEAK 12(12Q15) WILD-TYPE 42  2
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                          90                           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 
       41.39        46.13        76.11       128.58       154.59        45.21 
TCGA-2G-AAFI TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
       22.19        14.86        22.52        45.67        36.13        44.48 
TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       50.27        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       80.19        81.47        89.88        85.84        92.09        96.59 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW 
      127.92       120.20       132.10       158.33       144.85       161.06 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      181.28       175.20       180.07       199.23        59.90       204.16 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKH 
       73.91       110.10       182.10       211.89       186.31       225.60 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
      230.89       229.22       131.21        86.96        14.30        19.96 
TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 
       14.33         0.10        15.88        22.95        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        17.75        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-A9SE TCGA-XE-AANV TCGA-XE-AAO3 
       28.14         6.87        40.01        23.28        55.92        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOL TCGA-XY-A8S2 
       12.07         7.89         8.88        67.66         0.43        22.09 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I 
       68.02        64.57        36.59         0.56        28.47        17.62 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       37.02        49.25        27.55        22.39        57.07        20.84 

$`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       114.77       203.28        14.56        24.66        16.54 
TCGA-2G-AAG3 TCGA-2G-AAGC TCGA-2G-AAGK TCGA-2G-AAGO TCGA-2G-AAGV TCGA-2G-AAGZ 
       52.37        84.99       119.05       132.36       148.83       172.04 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAL5 
       59.80       232.80        17.82       208.44       216.92       244.50 
TCGA-4K-AA1H TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-VF-A8AC 
       17.03         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        24.76         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        15.48 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90S TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 
       27.72         9.24        31.92        71.24        51.72        28.41 
TCGA-ZM-AA0D TCGA-ZM-AA0E 
       27.88        26.66 

  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 
                      230.89                       244.50 
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                      45.900                       28.145 
[1] "0.1 - 230.9 (45.9)" "0.5 - 244.5 (28.1)"
[1] "hr=" "1.8"
D12V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(12Q15) MUTATED        11       18       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                           18                            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   49 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                         49                           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   79  3
  AMP PEAK 12(12Q15) WILD-TYPE 36  1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(12Q15) MUTATED     79    3
  AMP PEAK 12(12Q15) WILD-TYPE   36    1
   clus
vv  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE
  0                         79                           36
  1                          3                            1
[1] 2 2
[1] FALSE
D12V7, binary
                              cls
clus                            0  1
  AMP PEAK 12(12Q15) MUTATED   77 10
  AMP PEAK 12(12Q15) WILD-TYPE 33  9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(12Q15) MUTATED     77   10
  AMP PEAK 12(12Q15) WILD-TYPE   33    9
     clus
vv    AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE
  NO                          77                           33
  YES                         10                            9
[1] 2 2
[1] FALSE
D12V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(12Q15) MUTATED       2                         5    79
  AMP PEAK 12(12Q15) WILD-TYPE     2                         1    40
D12V9, multiclass
                           clus
vv                          AMP PEAK 12(12Q15) MUTATED
  ASIAN                                              2
  BLACK OR AFRICAN AMERICAN                          5
  WHITE                                             79
                           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"
D12V10, binary
                              cls
clus                            0  1
  AMP PEAK 12(12Q15) MUTATED    7 77
  AMP PEAK 12(12Q15) WILD-TYPE  5 34
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(12Q15) MUTATED      7   77
  AMP PEAK 12(12Q15) WILD-TYPE    5   34
                        clus
vv                       AMP PEAK 12(12Q15) MUTATED
  HISPANIC OR LATINO                              7
  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    18   1
  AMP PEAK 13(16Q21) WILD-TYPE 112   3
  AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE 
                          19                          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 
       76.11        45.21        22.19        75.58        73.35        81.47 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAH2 TCGA-SN-A84X 
       85.84        92.09       127.92       144.85       199.23        10.26 
TCGA-SN-A84Y TCGA-X3-A8G4 TCGA-XE-A9SE TCGA-XE-AAOC TCGA-YU-A90P TCGA-YU-A90Y 
       17.23        28.14        23.28         8.88        68.02         0.56 
TCGA-ZM-AA06 
       49.25 

$`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        41.39        46.13       114.77       128.58       154.59 
TCGA-2G-AAFG TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
      203.28        14.56        24.66        16.54        14.86        22.52 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG7 
       45.67        36.13        44.48        50.27        52.37        81.37 
TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGJ 
       75.25        73.45        80.19        84.99        89.88        96.59 
TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV 
      119.05       120.20       132.36       132.10       158.33       148.83 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH3 
      161.06       181.28       175.20       172.04       180.07        59.90 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL 
      204.16        73.91       110.10       182.10        59.80       232.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
      211.89       186.31        17.82       208.44       216.92       225.60 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
      230.89       229.22       244.50       131.21        86.96        14.30 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
       19.96        14.33        17.03         0.10        15.88        22.95 
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 
       17.75        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        24.76 
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        55.92        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 
       15.48        22.09        27.72         9.24        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       36.59        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        27.55        27.88        26.66        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  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 
                      199.23                       244.50 
  AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE 
                       68.02                        37.68 
[1] "0.6 - 199.2 (68.0)" "0.1 - 244.5 (37.7)"
[1] "hr=" "2.9"
D13V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(16Q21) MUTATED         1        3        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                            3                           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   11  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                         11                           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   16  1
  AMP PEAK 13(16Q21) WILD-TYPE 99  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(16Q21) MUTATED     16    1
  AMP PEAK 13(16Q21) WILD-TYPE   99    3
   clus
vv  AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE
  0                         16                           99
  1                          1                            3
[1] 2 2
[1] FALSE
D13V7, binary
                              cls
clus                            0  1
  AMP PEAK 13(16Q21) MUTATED   17  2
  AMP PEAK 13(16Q21) WILD-TYPE 93 17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(16Q21) MUTATED     17    2
  AMP PEAK 13(16Q21) WILD-TYPE   93   17
     clus
vv    AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE
  NO                          17                           93
  YES                          2                           17
[1] 2 2
[1] FALSE
D13V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(16Q21) MUTATED       0                         1    18
  AMP PEAK 13(16Q21) WILD-TYPE     4                         5   101
D13V9, multiclass
                           clus
vv                          AMP PEAK 13(16Q21) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             18
                           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"
D13V10, binary
                              cls
clus                            0  1
  AMP PEAK 13(16Q21) MUTATED    4 13
  AMP PEAK 13(16Q21) WILD-TYPE  8 98
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(16Q21) MUTATED      4   13
  AMP PEAK 13(16Q21) WILD-TYPE    8   98
                        clus
vv                       AMP PEAK 13(16Q21) MUTATED
  HISPANIC OR LATINO                              4
  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 91  2
  AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE 
                             41                              93 
  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 
       22.19        44.48        52.37        75.58        73.35        75.25 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAH0 
       85.84        92.09       127.92       132.10       144.85       180.07 
TCGA-2G-AAH2 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHP TCGA-2G-AAKH TCGA-2G-AAKL 
      199.23        73.91       110.10       186.31       225.60       230.89 
TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-4K-AA1G TCGA-4K-AAAL TCGA-S6-A8JW TCGA-SB-A6J6 
      229.22       131.21        14.33        15.88        22.95        13.58 
TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-W4-A7U4 TCGA-WZ-A7V3 
       10.26        17.23        17.75        37.18        24.26        24.76 
TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-AAOC TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W 
        0.16        28.14         8.88        68.02        64.57        36.59 
TCGA-YU-A90Y TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA06 
        0.56        17.62        51.72        37.02        49.25 

$`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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       203.28        45.21        14.56        24.66        16.54 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG7 
       14.86        22.52        45.67        36.13        50.27        81.37 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGJ 
       73.45        80.19        84.99        81.47        89.88        96.59 
TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW 
      119.05       120.20       132.36       158.33       148.83       161.06 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC 
      181.28       175.20       172.04        59.90       204.16       182.10 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80       232.80       211.89        17.82       208.44       216.92 
TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I 
      244.50        86.96        14.30        19.96        17.03         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-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       23.28        34.22        65.98         0.46        55.92        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ 
       12.07         7.89        16.87        67.66        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90S 
        0.43        15.48        22.09        27.72         9.24        31.92 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA61 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
       28.47        71.24        28.41        27.55        27.88        26.66 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       22.39        57.07        20.84 

  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 
                         230.89                          244.50 
  AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE 
                          51.72                           37.68 
[1] "0.2 - 230.9 (51.7)" "0.1 - 244.5 (37.7)"
[1] "hr=" "1.8"
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       20        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                              20
  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 60 29  3
D14V4, multiclass
    clus
vv   AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE
  T1                            16                              60
  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 84  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(20Q11.21) MUTATED     31    2
  AMP PEAK 14(20Q11.21) WILD-TYPE   84    2
   clus
vv  AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE
  0                            31                              84
  1                             2                               2
[1] 2 2
[1] FALSE
D14V7, binary
                                 cls
clus                               0  1
  AMP PEAK 14(20Q11.21) MUTATED   38  2
  AMP PEAK 14(20Q11.21) WILD-TYPE 72 17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(20Q11.21) MUTATED     38    2
  AMP PEAK 14(20Q11.21) WILD-TYPE   72   17
     clus
vv    AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE
  NO                             38                              72
  YES                             2                              17
[1] 2 2
[1] FALSE
D14V8, continuous
                                 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    82
D14V9, 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                                                  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"
D14V10, binary
                                 cls
clus                               0  1
  AMP PEAK 14(20Q11.21) MUTATED    3 32
  AMP PEAK 14(20Q11.21) WILD-TYPE  9 79
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(20Q11.21) MUTATED      3   32
  AMP PEAK 14(20Q11.21) WILD-TYPE    9   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                                   9
  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   53  1
  AMP PEAK 15(22Q11.21) WILD-TYPE 77  3
  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE 
                             54                              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 
       41.39        76.11       114.77       203.28        45.21        22.19 
TCGA-2G-AAG3 TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGO TCGA-2G-AAH2 TCGA-2G-AAH8 
       52.37        92.09       119.05       132.36       199.23        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHN TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2X-A9D6 
      110.10       182.10       211.89       208.44       225.60        19.96 
TCGA-4K-AA1G TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
       14.33        15.88        22.95        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        17.75        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-A9SE TCGA-XE-AANJ TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOD 
       23.28        65.98        55.92        93.93         7.89        67.66 
TCGA-XE-AAOL TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90W TCGA-YU-A90Y 
        0.43        27.72         9.24        68.02        36.59         0.56 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0H TCGA-ZM-AA0N 
       51.72        28.41        49.25        27.55        57.07        20.84 

$`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        46.13       128.58       154.59        14.56        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
       16.54        14.86        22.52        45.67        36.13        44.48 
TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       50.27        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGJ 
       80.19        84.99        81.47        89.88        85.84        96.59 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
      127.92       120.20       132.10       158.33       144.85       148.83 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH3 
      161.06       181.28       175.20       172.04       180.07        59.90 
TCGA-2G-AAH4 TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKG 
      204.16        59.80       232.80       186.31        17.82       216.92 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
      230.89       229.22       244.50       131.21        86.96        14.30 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-SN-A84W TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB 
       17.03         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        24.76         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        15.48        22.09        64.57 
TCGA-YU-A90S TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-ZM-AA05 TCGA-ZM-AA0D 
       31.92        28.47        71.24        17.62        37.02        27.88 
TCGA-ZM-AA0E TCGA-ZM-AA0F 
       26.66        22.39 

  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE 
                           0.16                            0.10 
  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE 
                          225.6                           244.5 
  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE 
                          36.69                           45.90 
[1] "0.2 - 225.6 (36.7)" "0.1 - 244.5 (45.9)"
[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        9        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                               9                              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   30 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                            30                              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   47  0
  AMP PEAK 15(22Q11.21) WILD-TYPE 68  4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(22Q11.21) MUTATED     47    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                            47                              68
  1                             0                               4
[1] 2 2
[1] FALSE
D15V7, binary
                                 cls
clus                               0  1
  AMP PEAK 15(22Q11.21) MUTATED   39 12
  AMP PEAK 15(22Q11.21) WILD-TYPE 71  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(22Q11.21) MUTATED     39   12
  AMP PEAK 15(22Q11.21) WILD-TYPE   71    7
     clus
vv    AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE
  NO                             39                              71
  YES                            12                               7
[1] 2 2
[1] FALSE
D15V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(22Q11.21) MUTATED       1                         3    48
  AMP PEAK 15(22Q11.21) WILD-TYPE     3                         3    71
D15V9, multiclass
                           clus
vv                          AMP PEAK 15(22Q11.21) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                48
                           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"
D15V10, binary
                                 cls
clus                               0  1
  AMP PEAK 15(22Q11.21) MUTATED    6 43
  AMP PEAK 15(22Q11.21) WILD-TYPE  6 68
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(22Q11.21) MUTATED      6   43
  AMP PEAK 15(22Q11.21) WILD-TYPE    6   68
                        clus
vv                       AMP PEAK 15(22Q11.21) MUTATED
  HISPANIC OR LATINO                                 6
  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 103   2
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            29                            105 
  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        76.11       114.77       154.59        73.35       132.10 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAHC TCGA-2G-AAHP 
      148.83       161.06       180.07       199.23       182.10       186.31 
TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-SB-A76C TCGA-SN-A84W TCGA-SN-A84Y TCGA-VF-A8AE 
       14.30        14.33         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        17.62        51.72        28.41 

$`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 
       41.39        46.13       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       14.56        24.66        16.54        14.86        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG7 
       36.13        44.48        50.27        52.37        75.58        81.37 
TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       75.25        73.45        80.19        84.99        81.47        89.88 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN 
       85.84        92.09        96.59       119.05       127.92       120.20 
TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      132.36       158.33       144.85       181.28       175.20       172.04 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHL 
       59.90       204.16        73.91       110.10        59.80       232.80 
TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
      211.89        17.82       208.44       216.92       225.60       230.89 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D6 TCGA-4K-AA1H 
      229.22       244.50       131.21        86.96        19.96        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        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        17.75        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        24.76         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-A9SE TCGA-XE-AANV TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       23.28        55.92        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        15.48        22.09        27.72 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 
        9.24        68.02        64.57        31.92        36.59        28.47 
TCGA-YU-A94D TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
       71.24        37.02        49.25        27.55        27.88        26.66 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       22.39        57.07        20.84 

  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 
                        199.23                         244.50 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         50.96                          40.01 
[1] "0.5 - 199.2 (51.0)" "0.1 - 244.5 (40.0)"
[1] "hr=" "7.7"
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       24       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                             24
  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 58 41  5
D16V4, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T1                           18                             58
  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 92  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     23    0
  DEL PEAK  1(1P36.31) WILD-TYPE   92    4
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                           23                             92
  1                            0                              4
[1] 2 2
[1] FALSE
D16V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED   25  3
  DEL PEAK  1(1P36.31) WILD-TYPE 85 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     25    3
  DEL PEAK  1(1P36.31) WILD-TYPE   85   16
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  NO                            25                             85
  YES                            3                             16
[1] 2 2
[1] FALSE
D16V8, continuous
                                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    94
D16V9, 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                                                 94
[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"
D16V10, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED    5 19
  DEL PEAK  1(1P36.31) WILD-TYPE  7 92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      5   19
  DEL PEAK  1(1P36.31) WILD-TYPE    7   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                                  7
  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 106   2
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                           26                           108 
  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        76.11       114.77       154.59        73.35        85.84 
TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGO TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAHC 
       96.59       127.92       132.36       180.07       199.23       182.10 
TCGA-2G-AAHP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-SB-A76C TCGA-SN-A84W TCGA-SO-A8JP 
      186.31        14.30        14.33         1.38         9.63        17.75 
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        64.57         0.56 
TCGA-YU-A94I TCGA-YU-AA61 
       17.62        28.41 

$`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 
       41.39        46.13       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       14.56        24.66        16.54        14.86        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG7 
       36.13        44.48        50.27        52.37        75.58        81.37 
TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       75.25        73.45        80.19        84.99        81.47        89.88 
TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       92.09       119.05       120.20       132.10       158.33       144.85 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH3 
      148.83       161.06       181.28       175.20       172.04        59.90 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
      204.16        73.91       110.10        59.80       232.80       211.89 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I 
      244.50       131.21        86.96        19.96        17.03         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A6IS 
       15.88        22.95        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        24.76         5.06 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE 
        0.82        28.14         6.87        18.38        40.01        23.28 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       34.22        65.98        55.92        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-A90S 
       15.48        22.09        27.72         9.24        68.02        31.92 
TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA06 
       36.59        28.47        71.24        51.72        37.02        49.25 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        27.88        26.66        22.39        57.07        20.84 

  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 
                       199.23                        244.50 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                       53.045                        40.700 
[1] "0.2 - 199.2 (53.0)" "0.1 - 244.5 (40.7)"
[1] "hr=" "9.3"
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       23       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                            23
  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 62 41  4
D17V4, multiclass
    clus
vv   DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  T1                          14                            62
  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 96  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED     19    1
  DEL PEAK  2(1P31.1) WILD-TYPE   96    3
   clus
vv  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  0                          19                            96
  1                           1                             3
[1] 2 2
[1] FALSE
D17V7, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P31.1) MUTATED   21  3
  DEL PEAK  2(1P31.1) WILD-TYPE 89 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED     21    3
  DEL PEAK  2(1P31.1) WILD-TYPE   89   16
     clus
vv    DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  NO                           21                            89
  YES                           3                            16
[1] 2 2
[1] FALSE
D17V8, continuous
                               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    97
D17V9, 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                                                97
[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"
D17V10, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P31.1) MUTATED    2 20
  DEL PEAK  2(1P31.1) WILD-TYPE 10 91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED      2   20
  DEL PEAK  2(1P31.1) WILD-TYPE   10   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                                10
  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 122   3
  DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE 
                             9                            125 
  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 
       81.37       186.31        18.15         1.38        28.14        65.98 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-ZM-AA0B 
        0.56        28.47        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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       203.28        45.21        22.19        14.56        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
       16.54        14.86        22.52        45.67        36.13        44.48 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAG9 
       50.27        52.37        75.58        73.35        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT 
      110.10       182.10        59.80       232.80       211.89        17.82 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      208.44       216.92       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        86.96        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A6IS 
        0.10        15.88        22.95         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        17.75        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        24.76         5.06         0.16         0.82 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANR 
        6.87        18.38        40.01        23.28        34.22         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       55.92        93.93        12.07         7.89        16.87         8.88 
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        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       27.72         9.24        68.02        64.57        31.92        36.59 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       71.24        17.62        51.72        28.41        37.02        49.25 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.88        26.66        22.39        57.07        20.84 

  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 
                        186.31                         244.50 
  DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE 
                         28.14                          41.69 
[1] "0.6 - 186.3 (28.1)" "0.1 - 244.5 (41.7)"
[1] "hr=" "7.2"
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       25       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                             25
  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 71 48  5
D18V4, multiclass
    clus
vv   DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE
  T1                            5                             71
  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 108   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  3(1Q42.12) MUTATED      7    0
  DEL PEAK  3(1Q42.12) WILD-TYPE  108    4
   clus
vv  DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE
  0                            7                            108
  1                            0                              4
[1] 2 2
[1] FALSE
D18V7, binary
                                cls
clus                               0   1
  DEL PEAK  3(1Q42.12) MUTATED     8   1
  DEL PEAK  3(1Q42.12) WILD-TYPE 102  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  3(1Q42.12) MUTATED      8    1
  DEL PEAK  3(1Q42.12) WILD-TYPE  102   18
     clus
vv    DEL PEAK  3(1Q42.12) MUTATED DEL PEAK  3(1Q42.12) WILD-TYPE
  NO                             8                            102
  YES                            1                             18
[1] 2 2
[1] FALSE
D18V8, continuous
                                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   112
D18V9, 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                                                112
[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"
D18V10, binary
                                cls
clus                               0   1
  DEL PEAK  3(1Q42.12) MUTATED     1   6
  DEL PEAK  3(1Q42.12) WILD-TYPE  11 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  3(1Q42.12) MUTATED      1    6
  DEL PEAK  3(1Q42.12) WILD-TYPE   11  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                                 11
  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 118   3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           13                           121 
  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        50.27        96.59       119.05       120.20       132.36 
TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-SN-A84Y TCGA-XE-A8H5 TCGA-XE-AAO4 TCGA-XE-AAOL 
      199.23       204.16        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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      203.28        45.21        22.19        14.56        24.66        16.54 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 
       14.86        22.52        45.67        36.13        44.48        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       75.58        73.35        81.37        75.25        73.45        80.19 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM 
       84.99        81.47        89.88        85.84        92.09       127.92 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      132.10       158.33       144.85       148.83       161.06       181.28 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA 
      175.20       172.04       180.07        59.90        73.91       110.10 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
      182.10        59.80       232.80       211.89       186.31        17.82 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      208.44       216.92       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        86.96        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        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        17.75        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        24.76         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A9SE TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        23.28        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOB 
       65.98         0.46        55.92        93.93         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S2 
        8.88        67.66        41.69        50.96        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       27.72         9.24        68.02        64.57        31.92        36.59 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
       28.47        71.24        17.62        51.72        28.41        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       49.25        27.55        27.88        26.66        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  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 
                       204.16                        244.50 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                        96.59                         37.68 
[1] "0.4 - 204.2 (96.6)" "0.1 - 244.5 (37.7)"
[1] "hr=" "4.9"
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       24       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                            24
  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 70 45  5
D19V4, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  T1                           6                            70
  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 103   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     12    0
  DEL PEAK  4(2Q37.3) WILD-TYPE  103    4
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                          12                           103
  1                           0                             4
[1] 2 2
[1] FALSE
D19V7, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.3) MUTATED   11  1
  DEL PEAK  4(2Q37.3) WILD-TYPE 99 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     11    1
  DEL PEAK  4(2Q37.3) WILD-TYPE   99   18
     clus
vv    DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  NO                           11                            99
  YES                           1                            18
[1] 2 2
[1] FALSE
D19V8, continuous
                               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   110
D19V9, 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                                               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     3   9
  DEL PEAK  4(2Q37.3) WILD-TYPE   9 102
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      3    9
  DEL PEAK  4(2Q37.3) WILD-TYPE    9  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                                 9
  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 91  3
  DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE 
                           40                            94 
  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 
      114.77       154.59        50.27        75.25        73.45        80.19 
TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAH2 
       81.47        85.84        96.59       120.20       132.36       199.23 
TCGA-2G-AAH3 TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAKD TCGA-2G-AAKL 
       59.90       182.10       232.80       211.89       208.44       230.89 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-4K-AA1G TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A9 
      131.21        86.96        14.33        17.23        17.75        36.79 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-XE-AANJ 
       35.61        33.07        24.76         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        15.48        22.09        68.02         0.56 
TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0H 
       28.47        37.02        49.25        57.07 

$`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        41.39        46.13        76.11       128.58       203.28 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
       45.21        22.19        14.56        24.66        16.54        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 
       22.52        45.67        36.13        44.48        52.37        75.58 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGI TCGA-2G-AAGK 
       73.35        81.37        84.99        89.88        92.09       119.05 
TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW 
      127.92       132.10       158.33       144.85       148.83       161.06 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH4 TCGA-2G-AAH8 
      181.28       175.20       172.04       180.07       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKG TCGA-2G-AAKH 
      110.10        59.80       186.31        17.82       216.92       225.60 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I 
      229.22       244.50        14.30        19.96        17.03         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
       15.88        22.95        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-A9SE TCGA-XE-AANI TCGA-XE-AANV 
        6.87        18.38        40.01        23.28        34.22        55.92 
TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF 
       93.93         7.89        16.87         8.88        67.66        41.69 
TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S 
       50.96         0.43        27.72         9.24        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA0B 
       36.59        71.24        17.62        51.72        28.41        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0N 
       27.88        26.66        22.39        20.84 

  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 
                        232.8                         244.5 
  DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE 
                       62.940                        36.885 
[1] "0.2 - 232.8 (62.9)" "0.1 - 244.5 (36.9)"
[1] "hr=" "1.7"
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       20        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                            20
  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 59 31  3
D20V4, multiclass
    clus
vv   DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE
  T1                          17                            59
  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 83  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.2) MUTATED     32    2
  DEL PEAK  5(3P26.2) WILD-TYPE   83    2
   clus
vv  DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE
  0                          32                            83
  1                           2                             2
[1] 2 2
[1] FALSE
D20V7, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P26.2) MUTATED   33  4
  DEL PEAK  5(3P26.2) WILD-TYPE 77 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.2) MUTATED     33    4
  DEL PEAK  5(3P26.2) WILD-TYPE   77   15
     clus
vv    DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE
  NO                           33                            77
  YES                           4                            15
[1] 2 2
[1] FALSE
D20V8, continuous
                               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    82
D20V9, 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                                                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"
D20V10, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P26.2) MUTATED    4 33
  DEL PEAK  5(3P26.2) WILD-TYPE  8 78
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.2) MUTATED      4   33
  DEL PEAK  5(3P26.2) WILD-TYPE    8   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                                 8
  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   96  4
  DEL PEAK  6(4Q22.2) WILD-TYPE 34  0
  DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE 
                          100                            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        41.39        76.11       114.77       128.58       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
      203.28        45.21        14.56        24.66        16.54        14.86 
TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 
       22.52        36.13        50.27        73.35        81.37        73.45 
TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGK 
       80.19        81.47        89.88        85.84        96.59       119.05 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW 
      120.20       132.36       132.10       158.33       148.83       161.06 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
      182.10        59.80       232.80       186.31        17.82       208.44 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      216.92       225.60       230.89       229.22       244.50       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
       86.96        14.30        14.33        15.88        22.95        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 
       17.75        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        24.76         5.06         0.16 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI 
       28.14         6.87        18.38        40.01        23.28        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB 
       65.98         0.46        55.92        93.93        12.07        16.87 
TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       50.96         0.43        15.48        22.09        27.72         9.24 
TCGA-YU-A90P TCGA-YU-A90Y TCGA-YU-A94I TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B 
       68.02         0.56        17.62        28.41        49.25        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0N 
       27.88        26.66        22.39        20.84 

$`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 
       46.13        22.19        45.67        44.48        52.37        75.58 
TCGA-2G-AAG8 TCGA-2G-AAGC TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAGX 
       75.25        84.99        92.09       127.92       144.85       181.28 
TCGA-2G-AAGY TCGA-2G-AAHA TCGA-2G-AAHN TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I 
      175.20       110.10       211.89        19.96        17.03         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        64.57        31.92        36.59        28.47 
TCGA-YU-A94D TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA0H 
       71.24        51.72        37.02        57.07 

  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 
                       244.50                        211.89 
  DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE 
                        36.46                         45.90 
[1] "0.2 - 244.5 (36.5)" "0.1 - 211.9 (45.9)"
[1] "hr="     "2.9e+08"
D21V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(4Q22.2) MUTATED        16       17        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                            17                             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   57 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                          57                            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   88  3
  DEL PEAK  6(4Q22.2) WILD-TYPE 27  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q22.2) MUTATED     88    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                          88                            27
  1                           3                             1
[1] 2 2
[1] FALSE
D21V7, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q22.2) MUTATED   83 13
  DEL PEAK  6(4Q22.2) WILD-TYPE 27  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q22.2) MUTATED     83   13
  DEL PEAK  6(4Q22.2) WILD-TYPE   27    6
     clus
vv    DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE
  NO                           83                            27
  YES                          13                             6
[1] 2 2
[1] FALSE
D21V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4Q22.2) MUTATED       2                         4    91
  DEL PEAK  6(4Q22.2) WILD-TYPE     2                         2    28
D21V9, multiclass
                           clus
vv                          DEL PEAK  6(4Q22.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              91
                           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"
D21V10, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q22.2) MUTATED   10 85
  DEL PEAK  6(4Q22.2) WILD-TYPE  2 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q22.2) MUTATED     10   85
  DEL PEAK  6(4Q22.2) WILD-TYPE    2   26
                        clus
vv                       DEL PEAK  6(4Q22.2) MUTATED
  HISPANIC OR LATINO                              10
  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 42  1
  DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE 
                           91                            43 
  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        76.11       114.77       128.58       154.59       203.28 
TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG3 
       45.21        14.56        22.52        36.13        50.27        52.37 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       73.35        81.37        73.45        80.19        84.99        81.47 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGV 
       89.88        96.59       119.05       127.92       132.10       148.83 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAHC TCGA-2G-AAHG 
      175.20       172.04       199.23        59.90       182.10        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
      232.80       211.89       186.31        17.82       208.44       216.92 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
      230.89       229.22       244.50        86.96        14.30        19.96 
TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
       14.33         0.10        15.88        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        17.75        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        15.48        22.09        27.72         9.24 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       68.02        64.57        28.47        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.55        27.88        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

$`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 
       41.39        46.13        22.19        24.66        16.54        14.86 
TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGG TCGA-2G-AAGI 
       45.67        44.48        75.58        75.25        85.84        92.09 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGX 
      120.20       132.36       158.33       144.85       161.06       181.28 
TCGA-2G-AAH0 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAKH TCGA-2G-AAL7 
      180.07       204.16        73.91       110.10       225.60       131.21 
TCGA-4K-AA1H TCGA-S6-A8JW TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 
       17.03        22.95        10.26        17.23        37.18        36.79 
TCGA-VF-A8AA TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-XE-A9SE TCGA-XE-AANR TCGA-XE-AANV 
       37.68        24.26        24.76        23.28         0.46        55.92 
TCGA-XE-AAOC TCGA-XE-AAOF TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D 
        8.88        41.69        31.92        36.59         0.56        71.24 
TCGA-ZM-AA0E 
       26.66 

  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 
                        244.5                         225.6 
  DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE 
                        40.01                         41.69 
[1] "0.1 - 244.5 (40.0)" "0.5 - 225.6 (41.7)"
[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       10        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                            10
  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 21 18  4
D22V4, multiclass
    clus
vv   DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE
  T1                          55                            21
  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 36  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5P15.2) MUTATED     79    2
  DEL PEAK  7(5P15.2) WILD-TYPE   36    2
   clus
vv  DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE
  0                          79                            36
  1                           2                             2
[1] 2 2
[1] FALSE
D22V7, binary
                               cls
clus                             0  1
  DEL PEAK  7(5P15.2) MUTATED   73 14
  DEL PEAK  7(5P15.2) WILD-TYPE 37  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5P15.2) MUTATED     73   14
  DEL PEAK  7(5P15.2) WILD-TYPE   37    5
     clus
vv    DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE
  NO                           73                            37
  YES                          14                             5
[1] 2 2
[1] FALSE
D22V8, continuous
                               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    38
D22V9, 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                                                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"
D22V10, binary
                               cls
clus                             0  1
  DEL PEAK  7(5P15.2) MUTATED    7 77
  DEL PEAK  7(5P15.2) WILD-TYPE  5 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5P15.2) MUTATED      7   77
  DEL PEAK  7(5P15.2) WILD-TYPE    5   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                                 5
  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   90  3
  DEL PEAK  8(5P14.3) WILD-TYPE 40  1
  DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE 
                           93                            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        76.11       114.77       128.58       154.59       203.28 
TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG3 TCGA-2G-AAG6 
       45.21        14.56        22.52        36.13        52.37        73.35 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       81.37        73.45        80.19        84.99        81.47        89.88 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGV TCGA-2G-AAGX 
       96.59       119.05       127.92       132.10       148.83       181.28 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC 
      175.20       172.04       199.23        59.90       204.16       182.10 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80       232.80       211.89       186.31        17.82       208.44 
TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 
      216.92       230.89       229.22       244.50        86.96        14.30 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JX TCGA-S6-A8JY 
       19.96        14.33         0.10        15.88        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        17.75        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-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       23.28        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        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A912 TCGA-YU-A94I 
       27.72         9.24        68.02        64.57        28.47        17.62 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       51.72        28.41        37.02        49.25        27.55        27.88 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       22.39        57.07        20.84 

$`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 
       41.39        46.13        22.19        24.66        16.54        14.86 
TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGG 
       45.67        44.48        50.27        75.58        75.25        85.84 
TCGA-2G-AAGI TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW 
       92.09       120.20       132.36       158.33       144.85       161.06 
TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAKH TCGA-2G-AAL7 TCGA-4K-AA1H 
      180.07        73.91       110.10       225.60       131.21        17.03 
TCGA-S6-A8JW TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 TCGA-VF-A8AA 
       22.95        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        24.76         0.46        55.92         8.88        41.69 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D TCGA-ZM-AA0E 
       31.92        36.59         0.56        71.24        26.66 

  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 
                        244.5                         225.6 
  DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE 
                        40.01                         41.69 
[1] "0.1 - 244.5 (40.0)" "0.5 - 225.6 (41.7)"
[1] "hr=" "1.1"
D23V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(5P14.3) MUTATED        16       18        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                            18                             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   58 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                          58                            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   81  2
  DEL PEAK  8(5P14.3) WILD-TYPE 34  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P14.3) MUTATED     81    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                          81                            34
  1                           2                             2
[1] 2 2
[1] FALSE
D23V7, binary
                               cls
clus                             0  1
  DEL PEAK  8(5P14.3) MUTATED   74 15
  DEL PEAK  8(5P14.3) WILD-TYPE 36  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P14.3) MUTATED     74   15
  DEL PEAK  8(5P14.3) WILD-TYPE   36    4
     clus
vv    DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE
  NO                           74                            36
  YES                          15                             4
[1] 2 2
[1] FALSE
D23V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(5P14.3) MUTATED       2                         5    83
  DEL PEAK  8(5P14.3) WILD-TYPE     2                         1    36
D23V9, multiclass
                           clus
vv                          DEL PEAK  8(5P14.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              83
                           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"
D23V10, binary
                               cls
clus                             0  1
  DEL PEAK  8(5P14.3) MUTATED    8 78
  DEL PEAK  8(5P14.3) WILD-TYPE  4 33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P14.3) MUTATED      8   78
  DEL PEAK  8(5P14.3) WILD-TYPE    4   33
                        clus
vv                       DEL PEAK  8(5P14.3) MUTATED
  HISPANIC OR LATINO                               8
  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   92  3
  DEL PEAK  9(5Q12.1) WILD-TYPE 38  1
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           95                            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        41.39        76.11       114.77       128.58       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG3 
      203.28        45.21        14.56        22.52        36.13        52.37 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       73.35        81.37        73.45        80.19        84.99        81.47 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGV 
       89.88        96.59       119.05       127.92       132.10       148.83 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      181.28       175.20       172.04       199.23        59.90       204.16 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
      182.10        59.80       232.80       211.89       186.31        17.82 
TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 
      216.92       230.89       229.22       244.50        86.96        14.30 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JX TCGA-S6-A8JY 
       19.96        14.33         0.10        15.88        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        17.75        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-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AAO3 TCGA-XE-AAO4 
       40.01        23.28        34.22        65.98        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        7.89        16.87        67.66        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W 
       22.09        27.72         9.24        68.02        64.57        36.59 
TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       28.47        17.62        51.72        28.41        37.02        49.25 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        27.88        22.39        57.07        20.84 

$`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 
       46.13        22.19        24.66        16.54        14.86        45.67 
TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGG TCGA-2G-AAGI 
       44.48        50.27        75.58        75.25        85.84        92.09 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAH0 
      120.20       132.36       158.33       144.85       161.06       180.07 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2G-AAL7 TCGA-4K-AA1H 
       73.91       110.10       208.44       225.60       131.21        17.03 
TCGA-S6-A8JW TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-W4-A7U4 
       22.95        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 
       24.76         0.46        55.92         8.88        41.69        31.92 
TCGA-YU-A90Y TCGA-YU-A94D TCGA-ZM-AA0E 
        0.56        71.24        26.66 

  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 
                        244.5                         225.6 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                        37.02                         45.67 
[1] "0.1 - 244.5 (37.0)" "0.5 - 225.6 (45.7)"
[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       20        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                            20                             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   61 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                          61                            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   82  2
  DEL PEAK  9(5Q12.1) WILD-TYPE 33  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     82    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                          82                            33
  1                           2                             2
[1] 2 2
[1] FALSE
D24V7, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED   74 17
  DEL PEAK  9(5Q12.1) WILD-TYPE 36  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     74   17
  DEL PEAK  9(5Q12.1) WILD-TYPE   36    2
     clus
vv    DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  NO                           74                            36
  YES                          17                             2
[1] 2 2
[1] FALSE
D24V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(5Q12.1) MUTATED       2                         5    85
  DEL PEAK  9(5Q12.1) WILD-TYPE     2                         1    34
D24V9, multiclass
                           clus
vv                          DEL PEAK  9(5Q12.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              85
                           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"
D24V10, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED    8 79
  DEL PEAK  9(5Q12.1) WILD-TYPE  4 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED      8   79
  DEL PEAK  9(5Q12.1) WILD-TYPE    4   32
                        clus
vv                       DEL PEAK  9(5Q12.1) MUTATED
  HISPANIC OR LATINO                               8
  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 112   3
  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE 
                           19                           115 
  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        73.35        81.47       119.05       127.92       144.85 
TCGA-2G-AAGW TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AALP TCGA-4K-AA1G TCGA-SB-A6J6 
      161.06       229.22       244.50        86.96        14.33        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        68.02        17.62 
TCGA-ZM-AA06 
       49.25 

$`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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       203.28        45.21        22.19        14.56        24.66 
TCGA-2G-AAFM TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       16.54        22.52        45.67        36.13        44.48        50.27 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       52.37        75.58        81.37        75.25        73.45        80.19 
TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGN 
       84.99        89.88        85.84        92.09        96.59       120.20 
TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY 
      132.36       132.10       158.33       148.83       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAL7 
       17.82       208.44       216.92       225.60       230.89       131.21 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
       14.30        19.96        17.03         0.10        15.88        22.95 
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 
       17.75        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        24.76         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI 
        0.16         0.82        18.38        40.01        23.28        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        55.92        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-A90Q TCGA-YU-A90S 
       15.48        22.09        27.72         9.24        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 
       36.59         0.56        28.47        71.24        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        27.55        27.88        26.66        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE 
                         6.87                          0.10 
  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE 
                        244.5                         232.8 
  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE 
                        68.02                         40.01 
[1] "6.9 - 244.5 (68.0)" "0.1 - 232.8 (40.0)"
[1] "hr=" "1.2"
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       23       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                            23
  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 66 42  6
D25V4, multiclass
    clus
vv   DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE
  T1                          10                            66
  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 99  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P22.3) MUTATED     16    1
  DEL PEAK 10(6P22.3) WILD-TYPE   99    3
   clus
vv  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE
  0                          16                            99
  1                           1                             3
[1] 2 2
[1] FALSE
D25V7, binary
                               cls
clus                             0  1
  DEL PEAK 10(6P22.3) MUTATED   19  0
  DEL PEAK 10(6P22.3) WILD-TYPE 91 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P22.3) MUTATED     19    0
  DEL PEAK 10(6P22.3) WILD-TYPE   91   19
     clus
vv    DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE
  NO                           19                            91
  YES                           0                            19
[1] 2 2
[1] FALSE
D25V8, continuous
                               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   101
D25V9, 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                                               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"
D25V10, binary
                               cls
clus                             0  1
  DEL PEAK 10(6P22.3) MUTATED    2 15
  DEL PEAK 10(6P22.3) WILD-TYPE 10 96
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P22.3) MUTATED      2   15
  DEL PEAK 10(6P22.3) WILD-TYPE   10   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                                10
  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 108   4
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                         22                         112 
  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 
       76.11        45.67        81.47        96.59       119.05       127.92 
TCGA-2G-AAGP TCGA-2G-AAGZ TCGA-2G-AAH4 TCGA-2G-AAHG TCGA-2G-AAKH TCGA-2G-AAKL 
      132.10       172.04       204.16        59.80       225.60       230.89 
TCGA-2G-AALP TCGA-4K-AA1G TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-VF-A8A8 TCGA-W4-A7U4 
       86.96        14.33         9.14        13.58        37.18        24.26 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-YU-A90P TCGA-YU-A94I 
       28.14         6.87        68.02        17.62 

$`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        41.39        46.13       114.77       128.58       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      203.28        45.21        22.19        14.56        24.66        16.54 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       14.86        22.52        36.13        44.48        50.27        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       75.58        73.35        81.37        75.25        73.45        80.19 
TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGN TCGA-2G-AAGO 
       84.99        89.88        85.84        92.09       120.20       132.36 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
      180.07       199.23        59.90        73.91       110.10       182.10 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
      232.80       211.89       186.31        17.82       208.44       216.92 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1H 
      229.22       244.50       131.21        14.30        19.96        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A76C TCGA-SN-A6IS 
        0.10        15.88        22.95        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        17.75        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 
       24.76         5.06         0.16         0.82        18.38        40.01 
TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       23.28        34.22        65.98         0.46        55.92        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        15.48        22.09        27.72         9.24 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       64.57        31.92        36.59         0.56        28.47        71.24 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       51.72        28.41        37.02        49.25        27.55        27.88 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       26.66        22.39        57.07        20.84 

  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                       6.87                        0.10 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                     230.89                      244.50 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                     72.065                      37.350 
[1] "6.9 - 230.9 (72.1)" "0.1 - 244.5 (37.4)"
[1] "hr="     "2.5e+08"
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       21       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                          21
  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 62 43  6
D26V4, multiclass
    clus
vv   DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  T1                        14                          62
  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 97  2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED     18    2
  DEL PEAK 11(6Q26) WILD-TYPE   97    2
   clus
vv  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  0                        18                          97
  1                         2                           2
[1] 2 2
[1] FALSE
D26V7, binary
                             cls
clus                           0  1
  DEL PEAK 11(6Q26) MUTATED   20  2
  DEL PEAK 11(6Q26) WILD-TYPE 90 17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED     20    2
  DEL PEAK 11(6Q26) WILD-TYPE   90   17
     clus
vv    DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  NO                         20                          90
  YES                         2                          17
[1] 2 2
[1] FALSE
D26V8, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q26) MUTATED       0                         1    20
  DEL PEAK 11(6Q26) WILD-TYPE     4                         5    99
D26V9, 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                                              99
[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"
D26V10, binary
                             cls
clus                           0  1
  DEL PEAK 11(6Q26) MUTATED    1 19
  DEL PEAK 11(6Q26) WILD-TYPE 11 92
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED      1   19
  DEL PEAK 11(6Q26) WILD-TYPE   11   92
                        clus
vv                       DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             1                          11
  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 127   4
  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE 
                             3                            131 
  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 
      127.92       175.20        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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       203.28        45.21        22.19        14.56        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
       16.54        14.86        22.52        45.67        36.13        44.48 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       50.27        52.37        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       92.09        96.59       119.05       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGZ 
      158.33       144.85       148.83       161.06       181.28       172.04 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
      180.07       199.23        59.90       204.16        73.91       110.10 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
      182.10        59.80       232.80       211.89       186.31        17.82 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      208.44       216.92       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        86.96        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        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        17.75 
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        24.76         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-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       23.28        34.22        65.98         0.46        55.92        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-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P 
        0.43        15.48        22.09        27.72         9.24        68.02 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       64.57        31.92        36.59         0.56        28.47        71.24 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
       17.62        51.72        28.41        37.02        49.25        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.88        26.66        22.39        57.07        20.84 

  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 
                         175.2                          244.5 
  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE 
                        127.92                          40.01 
[1] "51.0 - 175.2 (127.9)" "0.1 - 244.5 (40.0)"  
[1] "hr="     "9300000"
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       26       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                             26
  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 74 50  6
D27V4, multiclass
    clus
vv   DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE
  T1                            2                             74
  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 112   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(7Q11.22) MUTATED      3    0
  DEL PEAK 12(7Q11.22) WILD-TYPE  112    4
   clus
vv  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE
  0                            3                            112
  1                            0                              4
[1] 2 2
[1] FALSE
D27V7, binary
                                cls
clus                               0   1
  DEL PEAK 12(7Q11.22) MUTATED     3   0
  DEL PEAK 12(7Q11.22) WILD-TYPE 107  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(7Q11.22) MUTATED      3    0
  DEL PEAK 12(7Q11.22) WILD-TYPE  107   19
     clus
vv    DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE
  NO                             3                            107
  YES                            0                             19
[1] 2 2
[1] FALSE
D27V8, continuous
                                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   116
D27V9, 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                                                116
[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"
D27V10, binary
                                cls
clus                               0   1
  DEL PEAK 12(7Q11.22) MUTATED     1   2
  DEL PEAK 12(7Q11.22) WILD-TYPE  11 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(7Q11.22) MUTATED      1    2
  DEL PEAK 12(7Q11.22) WILD-TYPE   11  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                                 11
  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 116   4
  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE 
                           14                           120 
  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 
       45.21        52.37       127.92       158.33       161.06        10.26 
TCGA-SN-A84Y TCGA-WZ-A7V3 TCGA-X3-A8G4 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AAOJ 
       17.23        24.76        28.14        40.01        65.98        50.96 
TCGA-XY-A9T9 TCGA-ZM-AA0B 
        9.24        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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       203.28        22.19        14.56        24.66        16.54 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        22.52        45.67        36.13        44.48        50.27 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       75.58        73.35        81.37        75.25        73.45        80.19 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       84.99        81.47        89.88        85.84        92.09        96.59 
TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV 
      119.05       120.20       132.36       132.10       144.85       148.83 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
      181.28       175.20       172.04       180.07       199.23        59.90 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL 
      204.16        73.91       110.10       182.10        59.80       232.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
      211.89       186.31        17.82       208.44       216.92       225.60 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
      230.89       229.22       244.50       131.21        86.96        14.30 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
       19.96        14.33        17.03         0.10        15.88        22.95 
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 
       17.75        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-A9SE TCGA-XE-AANI 
        0.16         0.82         6.87        18.38        23.28        34.22 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
        8.88        67.66        41.69         0.43        15.48        22.09 
TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
       27.72        68.02        64.57        31.92        36.59         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
       28.47        71.24        17.62        51.72        28.41        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       49.25        27.88        26.66        22.39        57.07        20.84 

  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE 
                         9.24                          0.10 
  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE 
                       161.06                        244.50 
  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE 
                       42.610                        41.455 
[1] "9.2 - 161.1 (42.6)" "0.1 - 244.5 (41.5)"
[1] "hr="     "7.9e+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       25       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                            25
  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 67 46  6
D28V4, multiclass
    clus
vv   DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE
  T1                           9                            67
  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 102   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.1) MUTATED     13    0
  DEL PEAK 13(7Q36.1) WILD-TYPE  102    4
   clus
vv  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE
  0                          13                           102
  1                           0                             4
[1] 2 2
[1] FALSE
D28V7, binary
                               cls
clus                             0  1
  DEL PEAK 13(7Q36.1) MUTATED   12  2
  DEL PEAK 13(7Q36.1) WILD-TYPE 98 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.1) MUTATED     12    2
  DEL PEAK 13(7Q36.1) WILD-TYPE   98   17
     clus
vv    DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE
  NO                           12                            98
  YES                           2                            17
[1] 2 2
[1] FALSE
D28V8, continuous
                               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   106
D28V9, 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                                               106
[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"
D28V10, binary
                               cls
clus                              0   1
  DEL PEAK 13(7Q36.1) MUTATED     5   9
  DEL PEAK 13(7Q36.1) WILD-TYPE   7 102
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.1) MUTATED      5    9
  DEL PEAK 13(7Q36.1) WILD-TYPE    7  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                                 7
  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   61  2
  DEL PEAK 14(9P24.3) WILD-TYPE 69  2
  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE 
                           63                            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       114.77       128.58       154.59       203.28        14.56 
TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       50.27        73.35        81.37        73.45        80.19        84.99 
TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       81.47        85.84       119.05       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH3 
      132.10       158.33       148.83       175.20       172.04        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHG TCGA-2G-AAHT TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM 
       73.91        59.80        17.82       216.92       225.60       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JY 
      244.50       131.21        86.96         0.10        15.88         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-A9SE 
        0.82        28.14         6.87        18.38        40.01        23.28 
TCGA-XE-AANJ TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A9T9 TCGA-YU-A90P 
       65.98        41.69        50.96         0.43         9.24        68.02 
TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
       28.47        17.62        51.72        37.02        49.25        27.55 
TCGA-ZM-AA0E TCGA-ZM-AA0H TCGA-ZM-AA0N 
       26.66        57.07        20.84 

$`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 
       41.39        46.13        76.11        45.21        22.19        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
       16.54        14.86        22.52        45.67        36.13        44.48 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGF TCGA-2G-AAGI TCGA-2G-AAGJ 
       52.37        75.58        75.25        89.88        92.09        96.59 
TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH4 
      144.85       161.06       181.28       180.07       199.23       204.16 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKD 
      110.10       182.10       232.80       211.89       186.31       208.44 
TCGA-2G-AAKL TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW 
      230.89        14.30        19.96        14.33        17.03        22.95 
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        17.75 
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        24.76         5.06        34.22         0.46        55.92 
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 
       15.48        22.09        27.72        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-AA61 TCGA-ZM-AA0D TCGA-ZM-AA0F 
        0.56        71.24        28.41        27.88        22.39 

  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE 
                         0.10                          0.46 
  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE 
                        244.5                         232.8 
  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE 
                        57.07                         35.61 
[1] "0.1 - 244.5 (57.1)" "0.5 - 232.8 (35.6)"
[1] "hr=" "1.1"
D29V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(9P24.3) MUTATED         7       11        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                            11                            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   36 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                          36                            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   54  3
  DEL PEAK 14(9P24.3) WILD-TYPE 61  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P24.3) MUTATED     54    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                          54                            61
  1                           3                             1
[1] 2 2
[1] FALSE
D29V7, binary
                               cls
clus                             0  1
  DEL PEAK 14(9P24.3) MUTATED   49 11
  DEL PEAK 14(9P24.3) WILD-TYPE 61  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P24.3) MUTATED     49   11
  DEL PEAK 14(9P24.3) WILD-TYPE   61    8
     clus
vv    DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE
  NO                           49                            61
  YES                          11                             8
[1] 2 2
[1] FALSE
D29V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(9P24.3) MUTATED       2                         4    55
  DEL PEAK 14(9P24.3) WILD-TYPE     2                         2    64
D29V9, multiclass
                           clus
vv                          DEL PEAK 14(9P24.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              55
                           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"
D29V10, binary
                               cls
clus                             0  1
  DEL PEAK 14(9P24.3) MUTATED    6 53
  DEL PEAK 14(9P24.3) WILD-TYPE  6 58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P24.3) MUTATED      6   53
  DEL PEAK 14(9P24.3) WILD-TYPE    6   58
                        clus
vv                       DEL PEAK 14(9P24.3) MUTATED
  HISPANIC OR LATINO                               6
  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   57  2
  DEL PEAK 15(9P23) WILD-TYPE 73  2
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                         59                          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       114.77       128.58       154.59       203.28        14.56 
TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE 
       50.27        73.35        81.37        73.45        84.99        81.47 
TCGA-2G-AAGG TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       85.84       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAHG TCGA-2G-AAHT 
      158.33       148.83       175.20       172.04        59.80        17.82 
TCGA-2G-AAKG TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-4K-AA1I 
      216.92       229.22       244.50       131.21        86.96         0.10 
TCGA-4K-AAAL TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A84W TCGA-VF-A8AB TCGA-W4-A7U2 
       15.88         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-A9SE TCGA-XE-AANJ TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
       40.01        23.28        65.98        41.69        50.96         0.43 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 
        9.24        68.02        28.47        17.62        51.72        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0E TCGA-ZM-AA0H TCGA-ZM-AA0N 
       49.25        27.55        26.66        57.07        20.84 

$`DEL PEAK 15(9P23) WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL 
       41.39        46.13        76.11        45.21        22.19        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
       16.54        14.86        22.52        45.67        36.13        44.48 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGF TCGA-2G-AAGI 
       52.37        75.58        75.25        80.19        89.88        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAH0 TCGA-2G-AAH2 
       96.59       144.85       161.06       181.28       180.07       199.23 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL 
       59.90       204.16        73.91       110.10       182.10       232.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2X-A9D5 
      211.89       186.31       208.44       225.60       230.89        14.30 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A76C 
       19.96        14.33        17.03        22.95        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        17.75        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        24.76 
TCGA-WZ-A7V4 TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
        5.06        34.22         0.46        55.92        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        15.48        22.09 
TCGA-XY-A8S3 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D 
       27.72        64.57        31.92        36.59         0.56        71.24 
TCGA-YU-AA61 TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        27.88        22.39 

  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                       0.10                        0.46 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                      244.5                       232.8 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                      50.96                       36.59 
[1] "0.1 - 244.5 (51.0)" "0.5 - 232.8 (36.6)"
[1] "hr=" "1.2"
D30V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(9P23) MUTATED         6       11        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                          11                          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   34 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                        34                          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   50  3
  DEL PEAK 15(9P23) WILD-TYPE 65  1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED     50    3
  DEL PEAK 15(9P23) WILD-TYPE   65    1
   clus
vv  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  0                        50                          65
  1                         3                           1
[1] 2 2
[1] FALSE
D30V7, binary
                             cls
clus                           0  1
  DEL PEAK 15(9P23) MUTATED   45 11
  DEL PEAK 15(9P23) WILD-TYPE 65  8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED     45   11
  DEL PEAK 15(9P23) WILD-TYPE   65    8
     clus
vv    DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  NO                         45                          65
  YES                        11                           8
[1] 2 2
[1] FALSE
D30V8, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(9P23) MUTATED       2                         4    51
  DEL PEAK 15(9P23) WILD-TYPE     2                         2    68
D30V9, multiclass
                           clus
vv                          DEL PEAK 15(9P23) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         4
  WHITE                                            51
                           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"
D30V10, binary
                             cls
clus                           0  1
  DEL PEAK 15(9P23) MUTATED    6 49
  DEL PEAK 15(9P23) WILD-TYPE  6 62
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED      6   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                             6                           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 81  1
  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE 
                           52                            82 
  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       114.77       128.58       154.59        50.27        73.35 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG 
       81.37        73.45        80.19        84.99        89.88        85.84 
TCGA-2G-AAGJ TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV 
       96.59       120.20       132.36       132.10       158.33       148.83 
TCGA-2G-AAGX TCGA-2G-AAHG TCGA-2G-AAHT TCGA-2G-AAKG TCGA-2G-AAKM TCGA-2G-AAL5 
      181.28        59.80        17.82       216.92       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JY 
      131.21        86.96        14.30         0.10        15.88         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        17.75        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 
       22.09        27.72         9.24        68.02         0.56        28.47 
TCGA-YU-A94I TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0H 
       17.62        49.25        27.55        57.07 

$`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 
       41.39        46.13        76.11       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       14.56        24.66        16.54        14.86        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGE 
       36.13        44.48        52.37        75.58        75.25        81.47 
TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGY 
       92.09       119.05       127.92       144.85       161.06       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKD 
      110.10       182.10       232.80       211.89       186.31       208.44 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW 
      225.60       230.89        19.96        14.33        17.03        22.95 
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-A9SE 
       24.76         0.82         6.87        18.38        40.01        23.28 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        55.92        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOL TCGA-XY-A89B TCGA-YU-A90Q 
       16.87         8.88        67.66         0.43        15.48        64.57 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
       31.92        36.59        71.24        51.72        28.41        37.02 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0N 
       27.88        26.66        22.39        20.84 

  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE 
                         0.10                          0.43 
  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE 
                        244.5                         232.8 
  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE 
                       50.615                        37.430 
[1] "0.1 - 244.5 (50.6)" "0.4 - 232.8 (37.4)"
[1] "hr=" "4.3"
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       16       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                            16
  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 45 33  3
D31V4, multiclass
    clus
vv   DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE
  T1                          31                            45
  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 71  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9Q33.3) MUTATED     44    2
  DEL PEAK 16(9Q33.3) WILD-TYPE   71    2
   clus
vv  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE
  0                          44                            71
  1                           2                             2
[1] 2 2
[1] FALSE
D31V7, binary
                               cls
clus                             0  1
  DEL PEAK 16(9Q33.3) MUTATED   43  7
  DEL PEAK 16(9Q33.3) WILD-TYPE 67 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9Q33.3) MUTATED     43    7
  DEL PEAK 16(9Q33.3) WILD-TYPE   67   12
     clus
vv    DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE
  NO                           43                            67
  YES                           7                            12
[1] 2 2
[1] FALSE
D31V8, continuous
                               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    73
D31V9, 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                                                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"
D31V10, binary
                               cls
clus                             0  1
  DEL PEAK 16(9Q33.3) MUTATED    3 45
  DEL PEAK 16(9Q33.3) WILD-TYPE  9 66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9Q33.3) MUTATED      3   45
  DEL PEAK 16(9Q33.3) WILD-TYPE    9   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                                 9
  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 81  1
  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE 
                           52                            82 
  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       114.77       128.58       154.59        50.27        73.35 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG 
       81.37        73.45        80.19        84.99        89.88        85.84 
TCGA-2G-AAGJ TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV 
       96.59       120.20       132.36       132.10       158.33       148.83 
TCGA-2G-AAGX TCGA-2G-AAHG TCGA-2G-AAHT TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM 
      181.28        59.80        17.82       216.92       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JY 
      244.50        86.96        14.30         0.10        15.88         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        17.75        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 
       22.09        27.72         9.24        68.02         0.56        28.47 
TCGA-YU-A94I TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0H 
       17.62        49.25        27.55        57.07 

$`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 
       41.39        46.13        76.11       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       14.56        24.66        16.54        14.86        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGE 
       36.13        44.48        52.37        75.58        75.25        81.47 
TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGY 
       92.09       119.05       127.92       144.85       161.06       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKD 
      110.10       182.10       232.80       211.89       186.31       208.44 
TCGA-2G-AAKH TCGA-2G-AAL7 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW 
      225.60       131.21        19.96        14.33        17.03        22.95 
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        24.76 
TCGA-WZ-A8D5 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANJ 
        0.82         6.87        18.38        40.01        23.28        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-YU-A90Q 
        8.88        67.66        50.96         0.43        15.48        64.57 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
       31.92        36.59        71.24        51.72        28.41        37.02 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0N 
       27.88        26.66        22.39        20.84 

  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE 
                         0.10                          0.43 
  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE 
                        244.5                         232.8 
  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE 
                       49.760                        38.845 
[1] "0.1 - 244.5 (49.8)" "0.4 - 232.8 (38.8)"
[1] "hr=" "3.6"
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       15       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                            15
  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 45 33  3
D32V4, multiclass
    clus
vv   DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE
  T1                          31                            45
  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 71  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9Q34.2) MUTATED     44    2
  DEL PEAK 17(9Q34.2) WILD-TYPE   71    2
   clus
vv  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE
  0                          44                            71
  1                           2                             2
[1] 2 2
[1] FALSE
D32V7, binary
                               cls
clus                             0  1
  DEL PEAK 17(9Q34.2) MUTATED   43  7
  DEL PEAK 17(9Q34.2) WILD-TYPE 67 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9Q34.2) MUTATED     43    7
  DEL PEAK 17(9Q34.2) WILD-TYPE   67   12
     clus
vv    DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE
  NO                           43                            67
  YES                           7                            12
[1] 2 2
[1] FALSE
D32V8, continuous
                               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    73
D32V9, 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                                                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"
D32V10, binary
                               cls
clus                             0  1
  DEL PEAK 17(9Q34.2) MUTATED    2 46
  DEL PEAK 17(9Q34.2) WILD-TYPE 10 65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9Q34.2) MUTATED      2   46
  DEL PEAK 17(9Q34.2) WILD-TYPE   10   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                                10
  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   69  3
  DEL PEAK 18(10P15.3) WILD-TYPE 61  1
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                            72                             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 
       41.39       114.77       154.59        16.54        14.86        22.52 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 
       45.67        36.13        44.48        50.27        73.35        81.37 
TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGK 
       75.25        73.45        81.47        89.88        85.84       119.05 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGY 
      120.20       132.36       132.10       148.83       161.06       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG 
      172.04       199.23        59.90       204.16       182.10        59.80 
TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      186.31       208.44       216.92       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW 
      131.21        86.96        14.30        14.33        17.03        22.95 
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 
       17.75        37.18        35.61        41.52         4.90        24.26 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A9SE TCGA-XE-AANI 
        5.06         0.16        28.14         6.87        23.28        34.22 
TCGA-XE-AANJ TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P 
       65.98        16.87        41.69        22.09        27.72        68.02 
TCGA-YU-A90Y TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
        0.56        28.41        49.25        27.55        27.88        22.39 

$`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        46.13        76.11       128.58       203.28        45.21 
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAGA 
       22.19        14.56        24.66        52.37        75.58        80.19 
TCGA-2G-AAGC TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGS TCGA-2G-AAGT 
       84.99        92.09        96.59       127.92       158.33       144.85 
TCGA-2G-AAGX TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHL TCGA-2G-AAHN 
      181.28       180.07        73.91       110.10       232.80       211.89 
TCGA-2G-AAHT TCGA-2G-AAKH TCGA-2X-A9D6 TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JY 
       17.82       225.60        19.96         0.10        15.88         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 
       24.76         0.82        18.38        40.01         0.46        55.92 
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        15.48         9.24        64.57        31.92        36.59 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA0E 
       28.47        71.24        17.62        51.72        37.02        26.66 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  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 
                         244.5                          232.8 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                        43.085                         37.350 
[1] "0.2 - 244.5 (43.1)" "0.1 - 232.8 (37.4)"
[1] "hr=" "2.1"
D33V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(10P15.3) MUTATED         9       10        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                             10                             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   38 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                           38                             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   61  4
  DEL PEAK 18(10P15.3) WILD-TYPE 54  0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED     61    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                           61                             54
  1                            4                              0
[1] 2 2
[1] FALSE
D33V7, binary
                                cls
clus                              0  1
  DEL PEAK 18(10P15.3) MUTATED   64  6
  DEL PEAK 18(10P15.3) WILD-TYPE 46 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED     64    6
  DEL PEAK 18(10P15.3) WILD-TYPE   46   13
     clus
vv    DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  NO                            64                             46
  YES                            6                             13
[1] 2 2
[1] FALSE
D33V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(10P15.3) MUTATED       1                         1    70
  DEL PEAK 18(10P15.3) WILD-TYPE     3                         5    49
D33V9, multiclass
                           clus
vv                          DEL PEAK 18(10P15.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               70
                           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"
D33V10, binary
                                cls
clus                              0  1
  DEL PEAK 18(10P15.3) MUTATED    6 62
  DEL PEAK 18(10P15.3) WILD-TYPE  6 49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED      6   62
  DEL PEAK 18(10P15.3) WILD-TYPE    6   49
                        clus
vv                       DEL PEAK 18(10P15.3) MUTATED
  HISPANIC OR LATINO                                6
  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 71  1
  DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE 
                            62                             72 
  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 
      114.77       154.59        16.54        14.86        22.52        36.13 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE 
       73.35        81.37        75.25        73.45        84.99        81.47 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGP 
       89.88        85.84        96.59       119.05       120.20       132.10 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 
      148.83       161.06       175.20       172.04       199.23        59.90 
TCGA-2G-AAH4 TCGA-2G-AAHG TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
      204.16        59.80       186.31       208.44       216.92       225.60 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1H 
      230.89       229.22       131.21        86.96        14.30        17.03 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SN-A84W TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8AC 
       22.95        18.15         9.63        17.23        17.75        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        22.09 
TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-AA61 TCGA-ZM-AA06 
       27.72        68.02         0.56        28.47        28.41        49.25 
TCGA-ZM-AA0D TCGA-ZM-AA0F 
       27.88        22.39 

$`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        41.39        46.13        76.11       128.58       203.28 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFV TCGA-2G-AAFZ 
       45.21        22.19        14.56        24.66        45.67        44.48 
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAGA TCGA-2G-AAGI TCGA-2G-AAGM 
       50.27        52.37        75.58        80.19        92.09       127.92 
TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGX TCGA-2G-AAH0 TCGA-2G-AAH8 
      132.36       158.33       144.85       181.28       180.07        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAL5 
      110.10       182.10       232.80       211.89        17.82       244.50 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JY TCGA-SB-A6J6 
       19.96        14.33         0.10        15.88         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        24.76         0.82         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        23.28        34.22         0.46        55.92        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XY-A89B 
       12.07         7.89         8.88        67.66        50.96        15.48 
TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A94D TCGA-YU-A94I 
        9.24        64.57        31.92        36.59        71.24        17.62 
TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0E TCGA-ZM-AA0H TCGA-ZM-AA0N 
       51.72        37.02        27.55        26.66        57.07        20.84 

  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 
                        230.89                         244.50 
  DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE 
                         59.85                          37.10 
[1] "0.2 - 230.9 (59.8)" "0.1 - 244.5 (37.1)"
[1] "hr=" "3.2"
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       19        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                             19
  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 44 23  4
D34V4, multiclass
    clus
vv   DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE
  T1                           32                             44
  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 64  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q23.1) MUTATED     51    3
  DEL PEAK 19(10Q23.1) WILD-TYPE   64    1
   clus
vv  DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE
  0                           51                             64
  1                            3                              1
[1] 2 2
[1] FALSE
D34V7, binary
                                cls
clus                              0  1
  DEL PEAK 19(10Q23.1) MUTATED   55  4
  DEL PEAK 19(10Q23.1) WILD-TYPE 55 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q23.1) MUTATED     55    4
  DEL PEAK 19(10Q23.1) WILD-TYPE   55   15
     clus
vv    DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE
  NO                            55                             55
  YES                            4                             15
[1] 2 2
[1] FALSE
D34V8, continuous
                                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    62
D34V9, 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                                                 62
[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"
D34V10, binary
                                cls
clus                              0  1
  DEL PEAK 19(10Q23.1) MUTATED    3 54
  DEL PEAK 19(10Q23.1) WILD-TYPE  9 57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q23.1) MUTATED      3   54
  DEL PEAK 19(10Q23.1) WILD-TYPE    9   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                                  9
  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   63  3
  DEL PEAK 20(10Q26.3) WILD-TYPE 67  1
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                            66                             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 
       76.11       114.77       154.59        22.19        14.56        16.54 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       14.86        22.52        36.13        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGY 
      119.05       120.20       132.10       148.83       161.06       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHG TCGA-2G-AAHP 
      172.04       199.23        59.90       204.16        59.80       186.31 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
      208.44       216.92       225.60       230.89       229.22       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW TCGA-S6-A8JX 
       86.96        14.30        14.33        17.03        22.95        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        17.75        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-A9SE TCGA-XE-AAOB TCGA-XE-AAOF TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P 
       23.28        16.87        41.69        22.09        27.72        68.02 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0D TCGA-ZM-AA0F 
        0.56        28.47        28.41        49.25        27.88        22.39 

$`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        41.39        46.13       128.58       203.28        45.21 
TCGA-2G-AAFL TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 
       24.66        45.67        44.48        50.27        52.37        75.58 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT 
       92.09        96.59       127.92       132.36       158.33       144.85 
TCGA-2G-AAGX TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL 
      181.28       180.07        73.91       110.10       182.10       232.80 
TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAL5 TCGA-2X-A9D6 TCGA-4K-AA1I TCGA-4K-AAAL 
      211.89        17.82       244.50        19.96         0.10        15.88 
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        24.76         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        55.92 
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        15.48         9.24        64.57        31.92        36.59 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0E 
       71.24        17.62        51.72        37.02        27.55        26.66 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  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 
                        230.89                         244.50 
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                         45.47                          40.70 
[1] "0.2 - 230.9 (45.5)" "0.1 - 244.5 (40.7)"
[1] "hr=" "3"  
D35V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(10Q26.3) MUTATED        10        7        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                              7                             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   35 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                           35                             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   56  3
  DEL PEAK 20(10Q26.3) WILD-TYPE 59  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10Q26.3) MUTATED     56    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                           56                             59
  1                            3                              1
[1] 2 2
[1] FALSE
D35V7, binary
                                cls
clus                              0  1
  DEL PEAK 20(10Q26.3) MUTATED   58  6
  DEL PEAK 20(10Q26.3) WILD-TYPE 52 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10Q26.3) MUTATED     58    6
  DEL PEAK 20(10Q26.3) WILD-TYPE   52   13
     clus
vv    DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE
  NO                            58                             52
  YES                            6                             13
[1] 2 2
[1] FALSE
D35V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(10Q26.3) MUTATED       2                         2    62
  DEL PEAK 20(10Q26.3) WILD-TYPE     2                         4    57
D35V9, multiclass
                           clus
vv                          DEL PEAK 20(10Q26.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               62
                           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"
D35V10, binary
                                cls
clus                              0  1
  DEL PEAK 20(10Q26.3) MUTATED    4 57
  DEL PEAK 20(10Q26.3) WILD-TYPE  8 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10Q26.3) MUTATED      4   57
  DEL PEAK 20(10Q26.3) WILD-TYPE    8   54
                        clus
vv                       DEL PEAK 20(10Q26.3) MUTATED
  HISPANIC OR LATINO                                4
  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   83  2
  DEL PEAK 21(11P15.5) WILD-TYPE 47  2
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                            85                             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        76.11       114.77       128.58       154.59       203.28 
TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY 
       45.21        14.56        16.54        14.86        22.52        36.13 
TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE 
       50.27        73.35        81.37        73.45        84.99        81.47 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS 
       89.88        85.84       119.05       120.20       132.36       158.33 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 
      148.83       161.06       181.28       175.20       172.04       199.23 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       59.90       204.16       182.10        59.80       232.80       211.89 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAL7 TCGA-2G-AALP 
      186.31        17.82       208.44       216.92       131.21        86.96 
TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
       14.30        14.33        22.95        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        24.76         5.06         0.16         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        23.28        65.98         0.46        55.92 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XY-A89B TCGA-XY-A8S2 
       93.93        12.07        67.66        41.69        15.48        22.09 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90Y TCGA-YU-A912 TCGA-ZM-AA05 
        9.24        68.02        64.57         0.56        28.47        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       49.25        27.55        27.88        26.66        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

$`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 
       41.39        46.13        22.19        24.66        45.67        44.48 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGI TCGA-2G-AAGJ 
       52.37        75.58        75.25        80.19        92.09        96.59 
TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA 
      127.92       132.10       144.85       180.07        73.91       110.10 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2X-A9D6 TCGA-4K-AA1H 
      225.60       230.89       229.22       244.50        19.96        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA 
        0.10        15.88        10.26        17.75        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 
       27.72        31.92        36.59        71.24        17.62        51.72 
TCGA-YU-AA61 
       28.41 

  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 
                         232.8                          244.5 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                         45.21                          37.68 
[1] "0.2 - 232.8 (45.2)" "0.1 - 244.5 (37.7)"
[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       16        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                             16                             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   47 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                           47                             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   75  3
  DEL PEAK 21(11P15.5) WILD-TYPE 40  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED     75    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                           75                             40
  1                            3                              1
[1] 2 2
[1] FALSE
D36V7, binary
                                cls
clus                              0  1
  DEL PEAK 21(11P15.5) MUTATED   67 15
  DEL PEAK 21(11P15.5) WILD-TYPE 43  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED     67   15
  DEL PEAK 21(11P15.5) WILD-TYPE   43    4
     clus
vv    DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  NO                            67                             43
  YES                           15                              4
[1] 2 2
[1] FALSE
D36V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(11P15.5) MUTATED       3                         3    76
  DEL PEAK 21(11P15.5) WILD-TYPE     1                         3    43
D36V9, multiclass
                           clus
vv                          DEL PEAK 21(11P15.5) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               76
                           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"
D36V10, binary
                                cls
clus                              0  1
  DEL PEAK 21(11P15.5) MUTATED    9 72
  DEL PEAK 21(11P15.5) WILD-TYPE  3 39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED      9   72
  DEL PEAK 21(11P15.5) WILD-TYPE    3   39
                        clus
vv                       DEL PEAK 21(11P15.5) MUTATED
  HISPANIC OR LATINO                                9
  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   87  3
  DEL PEAK 22(11P12) WILD-TYPE 43  1
  DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE 
                          90                           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        41.39        76.11       114.77       128.58       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
      203.28        45.21        14.56        16.54        14.86        22.52 
TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA 
       36.13        50.27        73.35        81.37        73.45        80.19 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGK TCGA-2G-AAGN 
       84.99        81.47        89.88        85.84       119.05       120.20 
TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      132.36       158.33       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG 
      172.04       199.23        59.90       204.16       182.10        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
      232.80       211.89       186.31        17.82       208.44       216.92 
TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JW 
      229.22       131.21        86.96        14.33        17.03        22.95 
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 
       24.76         5.06         0.16         6.87        18.38        40.01 
TCGA-XE-A9SE TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       23.28        65.98         0.46        55.92        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A9T9 
        7.89        67.66        41.69        15.48        22.09         9.24 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-AA61 TCGA-ZM-AA05 
       68.02        64.57         0.56        28.47        28.41        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       49.25        27.88        26.66        22.39        57.07        20.84 

$`DEL PEAK 22(11P12) WILD-TYPE`
TCGA-2G-AAF1 TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 
       46.13        22.19        24.66        45.67        44.48        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGP 
       75.58        75.25        92.09        96.59       127.92       132.10 
TCGA-2G-AAGT TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAKH TCGA-2G-AAKL 
      144.85       180.07        73.91       110.10       225.60       230.89 
TCGA-2G-AAL5 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1I TCGA-4K-AAAL TCGA-SN-A84X 
      244.50        14.30        19.96         0.10        15.88        10.26 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U3 
       17.75        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        27.72        31.92        36.59        71.24        17.62 
TCGA-YU-AA4L TCGA-ZM-AA0B 
       51.72        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 
                       232.8                        244.5 
  DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE 
                       43.45                        37.43 
[1] "0.2 - 232.8 (43.5)" "0.1 - 244.5 (37.4)"
[1] "hr=" "1.8"
D37V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(11P12) MUTATED        13       17        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                           17                            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   49 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                         49                           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   79  3
  DEL PEAK 22(11P12) WILD-TYPE 36  1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(11P12) MUTATED     79    3
  DEL PEAK 22(11P12) WILD-TYPE   36    1
   clus
vv  DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE
  0                         79                           36
  1                          3                            1
[1] 2 2
[1] FALSE
D37V7, binary
                              cls
clus                            0  1
  DEL PEAK 22(11P12) MUTATED   70 17
  DEL PEAK 22(11P12) WILD-TYPE 40  2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(11P12) MUTATED     70   17
  DEL PEAK 22(11P12) WILD-TYPE   40    2
     clus
vv    DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE
  NO                          70                           40
  YES                         17                            2
[1] 2 2
[1] FALSE
D37V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(11P12) MUTATED       3                         3    81
  DEL PEAK 22(11P12) WILD-TYPE     1                         3    38
D37V9, multiclass
                           clus
vv                          DEL PEAK 22(11P12) MUTATED
  ASIAN                                              3
  BLACK OR AFRICAN AMERICAN                          3
  WHITE                                             81
                           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"
D37V10, binary
                              cls
clus                            0  1
  DEL PEAK 22(11P12) MUTATED    9 76
  DEL PEAK 22(11P12) WILD-TYPE  3 35
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(11P12) MUTATED      9   76
  DEL PEAK 22(11P12) WILD-TYPE    3   35
                        clus
vv                       DEL PEAK 22(11P12) MUTATED
  HISPANIC OR LATINO                              9
  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   101   3
  DEL PEAK 23(11Q12.3) WILD-TYPE  29   1
  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE 
                           104                             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        41.39        76.11       114.77       128.58       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
      203.28        45.21        14.56        16.54        14.86        22.52 
TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       36.13        50.27        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGK TCGA-2G-AAGN 
       80.19        81.47        89.88        85.84       119.05       120.20 
TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      132.36       158.33       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
      182.10        59.80       232.80       211.89       186.31        17.82 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP 
      208.44       216.92       230.89       229.22       131.21        86.96 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
       14.33        17.03         0.10        15.88        22.95        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 
       17.75        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        24.76         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOD 
        0.46        55.92        93.93        12.07         7.89        67.66 
TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       41.69         0.43        15.48        22.09        27.72         9.24 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-AA61 
       68.02        64.57        36.59         0.56        28.47        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        49.25        27.55        27.88        26.66        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

$`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 
       46.13        22.19        24.66        45.67        44.48        52.37 
TCGA-2G-AAG5 TCGA-2G-AAGC TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGP 
       75.58        84.99        92.09        96.59       127.92       132.10 
TCGA-2G-AAGT TCGA-2G-AAHA TCGA-2G-AAKH TCGA-2G-AAL5 TCGA-2X-A9D5 TCGA-2X-A9D6 
      144.85       110.10       225.60       244.50        14.30        19.96 
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        71.24        17.62        51.72 

  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE 
                           0.1                            4.9 
  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE 
                         232.8                          244.5 
  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE 
                        38.515                         45.900 
[1] "0.1 - 232.8 (38.5)" "4.9 - 244.5 (45.9)"
[1] "hr=" "1.1"
D38V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(11Q12.3) MUTATED        15       20        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                             20                              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   56 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                           56                             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   91  3
  DEL PEAK 23(11Q12.3) WILD-TYPE 24  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q12.3) MUTATED     91    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                           91                             24
  1                            3                              1
[1] 2 2
[1] FALSE
D38V7, binary
                                cls
clus                              0  1
  DEL PEAK 23(11Q12.3) MUTATED   81 18
  DEL PEAK 23(11Q12.3) WILD-TYPE 29  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q12.3) MUTATED     81   18
  DEL PEAK 23(11Q12.3) WILD-TYPE   29    1
     clus
vv    DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE
  NO                            81                             29
  YES                           18                              1
[1] 2 2
[1] FALSE
D38V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(11Q12.3) MUTATED       3                         3    95
  DEL PEAK 23(11Q12.3) WILD-TYPE     1                         3    24
D38V9, multiclass
                           clus
vv                          DEL PEAK 23(11Q12.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               95
                           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"
D38V10, binary
                                cls
clus                              0  1
  DEL PEAK 23(11Q12.3) MUTATED    9 89
  DEL PEAK 23(11Q12.3) WILD-TYPE  3 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q12.3) MUTATED      9   89
  DEL PEAK 23(11Q12.3) WILD-TYPE    3   22
                        clus
vv                       DEL PEAK 23(11Q12.3) MUTATED
  HISPANIC OR LATINO                                9
  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   107   3
  DEL PEAK 24(11Q24.2) WILD-TYPE  23   1
  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE 
                           110                             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        41.39        76.11       114.77       128.58       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
      203.28        45.21        14.56        16.54        14.86        22.52 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        50.27        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
       92.09       119.05       120.20       132.36       132.10       158.33 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      148.83       161.06       181.28       175.20       172.04       180.07 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHC TCGA-2G-AAHG 
      199.23        59.90       204.16        73.91       182.10        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
      232.80       211.89       186.31        17.82       208.44       216.92 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      225.60       230.89       229.22       244.50       131.21        86.96 
TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
       14.30        14.33         0.10        15.88        22.95        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 
       17.75        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        24.76         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       67.66        41.69         0.43        15.48        22.09        27.72 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-AA61 
        9.24        68.02        64.57        36.59        28.47        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        49.25        27.55        27.88        26.66        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

$`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 
       46.13        22.19        24.66        45.67        52.37        75.58 
TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAHA TCGA-2X-A9D6 TCGA-4K-AA1H 
       96.59       127.92       144.85       110.10        19.96        17.03 
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        71.24        17.62        51.72 

  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE 
                          0.10                           0.56 
  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE 
                        244.50                         144.85 
  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE 
                        41.605                         37.430 
[1] "0.1 - 244.5 (41.6)" "0.6 - 144.8 (37.4)"
[1] "hr=" "2.3"
D39V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(11Q24.2) MUTATED        17       19        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                             19                              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   62 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                           62                             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   97  4
  DEL PEAK 24(11Q24.2) WILD-TYPE 18  0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(11Q24.2) MUTATED     97    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                           97                             18
  1                            4                              0
[1] 2 2
[1] FALSE
D39V7, binary
                                cls
clus                              0  1
  DEL PEAK 24(11Q24.2) MUTATED   87 18
  DEL PEAK 24(11Q24.2) WILD-TYPE 23  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(11Q24.2) MUTATED     87   18
  DEL PEAK 24(11Q24.2) WILD-TYPE   23    1
     clus
vv    DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE
  NO                            87                             23
  YES                           18                              1
[1] 2 2
[1] FALSE
D39V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(11Q24.2) MUTATED       3                         2   102
  DEL PEAK 24(11Q24.2) WILD-TYPE     1                         4    17
D39V9, multiclass
                           clus
vv                          DEL PEAK 24(11Q24.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                              102
                           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"
D39V10, binary
                                cls
clus                              0  1
  DEL PEAK 24(11Q24.2) MUTATED    9 96
  DEL PEAK 24(11Q24.2) WILD-TYPE  3 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(11Q24.2) MUTATED      9   96
  DEL PEAK 24(11Q24.2) WILD-TYPE    3   15
                        clus
vv                       DEL PEAK 24(11Q24.2) MUTATED
  HISPANIC OR LATINO                                9
  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   98  4
  DEL PEAK 25(13Q34) WILD-TYPE 32  0
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                         102                           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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       203.28        45.21        14.56        24.66        16.54 
TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 
       14.86        36.13        50.27        73.35        81.37        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGK 
       80.19        84.99        89.88        85.84        96.59       119.05 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGX 
      127.92       120.20       132.10       158.33       148.83       181.28 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH8 TCGA-2G-AAHA 
      175.20       172.04       180.07       199.23        73.91       110.10 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
      182.10        59.80       232.80       211.89       186.31        17.82 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      208.44       216.92       225.60       230.89       229.22       244.50 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JX TCGA-S6-A8JY 
       86.96        14.30         0.10        15.88        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        17.75 
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        24.76         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOF 
        0.46        93.93        12.07         7.89        16.87        41.69 
TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       50.96         0.43        15.48        22.09        27.72         9.24 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I 
       68.02        64.57        36.59         0.56        28.47        17.62 
TCGA-YU-AA4L TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0N 
       51.72        49.25        27.55        27.88        26.66        20.84 

$`DEL PEAK 25(13Q34) WILD-TYPE`
TCGA-2G-AAFI TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 
       22.19        22.52        45.67        44.48        52.37        75.58 
TCGA-2G-AAG8 TCGA-2G-AAGE TCGA-2G-AAGI TCGA-2G-AAGO TCGA-2G-AAGT TCGA-2G-AAGW 
       75.25        81.47        92.09       132.36       144.85       161.06 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAL7 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
       59.90       204.16       131.21        19.96        14.33        17.03 
TCGA-S6-A8JW TCGA-SN-A84X TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-W4-A7U4 TCGA-XE-AANV 
       22.95        10.26        37.18        37.68        24.26        55.92 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-YU-A90S TCGA-YU-A94D TCGA-YU-AA61 TCGA-ZM-AA05 
        8.88        67.66        31.92        71.24        28.41        37.02 
TCGA-ZM-AA0F TCGA-ZM-AA0H 
       22.39        57.07 

  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                        0.10                         8.88 
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                      244.50                       204.16 
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                      40.700                       45.075 
[1] "0.1 - 244.5 (40.7)" "8.9 - 204.2 (45.1)"
[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       21        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                           21                            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   61 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                         61                           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   87  3
  DEL PEAK 25(13Q34) WILD-TYPE 28  1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(13Q34) MUTATED     87    3
  DEL PEAK 25(13Q34) WILD-TYPE   28    1
   clus
vv  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE
  0                         87                           28
  1                          3                            1
[1] 2 2
[1] FALSE
D40V7, binary
                              cls
clus                            0  1
  DEL PEAK 25(13Q34) MUTATED   80 17
  DEL PEAK 25(13Q34) WILD-TYPE 30  2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(13Q34) MUTATED     80   17
  DEL PEAK 25(13Q34) WILD-TYPE   30    2
     clus
vv    DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE
  NO                          80                           30
  YES                         17                            2
[1] 2 2
[1] FALSE
D40V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(13Q34) MUTATED       4                         6    89
  DEL PEAK 25(13Q34) WILD-TYPE     0                         0    30
D40V9, multiclass
                           clus
vv                          DEL PEAK 25(13Q34) MUTATED
  ASIAN                                              4
  BLACK OR AFRICAN AMERICAN                          6
  WHITE                                             89
                           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"
D40V10, binary
                              cls
clus                            0  1
  DEL PEAK 25(13Q34) MUTATED   10 84
  DEL PEAK 25(13Q34) WILD-TYPE  2 27
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(13Q34) MUTATED     10   84
  DEL PEAK 25(13Q34) WILD-TYPE    2   27
                        clus
vv                       DEL PEAK 25(13Q34) MUTATED
  HISPANIC OR LATINO                             10
  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   60  1
  DEL PEAK 26(16Q23.1) WILD-TYPE 70  3
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            61                             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 
       76.11       114.77       128.58       154.59       203.28        45.21 
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAG3 
       22.19        14.56        24.66        14.86        36.13        52.37 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGJ 
       81.37        73.45        80.19        84.99        89.88        96.59 
TCGA-2G-AAGP TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
      132.10       161.06       175.20       180.07       199.23        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       73.91        59.80       232.80       186.31        17.82       208.44 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      216.92       225.60       230.89       229.22       244.50       131.21 
TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-SB-A6J6 TCGA-SB-A76C TCGA-VF-A8AC TCGA-W4-A7U2 
       14.30        14.33        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 
       24.76         0.16         0.82        28.14         6.87        40.01 
TCGA-XE-A9SE TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAO6 TCGA-XE-AAOJ TCGA-XY-A89B 
       23.28        65.98         0.46         7.89        50.96        15.48 
TCGA-XY-A8S2 TCGA-XY-A9T9 TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA0D 
       22.09         9.24        17.62        51.72        28.41        27.88 
TCGA-ZM-AA0N 
       20.84 

$`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        41.39        46.13        16.54        22.52        45.67 
TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAGE 
       44.48        50.27        75.58        73.35        75.25        81.47 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       85.84        92.09       119.05       127.92       120.20       132.36 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAH4 
      158.33       144.85       148.83       181.28       172.04       204.16 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHN TCGA-2G-AALP TCGA-2X-A9D6 TCGA-4K-AA1H 
      110.10       182.10       211.89        86.96        19.96        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SN-A6IS 
        0.10        15.88        22.95        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        17.75        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        55.92        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        27.72 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       68.02        64.57        31.92        36.59         0.56        28.47 
TCGA-YU-A94D TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0E TCGA-ZM-AA0F 
       71.24        37.02        49.25        27.55        26.66        22.39 
TCGA-ZM-AA0H 
       57.07 

  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 
                        244.50                         211.89 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                         51.72                          37.02 
[1] "0.2 - 244.5 (51.7)" "0.1 - 211.9 (37.0)"
[1] "hr="   "5e+08"
D41V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(16Q23.1) MUTATED        12        9        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                              9                             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   34 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                           34                             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   55  0
  DEL PEAK 26(16Q23.1) WILD-TYPE 60  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED     55    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                           55                             60
  1                            0                              4
[1] 2 2
[1] FALSE
D41V7, binary
                                cls
clus                              0  1
  DEL PEAK 26(16Q23.1) MUTATED   46 12
  DEL PEAK 26(16Q23.1) WILD-TYPE 64  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED     46   12
  DEL PEAK 26(16Q23.1) WILD-TYPE   64    7
     clus
vv    DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  NO                            46                             64
  YES                           12                              7
[1] 2 2
[1] FALSE
D41V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(16Q23.1) MUTATED       1                         2    56
  DEL PEAK 26(16Q23.1) WILD-TYPE     3                         4    63
D41V9, multiclass
                           clus
vv                          DEL PEAK 26(16Q23.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               56
                           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"
D41V10, binary
                                cls
clus                              0  1
  DEL PEAK 26(16Q23.1) MUTATED    6 52
  DEL PEAK 26(16Q23.1) WILD-TYPE  6 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED      6   52
  DEL PEAK 26(16Q23.1) WILD-TYPE    6   59
                        clus
vv                       DEL PEAK 26(16Q23.1) MUTATED
  HISPANIC OR LATINO                                6
  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   102   4
  DEL PEAK 27(18P11.32) WILD-TYPE  28   0
  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE 
                            106                              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        46.13        76.11       114.77       128.58       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
      203.28        45.21        24.66        16.54        14.86        22.52 
TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        50.27        52.37        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS 
       96.59       119.05       127.92       120.20       132.36       158.33 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      148.83       161.06       181.28       175.20       172.04       180.07 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL 
      199.23        59.90       204.16       182.10        59.80       232.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL 
      211.89       186.31        17.82       208.44       216.92       230.89 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1I 
      229.22       244.50       131.21        86.96        14.30         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
       15.88        22.95        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        17.75        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        24.76         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE 
        0.82        28.14         6.87        18.38        40.01        23.28 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB 
       34.22        65.98         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-A8S2 
       67.66        41.69        50.96         0.43        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y 
       27.72         9.24        68.02        64.57        36.59         0.56 
TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B 
       28.47        17.62        51.72        28.41        49.25        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0N 
       27.88        26.66        22.39        20.84 

$`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 
       41.39        22.19        14.56        45.67        44.48        75.58 
TCGA-2G-AAGI TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAKH 
       92.09       132.10       144.85        73.91       110.10       225.60 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A84X 
       19.96        14.33        17.03         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        55.92         7.89         8.88 
TCGA-YU-A90S TCGA-YU-A94D TCGA-ZM-AA05 TCGA-ZM-AA0H 
       31.92        71.24        37.02        57.07 

  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE 
                           0.10                            7.89 
  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE 
                          244.5                           225.6 
  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE 
                          43.45                           37.10 
[1] "0.1 - 244.5 (43.5)" "7.9 - 225.6 (37.1)"
[1] "hr="     "9.4e+07"
D42V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(18P11.32) MUTATED        17       18        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                              18                               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   61 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                            61                              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   90  3
  DEL PEAK 27(18P11.32) WILD-TYPE 25  1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(18P11.32) MUTATED     90    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                            90                              25
  1                             3                               1
[1] 2 2
[1] FALSE
D42V7, binary
                                 cls
clus                               0  1
  DEL PEAK 27(18P11.32) MUTATED   86 15
  DEL PEAK 27(18P11.32) WILD-TYPE 24  4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(18P11.32) MUTATED     86   15
  DEL PEAK 27(18P11.32) WILD-TYPE   24    4
     clus
vv    DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE
  NO                             86                              24
  YES                            15                               4
[1] 2 2
[1] FALSE
D42V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(18P11.32) MUTATED       3                         6    94
  DEL PEAK 27(18P11.32) WILD-TYPE     1                         0    25
D42V9, multiclass
                           clus
vv                          DEL PEAK 27(18P11.32) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                94
                           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"
D42V10, binary
                                 cls
clus                               0  1
  DEL PEAK 27(18P11.32) MUTATED   10 87
  DEL PEAK 27(18P11.32) WILD-TYPE  2 24
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(18P11.32) MUTATED     10   87
  DEL PEAK 27(18P11.32) WILD-TYPE    2   24
                        clus
vv                       DEL PEAK 27(18P11.32) MUTATED
  HISPANIC OR LATINO                                10
  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   109   4
  DEL PEAK 28(18Q22.2) WILD-TYPE  21   0
  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE 
                           113                             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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      154.59       203.28        45.21        22.19        14.56        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.54        14.86        22.52        36.13        50.27        52.37 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       73.35        81.37        75.25        73.45        80.19        84.99 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       81.47        89.88        85.84        92.09        96.59       119.05 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
      127.92       120.20       132.36       158.33       144.85       148.83 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
      161.06       181.28       175.20       172.04       180.07       199.23 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP 
       59.90       204.16       182.10        59.80       232.80       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
       17.82       208.44       216.92       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
      131.21        86.96        14.30         0.10        15.88        22.95 
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        17.75        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        24.76         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE 
        0.82        28.14         6.87        18.38        40.01        23.28 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       34.22        65.98         0.46        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
       16.87        67.66        41.69        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W 
       22.09        27.72         9.24        68.02        64.57        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA06 
        0.56        28.47        17.62        51.72        28.41        49.25 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0N 
       27.55        27.88        26.66        22.39        20.84 

$`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 
       45.67        44.48        75.58       132.10        73.91       110.10 
TCGA-2G-AAHN TCGA-2G-AAKH TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-SN-A84X 
      211.89       225.60        19.96        14.33        17.03        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        55.92         8.88        31.92 
TCGA-YU-A94D TCGA-ZM-AA05 TCGA-ZM-AA0H 
       71.24        37.02        57.07 

  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE 
                          0.10                           8.88 
  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE 
                         244.5                          225.6 
  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE 
                         41.39                          44.48 
[1] "0.1 - 244.5 (41.4)" "8.9 - 225.6 (44.5)"
[1] "hr="     "8.7e+07"
D43V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(18Q22.2) MUTATED        17       20        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                             20                              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   66 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                           66                             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   97  3
  DEL PEAK 28(18Q22.2) WILD-TYPE 18  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q22.2) MUTATED     97    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                           97                             18
  1                            3                              1
[1] 2 2
[1] FALSE
D43V7, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q22.2) MUTATED   92 16
  DEL PEAK 28(18Q22.2) WILD-TYPE 18  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q22.2) MUTATED     92   16
  DEL PEAK 28(18Q22.2) WILD-TYPE   18    3
     clus
vv    DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE
  NO                            92                             18
  YES                           16                              3
[1] 2 2
[1] FALSE
D43V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(18Q22.2) MUTATED       4                         6   100
  DEL PEAK 28(18Q22.2) WILD-TYPE     0                         0    19
D43V9, multiclass
                           clus
vv                          DEL PEAK 28(18Q22.2) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                              100
                           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"
D43V10, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q22.2) MUTATED   10 94
  DEL PEAK 28(18Q22.2) WILD-TYPE  2 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q22.2) MUTATED     10   94
  DEL PEAK 28(18Q22.2) WILD-TYPE    2   17
                        clus
vv                       DEL PEAK 28(18Q22.2) MUTATED
  HISPANIC OR LATINO                               10
  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 86  1
  DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE 
                             47                              87 
  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        16.54        14.86        36.13        50.27        73.35 
TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGG 
       81.37        75.25        80.19        84.99        81.47        85.84 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH4 
      158.33       148.83       161.06       181.28       175.20       204.16 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
      208.44       216.92       225.60       230.89       229.22       131.21 
TCGA-2G-AALP TCGA-S6-A8JX TCGA-SN-A84W TCGA-SN-A84Y TCGA-VF-A8AD TCGA-W4-A7U3 
       86.96        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 
       22.09        27.72        68.02         0.56        51.72 

$`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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFO 
      154.59       203.28        45.21        22.19        24.66        22.52 
TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG9 TCGA-2G-AAGF 
       45.67        44.48        52.37        75.58        73.45        89.88 
TCGA-2G-AAGI TCGA-2G-AAGT TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
       92.09       144.85       172.04       180.07       199.23        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       73.91       110.10       182.10        59.80       232.80       211.89 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAL5 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      186.31        17.82       244.50        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JY TCGA-SB-A6J6 
       17.03         0.10        15.88        22.95         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        17.75        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        24.76 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE 
        5.06         0.16         0.82        18.38        40.01        23.28 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        55.92        93.93        12.07         7.89 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A9T9 
        8.88        67.66        41.69         0.43        15.48         9.24 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       64.57        31.92        36.59        28.47        71.24        17.62 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
       28.41        37.02        49.25        27.55        27.88        26.66 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       22.39        57.07        20.84 

  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 
                         230.89                          244.50 
  DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE 
                          80.19                           36.59 
[1] "0.6 - 230.9 (80.2)" "0.1 - 244.5 (36.6)"
[1] "hr=" "4.6"
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       23        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                              23
  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 53 29  4
D44V4, multiclass
    clus
vv   DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE
  T1                            23                              53
  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 74  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.41) MUTATED     41    2
  DEL PEAK 29(19Q13.41) WILD-TYPE   74    2
   clus
vv  DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE
  0                            41                              74
  1                             2                               2
[1] 2 2
[1] FALSE
D44V7, binary
                                 cls
clus                               0  1
  DEL PEAK 29(19Q13.41) MUTATED   47  0
  DEL PEAK 29(19Q13.41) WILD-TYPE 63 19
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.41) MUTATED     47    0
  DEL PEAK 29(19Q13.41) WILD-TYPE   63   19
     clus
vv    DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE
  NO                             47                              63
  YES                             0                              19
[1] 2 2
[1] FALSE
D44V8, continuous
                                 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    76
D44V9, 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                                                  76
[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"
D44V10, binary
                                 cls
clus                               0  1
  DEL PEAK 29(19Q13.41) MUTATED    4 39
  DEL PEAK 29(19Q13.41) WILD-TYPE  8 72
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.41) MUTATED      4   39
  DEL PEAK 29(19Q13.41) WILD-TYPE    8   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                                   8
  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 103   4
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            27                            107 
  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 
       76.11        14.86        73.35        81.37        73.45        96.59 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGZ TCGA-2G-AAH4 
      132.10       158.33       161.06       181.28       172.04       204.16 
TCGA-2G-AAL5 TCGA-2G-AALP TCGA-S6-A8JY TCGA-SN-A84Y TCGA-VF-A8AC TCGA-WZ-A7V3 
      244.50        86.96         9.14        17.23        35.61        24.76 
TCGA-XE-A8H1 TCGA-XE-AANJ TCGA-XE-AAO6 TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
        6.87        65.98         7.89        22.09        27.72         9.24 
TCGA-YU-A912 TCGA-ZM-AA0B TCGA-ZM-AA0N 
       28.47        27.55        20.84 

$`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        41.39        46.13       114.77       128.58       154.59 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      203.28        45.21        22.19        14.56        24.66        16.54 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       22.52        45.67        36.13        44.48        50.27        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       75.58        75.25        80.19        84.99        81.47        89.88 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       85.84        92.09       119.05       127.92       120.20       132.36 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGY TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
      144.85       148.83       175.20       180.07       199.23        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       73.91       110.10       182.10        59.80       232.80       211.89 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
      186.31        17.82       208.44       216.92       225.60       230.89 
TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      229.22       131.21        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C 
        0.10        15.88        22.95        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        17.75        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-A9SE TCGA-XE-AANI TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        23.28        34.22         0.46        55.92        93.93 
TCGA-XE-AAO4 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ 
       12.07        16.87         8.88        67.66        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
        0.43        15.48        68.02        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        0.56        71.24        17.62        51.72        28.41        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       49.25        27.88        26.66        22.39        57.07 

  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                          6.87                           0.10 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                         244.5                          232.8 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                         65.98                          41.39 
[1] "6.9 - 244.5 (66.0)" "0.1 - 232.8 (41.4)"
[1] "hr="     "2.7e+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       21       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                             21
  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 59 41  6
D45V4, multiclass
    clus
vv   DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  T1                           17                             59
  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 92  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED     23    2
  DEL PEAK 30(20P12.1) WILD-TYPE   92    2
   clus
vv  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  0                           23                             92
  1                            2                              2
[1] 2 2
[1] FALSE
D45V7, binary
                                cls
clus                              0  1
  DEL PEAK 30(20P12.1) MUTATED   24  3
  DEL PEAK 30(20P12.1) WILD-TYPE 86 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED     24    3
  DEL PEAK 30(20P12.1) WILD-TYPE   86   16
     clus
vv    DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  NO                            24                             86
  YES                            3                             16
[1] 2 2
[1] FALSE
D45V8, continuous
                                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    94
D45V9, 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                                                 94
[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"
D45V10, binary
                                cls
clus                              0  1
  DEL PEAK 30(20P12.1) MUTATED    3 23
  DEL PEAK 30(20P12.1) WILD-TYPE  9 88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED      3   23
  DEL PEAK 30(20P12.1) WILD-TYPE    9   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                                  9
  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 107   4
  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE 
                           23                           111 
  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        75.58        81.37        96.59       132.36       148.83 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHG TCGA-2G-AAHP TCGA-2G-AAL5 TCGA-2X-A9D5 
       59.90       204.16        59.80       186.31       244.50        14.30 
TCGA-S6-A8JY TCGA-SN-A84W TCGA-SO-A8JP TCGA-W4-A7U2 TCGA-XE-AANI TCGA-XE-AANJ 
        9.14         9.63        17.75        41.52        34.22        65.98 
TCGA-XE-AAOJ TCGA-YU-A912 TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA0N 
       50.96        28.47        17.62        51.72        20.84 

$`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        41.39        46.13        76.11       114.77       128.58 
TCGA-2G-AAFE TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM 
      154.59       203.28        45.21        22.19        24.66        16.54 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        22.52        45.67        36.13        44.48        50.27 
TCGA-2G-AAG3 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       52.37        73.35        75.25        73.45        80.19        84.99 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM 
       81.47        89.88        85.84        92.09       119.05       127.92 
TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGX 
      120.20       132.10       158.33       144.85       161.06       181.28 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH8 TCGA-2G-AAHA 
      175.20       172.04       180.07       199.23        73.91       110.10 
TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
      182.10       232.80       211.89        17.82       208.44       216.92 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D6 
      225.60       230.89       229.22       131.21        86.96        19.96 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
       14.33        17.03         0.10        15.88        22.95        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        24.76         5.06         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANR 
       28.14         6.87        18.38        40.01        23.28         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       55.92        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        15.48        22.09        27.72 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        9.24        68.02        64.57        31.92        36.59         0.56 
TCGA-YU-A94D TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       71.24        28.41        37.02        49.25        27.55        27.88 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       26.66        22.39        57.07 

  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE 
                         9.14                          0.10 
  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE 
                        244.5                         232.8 
  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE 
                        51.72                         37.68 
[1] "9.1 - 244.5 (51.7)" "0.1 - 232.8 (37.7)"
[1] "hr="     "2.6e+08"
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       24       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                            24
  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 59 45  6
D46V4, multiclass
    clus
vv   DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE
  T1                          17                            59
  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 96  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 31(XP21.1) MUTATED     19    0
  DEL PEAK 31(XP21.1) WILD-TYPE   96    4
   clus
vv  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE
  0                          19                            96
  1                           0                             4
[1] 2 2
[1] FALSE
D46V7, binary
                               cls
clus                             0  1
  DEL PEAK 31(XP21.1) MUTATED   21  2
  DEL PEAK 31(XP21.1) WILD-TYPE 89 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 31(XP21.1) MUTATED     21    2
  DEL PEAK 31(XP21.1) WILD-TYPE   89   17
     clus
vv    DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE
  NO                           21                            89
  YES                           2                            17
[1] 2 2
[1] FALSE
D46V8, continuous
                               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   101
D46V9, 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                                               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"
D46V10, binary
                               cls
clus                             0  1
  DEL PEAK 31(XP21.1) MUTATED    3 17
  DEL PEAK 31(XP21.1) WILD-TYPE  9 94
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 31(XP21.1) MUTATED      3   17
  DEL PEAK 31(XP21.1) WILD-TYPE    9   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                                 9
  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 105   4
  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE 
                           25                           109 
  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 
      114.77       154.59        14.56        75.58        81.37       119.05 
TCGA-2G-AAGV TCGA-2G-AAGY TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHG TCGA-2G-AAHP 
      148.83       175.20        59.90       204.16        59.80       186.31 
TCGA-2G-AAHT TCGA-2G-AAL5 TCGA-2G-AALP TCGA-S6-A8JY TCGA-SN-A84W TCGA-W4-A7U2 
       17.82       244.50        86.96         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        27.72        28.47 
TCGA-YU-AA61 
       28.41 

$`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        41.39        46.13        76.11       128.58       203.28 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
       45.21        22.19        24.66        16.54        14.86        22.52 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG6 
       45.67        36.13        44.48        50.27        52.37        73.35 
TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       75.25        73.45        80.19        84.99        81.47        89.88 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       85.84        92.09        96.59       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGZ 
      132.10       158.33       144.85       161.06       181.28       172.04 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL 
      180.07       199.23        73.91       110.10       182.10       232.80 
TCGA-2G-AAHN TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
      211.89       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL7 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
      131.21        14.30        19.96        14.33        17.03         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       15.88        22.95        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        17.75        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 
       24.76         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A9SE TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       18.38        23.28         0.46        55.92        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-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       15.48        22.09         9.24        68.02        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-ZM-AA05 
       36.59         0.56        71.24        17.62        51.72        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       49.25        27.55        27.88        26.66        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE 
                         9.14                          0.10 
  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE 
                        244.5                         232.8 
  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE 
                        59.90                         37.02 
[1] "9.1 - 244.5 (59.9)" "0.1 - 232.8 (37.0)"
[1] "hr="     "2.7e+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       26       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                            26
  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 59 43  6
D47V4, multiclass
    clus
vv   DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE
  T1                          17                            59
  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 94  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 32(XQ27.3) MUTATED     21    1
  DEL PEAK 32(XQ27.3) WILD-TYPE   94    3
   clus
vv  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE
  0                          21                            94
  1                           1                             3
[1] 2 2
[1] FALSE
D47V7, binary
                               cls
clus                             0  1
  DEL PEAK 32(XQ27.3) MUTATED   20  5
  DEL PEAK 32(XQ27.3) WILD-TYPE 90 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 32(XQ27.3) MUTATED     20    5
  DEL PEAK 32(XQ27.3) WILD-TYPE   90   14
     clus
vv    DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE
  NO                           20                            90
  YES                           5                            14
[1] 2 2
[1] FALSE
D47V8, continuous
                               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    97
D47V9, 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                                                97
[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"
D47V10, binary
                               cls
clus                             0  1
  DEL PEAK 32(XQ27.3) MUTATED    4 19
  DEL PEAK 32(XQ27.3) WILD-TYPE  8 92
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 32(XQ27.3) MUTATED      4   19
  DEL PEAK 32(XQ27.3) WILD-TYPE    8   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                                 8
  NOT HISPANIC OR LATINO                            92
[1] 2 2
[1] FALSE
