[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[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/11541779/TGCT-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/TGCT-TP/11544840/transformed.cor.cli.txt"

nPatients in clinical file=31, in cluster file=150, common to both=31
[1] "Reduce the number of clustering variables from 47 to 42."
[1] 42 31
[1] "AMP PEAK  1(1Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                           13                            18 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                           13                            18 
[1] "AMP PEAK  2(2P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE 
                           16                            15 
  AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE 
                           16                            15 
[1] "AMP PEAK  3(3Q27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                           12                            19 
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                           12                            19 
[1] "AMP PEAK  4(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                          4                          27 
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                          4                          27 
[1] "AMP PEAK  6(7Q11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE 
                            28                              3 
  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE 
                            28                              3 
[1] "AMP PEAK  7(8Q11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE 
                            28                              3 
  AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE 
                            28                              3 
[1] "AMP PEAK  8(8Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE 
                           25                             6 
  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE 
                           25                             6 
[1] "AMP PEAK 12(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                          22                            9 
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                          22                            9 
[1] "AMP PEAK 13(16Q21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE 
                           6                           25 
  AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE 
                           6                           25 
[1] "AMP PEAK 14(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE 
                             11                              20 
  AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE 
                             11                              20 
[1] "AMP PEAK 15(22Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE 
                             10                              21 
  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE 
                             10                              21 
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                             7                             24 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                             7                             24 
[1] "DEL PEAK  2(1P31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                            8                            23 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                            8                            23 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            5                            26 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            5                            26 
[1] "DEL PEAK  5(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE 
                           14                            17 
  DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE 
                           14                            17 
[1] "DEL PEAK  6(4Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE 
                           25                             6 
  DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE 
                           25                             6 
[1] "DEL PEAK  7(5P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE 
                           21                            10 
  DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE 
                           21                            10 
[1] "DEL PEAK  8(5P14.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE 
                           22                             9 
  DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE 
                           22                             9 
[1] "DEL PEAK  9(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           21                            10 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           21                            10 
[1] "DEL PEAK 10(6P22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE 
                            7                            24 
  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE 
                            7                            24 
[1] "DEL PEAK 11(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                          8                          23 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                          8                          23 
[1] "DEL PEAK 12(7Q11.22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE 
                             3                             28 
  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE 
                             3                             28 
[1] "DEL PEAK 13(7Q36.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE 
                            4                            27 
  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE 
                            4                            27 
[1] "DEL PEAK 14(9P24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE 
                           19                            12 
  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE 
                           19                            12 
[1] "DEL PEAK 15(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                         19                          12 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                         19                          12 
[1] "DEL PEAK 16(9Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE 
                           16                            15 
  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE 
                           16                            15 
[1] "DEL PEAK 17(9Q34.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE 
                           14                            17 
  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE 
                           14                            17 
[1] "DEL PEAK 18(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                            22                              9 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                            22                              9 
[1] "DEL PEAK 19(10Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE 
                            20                             11 
  DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE 
                            20                             11 
[1] "DEL PEAK 20(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                            18                             13 
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                            18                             13 
[1] "DEL PEAK 21(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                            18                             13 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                            18                             13 
[1] "DEL PEAK 22(11P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE 
                          19                           12 
  DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE 
                          19                           12 
[1] "DEL PEAK 23(11Q12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE 
                            23                              8 
  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE 
                            23                              8 
[1] "DEL PEAK 24(11Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE 
                            26                              5 
  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE 
                            26                              5 
[1] "DEL PEAK 25(13Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                          22                            9 
  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE 
                          22                            9 
[1] "DEL PEAK 26(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            15                             16 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            15                             16 
[1] "DEL PEAK 27(18P11.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE 
                             26                               5 
  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE 
                             26                               5 
[1] "DEL PEAK 28(18Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE 
                            27                              4 
  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE 
                            27                              4 
[1] "DEL PEAK 29(19Q13.41) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE 
                             18                              13 
  DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE 
                             18                              13 
[1] "DEL PEAK 30(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                             7                             24 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                             7                             24 
[1] "DEL PEAK 31(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE 
                            7                            24 
  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE 
                            7                            24 
[1] "DEL PEAK 32(XQ27.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE 
                            7                            24 
  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE 
                            7                            24 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONTHERAPY"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCHNUMBER"                           

Input Data has 15 rows and 31 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-2G-AAF6 TCGA-2G-AAFL TCGA-2G-AAFZ TCGA-2G-AAG9 TCGA-2G-AAGE TCGA-2G-AAGG 
        3113          428         1122         1926         2080         2067 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
        2801         2284         1814         3236         3498         3669 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG 
        3922         1869         2462         3823         1817         1819 
TCGA-2G-AAKD TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2X-A9D6 TCGA-SO-A8JP TCGA-X3-A8G4 
        3726         2651         3991            4          107          856 
TCGA-XE-A8H1 TCGA-XE-AANR TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A8S3 TCGA-ZM-AA05 
         209           14         1550           13          424          757 
TCGA-ZM-AA06 
        1197 
Variable 1:'AGE':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
Variable 3:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RACE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "ETHNICITY"            
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 31 columns, 0 survival variables, and 5 non-survival variables.
AGE, nv=19, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=10, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 
15 14  2 
[1] "table(vv)"
vv
   T1 T2+T3 
   15    16 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 
15 14  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 15

$Class1_nSamples
[1] 16

$Class0_label
[1] "T1"

$Class1_label
[1] "T2+T3"


   T1 T2+T3 
   15    16 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q21.2) MUTATION ANALYSIS
D1V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  1(1Q21.2) MUTATED         2        0        1        1         1
  AMP PEAK  1(1Q21.2) WILD-TYPE       3        1        1        2         0
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  AMP PEAK  1(1Q21.2) MUTATED           1         0          0          1
  AMP PEAK  1(1Q21.2) WILD-TYPE         0         2          2          0
                               vv
clus                            STAGE IS
  AMP PEAK  1(1Q21.2) MUTATED          6
  AMP PEAK  1(1Q21.2) WILD-TYPE        7
D1V2, multiclass
            clus
vv           AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             0                             1
  STAGE IB                             1                             1
  STAGE II                             1                             2
  STAGE IIA                            1                             0
  STAGE IIC                            1                             0
  STAGE III                            0                             2
  STAGE IIIB                           0                             2
  STAGE IIIC                           1                             0
  STAGE IS                             6                             7
[1] 10  2
[1] 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    6     7
  AMP PEAK  1(1Q21.2) WILD-TYPE  9     9
D1V3, multiclass
       clus
vv      AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  T1                              6                             9
  T2+T3                           7                             9
[1] 2 2
[1] FALSE
D1V4, binary
                               cls
clus                            0 1
  AMP PEAK  1(1Q21.2) MUTATED   6 2
  AMP PEAK  1(1Q21.2) WILD-TYPE 7 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED      6    2
  AMP PEAK  1(1Q21.2) WILD-TYPE    7    2
   clus
vv  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  0                           6                             7
  1                           2                             2
[1] 2 2
[1] FALSE
D1V5, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q21.2) MUTATED    1 12
  AMP PEAK  1(1Q21.2) WILD-TYPE  2 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED      1   12
  AMP PEAK  1(1Q21.2) WILD-TYPE    2   16
                        clus
vv                       AMP PEAK  1(1Q21.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          12
                        clus
vv                       AMP PEAK  1(1Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            16
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(2P24.1) MUTATION ANALYSIS
D2V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  2(2P24.1) MUTATED         2        1        1        0         1
  AMP PEAK  2(2P24.1) WILD-TYPE       3        0        1        3         0
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  AMP PEAK  2(2P24.1) MUTATED           0         1          0          1
  AMP PEAK  2(2P24.1) WILD-TYPE         1         1          2          0
                               vv
clus                            STAGE IS
  AMP PEAK  2(2P24.1) MUTATED          9
  AMP PEAK  2(2P24.1) WILD-TYPE        4
D2V2, multiclass
            clus
vv           AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             1                             0
  STAGE IB                             1                             1
  STAGE II                             0                             3
  STAGE IIA                            1                             0
  STAGE IIC                            0                             1
  STAGE III                            1                             1
  STAGE IIIB                           0                             2
  STAGE IIIC                           1                             0
  STAGE IS                             9                             4
[1] 10  2
[1] 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   10     6
  AMP PEAK  2(2P24.1) WILD-TYPE  5    10
D2V3, multiclass
       clus
vv      AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE
  T1                             10                             5
  T2+T3                           6                            10
[1] 2 2
[1] FALSE
D2V4, binary
                               cls
clus                            0 1
  AMP PEAK  2(2P24.1) MUTATED   9 2
  AMP PEAK  2(2P24.1) WILD-TYPE 4 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P24.1) MUTATED      9    2
  AMP PEAK  2(2P24.1) WILD-TYPE    4    2
   clus
vv  AMP PEAK  2(2P24.1) MUTATED AMP PEAK  2(2P24.1) WILD-TYPE
  0                           9                             4
  1                           2                             2
[1] 2 2
[1] FALSE
D2V5, binary
                               cls
clus                             0  1
  AMP PEAK  2(2P24.1) MUTATED    0 16
  AMP PEAK  2(2P24.1) WILD-TYPE  3 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P24.1) MUTATED      0   16
  AMP PEAK  2(2P24.1) WILD-TYPE    3   12
                        clus
vv                       AMP PEAK  2(2P24.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          16
                        clus
vv                       AMP PEAK  2(2P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            12
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(3Q27.3) MUTATION ANALYSIS
D3V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  3(3Q27.3) MUTATED         0        1        0        0         1
  AMP PEAK  3(3Q27.3) WILD-TYPE       5        0        2        3         0
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  AMP PEAK  3(3Q27.3) MUTATED           0         2          0          1
  AMP PEAK  3(3Q27.3) WILD-TYPE         1         0          2          0
                               vv
clus                            STAGE IS
  AMP PEAK  3(3Q27.3) MUTATED          7
  AMP PEAK  3(3Q27.3) WILD-TYPE        6
D3V2, multiclass
            clus
vv           AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             1                             0
  STAGE IB                             0                             2
  STAGE II                             0                             3
  STAGE IIA                            1                             0
  STAGE IIC                            0                             1
  STAGE III                            2                             0
  STAGE IIIB                           0                             2
  STAGE IIIC                           1                             0
  STAGE IS                             7                             6
[1] 10  2
[1] 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    6     6
  AMP PEAK  3(3Q27.3) WILD-TYPE  9    10
D3V3, multiclass
       clus
vv      AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  T1                              6                             9
  T2+T3                           6                            10
[1] 2 2
[1] FALSE
D3V4, binary
                               cls
clus                            0 1
  AMP PEAK  3(3Q27.3) MUTATED   6 2
  AMP PEAK  3(3Q27.3) WILD-TYPE 7 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q27.3) MUTATED      6    2
  AMP PEAK  3(3Q27.3) WILD-TYPE    7    2
   clus
vv  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  0                           6                             7
  1                           2                             2
[1] 2 2
[1] FALSE
D3V5, binary
                               cls
clus                             0  1
  AMP PEAK  3(3Q27.3) MUTATED    1 11
  AMP PEAK  3(3Q27.3) WILD-TYPE  2 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q27.3) MUTATED      1   11
  AMP PEAK  3(3Q27.3) WILD-TYPE    2   17
                        clus
vv                       AMP PEAK  3(3Q27.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          11
                        clus
vv                       AMP PEAK  3(3Q27.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            17
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(4Q12) MUTATION ANALYSIS
D4V1, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  4(4Q12) MUTATED         1        0        0        0         0
  AMP PEAK  4(4Q12) WILD-TYPE       4        1        2        3         1
                             vv
clus                          STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  AMP PEAK  4(4Q12) MUTATED           0         1          0          0
  AMP PEAK  4(4Q12) WILD-TYPE         1         1          2          1
                             vv
clus                          STAGE IS
  AMP PEAK  4(4Q12) MUTATED          2
  AMP PEAK  4(4Q12) WILD-TYPE       11
D4V2, multiclass
            clus
vv           AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  STAGE I                            1                           4
  STAGE IA                           0                           1
  STAGE IB                           0                           2
  STAGE II                           0                           3
  STAGE IIA                          0                           1
  STAGE IIC                          0                           1
  STAGE III                          1                           1
  STAGE IIIB                         0                           2
  STAGE IIIC                         0                           1
  STAGE IS                           2                          11
[1] 10  2
[1] 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    2     2
  AMP PEAK  4(4Q12) WILD-TYPE 13    14
D4V3, multiclass
       clus
vv      AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  T1                            2                          13
  T2+T3                         2                          14
[1] 2 2
[1] FALSE
D4V4, binary
                             cls
clus                           0  1
  AMP PEAK  4(4Q12) MUTATED    2  0
  AMP PEAK  4(4Q12) WILD-TYPE 11  4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(4Q12) MUTATED      2    0
  AMP PEAK  4(4Q12) WILD-TYPE   11    4
   clus
vv  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  0                         2                          11
  1                         0                           4
[1] 2 2
[1] FALSE
D4V5, binary
                             cls
clus                           0  1
  AMP PEAK  4(4Q12) MUTATED    0  4
  AMP PEAK  4(4Q12) WILD-TYPE  3 24
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(4Q12) MUTATED      0    4
  AMP PEAK  4(4Q12) WILD-TYPE    3   24
                        clus
vv                       AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             0                           3
  NOT HISPANIC OR LATINO                         4                          24
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  6(7Q11.22) MUTATION ANALYSIS
D5V1, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  6(7Q11.22) MUTATED         4        1        2        3         1
  AMP PEAK  6(7Q11.22) WILD-TYPE       1        0        0        0         0
                                vv
clus                             STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  AMP PEAK  6(7Q11.22) MUTATED           1         2          2          1
  AMP PEAK  6(7Q11.22) WILD-TYPE         0         0          0          0
                                vv
clus                             STAGE IS
  AMP PEAK  6(7Q11.22) MUTATED         11
  AMP PEAK  6(7Q11.22) WILD-TYPE        2
D5V2, multiclass
            clus
vv           AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                              1                              0
  STAGE IB                              2                              0
  STAGE II                              3                              0
  STAGE IIA                             1                              0
  STAGE IIC                             1                              0
  STAGE III                             2                              0
  STAGE IIIB                            2                              0
  STAGE IIIC                            1                              0
  STAGE IS                             11                              2
[1] 10  2
[1] 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   13    15
  AMP PEAK  6(7Q11.22) WILD-TYPE  2     1
D5V3, multiclass
       clus
vv      AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE
  T1                              13                              2
  T2+T3                           15                              1
[1] 2 2
[1] FALSE
D5V4, binary
                                cls
clus                              0  1
  AMP PEAK  6(7Q11.22) MUTATED   11  4
  AMP PEAK  6(7Q11.22) WILD-TYPE  2  0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(7Q11.22) MUTATED     11    4
  AMP PEAK  6(7Q11.22) WILD-TYPE    2    0
   clus
vv  AMP PEAK  6(7Q11.22) MUTATED AMP PEAK  6(7Q11.22) WILD-TYPE
  0                           11                              2
  1                            4                              0
[1] 2 2
[1] FALSE
D5V5, binary
                                cls
clus                              0  1
  AMP PEAK  6(7Q11.22) MUTATED    2 26
  AMP PEAK  6(7Q11.22) WILD-TYPE  1  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(7Q11.22) MUTATED      2   26
  AMP PEAK  6(7Q11.22) WILD-TYPE    1    2
                        clus
vv                       AMP PEAK  6(7Q11.22) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           26
                        clus
vv                       AMP PEAK  6(7Q11.22) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                              2
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  7(8Q11.23) MUTATION ANALYSIS
D6V1, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  7(8Q11.23) MUTATED         5        0        1        2         1
  AMP PEAK  7(8Q11.23) WILD-TYPE       0        1        1        1         0
                                vv
clus                             STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  AMP PEAK  7(8Q11.23) MUTATED           1         2          2          1
  AMP PEAK  7(8Q11.23) WILD-TYPE         0         0          0          0
                                vv
clus                             STAGE IS
  AMP PEAK  7(8Q11.23) MUTATED         13
  AMP PEAK  7(8Q11.23) WILD-TYPE        0
D6V2, multiclass
            clus
vv           AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE
  STAGE I                               5                              0
  STAGE IA                              0                              1
  STAGE IB                              1                              1
  STAGE II                              2                              1
  STAGE IIA                             1                              0
  STAGE IIC                             1                              0
  STAGE III                             2                              0
  STAGE IIIB                            2                              0
  STAGE IIIC                            1                              0
  STAGE IS                             13                              0
[1] 10  2
[1] 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   13    15
  AMP PEAK  7(8Q11.23) WILD-TYPE  2     1
D6V3, multiclass
       clus
vv      AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE
  T1                              13                              2
  T2+T3                           15                              1
[1] 2 2
[1] FALSE
D6V4, binary
                                cls
clus                              0  1
  AMP PEAK  7(8Q11.23) MUTATED   11  4
  AMP PEAK  7(8Q11.23) WILD-TYPE  2  0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q11.23) MUTATED     11    4
  AMP PEAK  7(8Q11.23) WILD-TYPE    2    0
   clus
vv  AMP PEAK  7(8Q11.23) MUTATED AMP PEAK  7(8Q11.23) WILD-TYPE
  0                           11                              2
  1                            4                              0
[1] 2 2
[1] FALSE
D6V5, binary
                                cls
clus                              0  1
  AMP PEAK  7(8Q11.23) MUTATED    3 25
  AMP PEAK  7(8Q11.23) WILD-TYPE  0  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q11.23) MUTATED      3   25
  AMP PEAK  7(8Q11.23) WILD-TYPE    0    3
                        clus
vv                       AMP PEAK  7(8Q11.23) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           25
                        clus
vv                       AMP PEAK  7(8Q11.23) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                              3
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  8(8Q23.3) MUTATION ANALYSIS
D7V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  8(8Q23.3) MUTATED         5        0        1        2         1
  AMP PEAK  8(8Q23.3) WILD-TYPE       0        1        1        1         0
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  AMP PEAK  8(8Q23.3) MUTATED           1         2          2          1
  AMP PEAK  8(8Q23.3) WILD-TYPE         0         0          0          0
                               vv
clus                            STAGE IS
  AMP PEAK  8(8Q23.3) MUTATED         10
  AMP PEAK  8(8Q23.3) WILD-TYPE        3
D7V2, multiclass
            clus
vv           AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE
  STAGE I                              5                             0
  STAGE IA                             0                             1
  STAGE IB                             1                             1
  STAGE II                             2                             1
  STAGE IIA                            1                             0
  STAGE IIC                            1                             0
  STAGE III                            2                             0
  STAGE IIIB                           2                             0
  STAGE IIIC                           1                             0
  STAGE IS                            10                             3
[1] 10  2
[1] 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   10    15
  AMP PEAK  8(8Q23.3) WILD-TYPE  5     1
D7V3, multiclass
       clus
vv      AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE
  T1                             10                             5
  T2+T3                          15                             1
[1] 2 2
[1] FALSE
D7V4, binary
                               cls
clus                            0 1
  AMP PEAK  8(8Q23.3) MUTATED   9 4
  AMP PEAK  8(8Q23.3) WILD-TYPE 4 0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q23.3) MUTATED      9    4
  AMP PEAK  8(8Q23.3) WILD-TYPE    4    0
   clus
vv  AMP PEAK  8(8Q23.3) MUTATED AMP PEAK  8(8Q23.3) WILD-TYPE
  0                           9                             4
  1                           4                             0
[1] 2 2
[1] FALSE
D7V5, binary
                               cls
clus                             0  1
  AMP PEAK  8(8Q23.3) MUTATED    2 23
  AMP PEAK  8(8Q23.3) WILD-TYPE  1  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q23.3) MUTATED      2   23
  AMP PEAK  8(8Q23.3) WILD-TYPE    1    5
                        clus
vv                       AMP PEAK  8(8Q23.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          23
                        clus
vv                       AMP PEAK  8(8Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                             5
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK 12(12Q15) MUTATION ANALYSIS
D8V1, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(12Q15) MUTATED         3        1        1        2         1
  AMP PEAK 12(12Q15) WILD-TYPE       2        0        1        1         0
                              vv
clus                           STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  AMP PEAK 12(12Q15) MUTATED           1         1          2          1
  AMP PEAK 12(12Q15) WILD-TYPE         0         1          0          0
                              vv
clus                           STAGE IS
  AMP PEAK 12(12Q15) MUTATED          9
  AMP PEAK 12(12Q15) WILD-TYPE        4
D8V2, multiclass
            clus
vv           AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE
  STAGE I                             3                            2
  STAGE IA                            1                            0
  STAGE IB                            1                            1
  STAGE II                            2                            1
  STAGE IIA                           1                            0
  STAGE IIC                           1                            0
  STAGE III                           1                            1
  STAGE IIIB                          2                            0
  STAGE IIIC                          1                            0
  STAGE IS                            9                            4
[1] 10  2
[1] 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   11    11
  AMP PEAK 12(12Q15) WILD-TYPE  4     5
D8V3, multiclass
       clus
vv      AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE
  T1                            11                            4
  T2+T3                         11                            5
[1] 2 2
[1] FALSE
D8V4, binary
                              cls
clus                           0 1
  AMP PEAK 12(12Q15) MUTATED   9 4
  AMP PEAK 12(12Q15) WILD-TYPE 4 0
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(12Q15) MUTATED      9    4
  AMP PEAK 12(12Q15) WILD-TYPE    4    0
   clus
vv  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE
  0                          9                            4
  1                          4                            0
[1] 2 2
[1] FALSE
D8V5, binary
                              cls
clus                            0  1
  AMP PEAK 12(12Q15) MUTATED    1 21
  AMP PEAK 12(12Q15) WILD-TYPE  2  7
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(12Q15) MUTATED      1   21
  AMP PEAK 12(12Q15) WILD-TYPE    2    7
                        clus
vv                       AMP PEAK 12(12Q15) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         21
                        clus
vv                       AMP PEAK 12(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            7
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK 13(16Q21) MUTATION ANALYSIS
D9V1, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(16Q21) MUTATED         0        0        1        0         0
  AMP PEAK 13(16Q21) WILD-TYPE       5        1        1        3         1
                              vv
clus                           STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  AMP PEAK 13(16Q21) MUTATED           0         0          0          1
  AMP PEAK 13(16Q21) WILD-TYPE         1         2          2          0
                              vv
clus                           STAGE IS
  AMP PEAK 13(16Q21) MUTATED          4
  AMP PEAK 13(16Q21) WILD-TYPE        9
D9V2, multiclass
            clus
vv           AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE
  STAGE I                             0                            5
  STAGE IA                            0                            1
  STAGE IB                            1                            1
  STAGE II                            0                            3
  STAGE IIA                           0                            1
  STAGE IIC                           0                            1
  STAGE III                           0                            2
  STAGE IIIB                          0                            2
  STAGE IIIC                          1                            0
  STAGE IS                            4                            9
[1] 10  2
[1] 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    3     3
  AMP PEAK 13(16Q21) WILD-TYPE 12    13
D9V3, multiclass
       clus
vv      AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE
  T1                             3                           12
  T2+T3                          3                           13
[1] 2 2
[1] FALSE
D9V4, binary
                              cls
clus                           0 1
  AMP PEAK 13(16Q21) MUTATED   4 1
  AMP PEAK 13(16Q21) WILD-TYPE 9 3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(16Q21) MUTATED      4    1
  AMP PEAK 13(16Q21) WILD-TYPE    9    3
   clus
vv  AMP PEAK 13(16Q21) MUTATED AMP PEAK 13(16Q21) WILD-TYPE
  0                          4                            9
  1                          1                            3
[1] 2 2
[1] FALSE
D9V5, binary
                              cls
clus                            0  1
  AMP PEAK 13(16Q21) MUTATED    0  6
  AMP PEAK 13(16Q21) WILD-TYPE  3 22
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(16Q21) MUTATED      0    6
  AMP PEAK 13(16Q21) WILD-TYPE    3   22
                        clus
vv                       AMP PEAK 13(16Q21) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                          6
                        clus
vv                       AMP PEAK 13(16Q21) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           22
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 14(20Q11.21) MUTATION ANALYSIS
D10V1, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(20Q11.21) MUTATED         1        0        1        1         1
  AMP PEAK 14(20Q11.21) WILD-TYPE       4        1        1        2         0
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  AMP PEAK 14(20Q11.21) MUTATED           1         1          0          1
  AMP PEAK 14(20Q11.21) WILD-TYPE         0         1          2          0
                                 vv
clus                              STAGE IS
  AMP PEAK 14(20Q11.21) MUTATED          4
  AMP PEAK 14(20Q11.21) WILD-TYPE        9
D10V2, multiclass
            clus
vv           AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                               0                               1
  STAGE IB                               1                               1
  STAGE II                               1                               2
  STAGE IIA                              1                               0
  STAGE IIC                              1                               0
  STAGE III                              1                               1
  STAGE IIIB                             0                               2
  STAGE IIIC                             1                               0
  STAGE IS                               4                               9
[1] 10  2
[1] 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    3     8
  AMP PEAK 14(20Q11.21) WILD-TYPE 12     8
D10V3, multiclass
       clus
vv      AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE
  T1                                3                              12
  T2+T3                             8                               8
[1] 2 2
[1] FALSE
D10V4, binary
                                 cls
clus                              0 1
  AMP PEAK 14(20Q11.21) MUTATED   5 2
  AMP PEAK 14(20Q11.21) WILD-TYPE 8 2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(20Q11.21) MUTATED      5    2
  AMP PEAK 14(20Q11.21) WILD-TYPE    8    2
   clus
vv  AMP PEAK 14(20Q11.21) MUTATED AMP PEAK 14(20Q11.21) WILD-TYPE
  0                             5                               8
  1                             2                               2
[1] 2 2
[1] FALSE
D10V5, binary
                                 cls
clus                               0  1
  AMP PEAK 14(20Q11.21) MUTATED    0 11
  AMP PEAK 14(20Q11.21) WILD-TYPE  3 17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(20Q11.21) MUTATED      0   11
  AMP PEAK 14(20Q11.21) WILD-TYPE    3   17
                        clus
vv                       AMP PEAK 14(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            11
                        clus
vv                       AMP PEAK 14(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                              17
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 15(22Q11.21) MUTATION ANALYSIS
D11V1, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(22Q11.21) MUTATED         3        0        1        0         0
  AMP PEAK 15(22Q11.21) WILD-TYPE       2        1        1        3         1
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  AMP PEAK 15(22Q11.21) MUTATED           0         1          0          0
  AMP PEAK 15(22Q11.21) WILD-TYPE         1         1          2          1
                                 vv
clus                              STAGE IS
  AMP PEAK 15(22Q11.21) MUTATED          5
  AMP PEAK 15(22Q11.21) WILD-TYPE        8
D11V2, multiclass
            clus
vv           AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE
  STAGE I                                3                               2
  STAGE IA                               0                               1
  STAGE IB                               1                               1
  STAGE II                               0                               3
  STAGE IIA                              0                               1
  STAGE IIC                              0                               1
  STAGE III                              1                               1
  STAGE IIIB                             0                               2
  STAGE IIIC                             0                               1
  STAGE IS                               5                               8
[1] 10  2
[1] 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    6     4
  AMP PEAK 15(22Q11.21) WILD-TYPE  9    12
D11V3, multiclass
       clus
vv      AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE
  T1                                6                               9
  T2+T3                             4                              12
[1] 2 2
[1] FALSE
D11V4, binary
                                 cls
clus                              0 1
  AMP PEAK 15(22Q11.21) MUTATED   4 0
  AMP PEAK 15(22Q11.21) WILD-TYPE 9 4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(22Q11.21) MUTATED      4    0
  AMP PEAK 15(22Q11.21) WILD-TYPE    9    4
   clus
vv  AMP PEAK 15(22Q11.21) MUTATED AMP PEAK 15(22Q11.21) WILD-TYPE
  0                             4                               9
  1                             0                               4
[1] 2 2
[1] FALSE
D11V5, binary
                                 cls
clus                               0  1
  AMP PEAK 15(22Q11.21) MUTATED    0 10
  AMP PEAK 15(22Q11.21) WILD-TYPE  3 18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(22Q11.21) MUTATED      0   10
  AMP PEAK 15(22Q11.21) WILD-TYPE    3   18
                        clus
vv                       AMP PEAK 15(22Q11.21) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            10
                        clus
vv                       AMP PEAK 15(22Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                              18
[1] 2 2
[1] FALSE

Clustering(12) Variable = DEL PEAK  1(1P36.31) MUTATION ANALYSIS
D12V1, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  1(1P36.31) MUTATED         1        0        0        1         1
  DEL PEAK  1(1P36.31) WILD-TYPE       4        1        2        2         0
                                vv
clus                             STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK  1(1P36.31) MUTATED           0         0          0          0
  DEL PEAK  1(1P36.31) WILD-TYPE         1         2          2          1
                                vv
clus                             STAGE IS
  DEL PEAK  1(1P36.31) MUTATED          4
  DEL PEAK  1(1P36.31) WILD-TYPE        9
D12V2, multiclass
            clus
vv           DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                              0                              1
  STAGE IB                              0                              2
  STAGE II                              1                              2
  STAGE IIA                             1                              0
  STAGE IIC                             0                              1
  STAGE III                             0                              2
  STAGE IIIB                            0                              2
  STAGE IIIC                            0                              1
  STAGE IS                              4                              9
[1] 10  2
[1] 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    5     2
  DEL PEAK  1(1P36.31) WILD-TYPE 10    14
D12V3, multiclass
       clus
vv      DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T1                               5                             10
  T2+T3                            2                             14
[1] 2 2
[1] FALSE
D12V4, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED    2  1
  DEL PEAK  1(1P36.31) WILD-TYPE 11  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      2    1
  DEL PEAK  1(1P36.31) WILD-TYPE   11    3
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                            2                             11
  1                            1                              3
[1] 2 2
[1] FALSE
D12V5, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED    2  5
  DEL PEAK  1(1P36.31) WILD-TYPE  1 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      2    5
  DEL PEAK  1(1P36.31) WILD-TYPE    1   23
                        clus
vv                       DEL PEAK  1(1P36.31) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            5
                        clus
vv                       DEL PEAK  1(1P36.31) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             23
[1] 2 2
[1] FALSE

Clustering(13) Variable = DEL PEAK  2(1P31.1) MUTATION ANALYSIS
D13V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  2(1P31.1) MUTATED         2        1        0        0         0
  DEL PEAK  2(1P31.1) WILD-TYPE       3        0        2        3         1
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK  2(1P31.1) MUTATED           0         0          0          1
  DEL PEAK  2(1P31.1) WILD-TYPE         1         2          2          0
                               vv
clus                            STAGE IS
  DEL PEAK  2(1P31.1) MUTATED          4
  DEL PEAK  2(1P31.1) WILD-TYPE        9
D13V2, multiclass
            clus
vv           DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             1                             0
  STAGE IB                             0                             2
  STAGE II                             0                             3
  STAGE IIA                            0                             1
  STAGE IIC                            0                             1
  STAGE III                            0                             2
  STAGE IIIB                           0                             2
  STAGE IIIC                           1                             0
  STAGE IS                             4                             9
[1] 10  2
[1] 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    4     4
  DEL PEAK  2(1P31.1) WILD-TYPE 11    12
D13V3, multiclass
       clus
vv      DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  T1                              4                            11
  T2+T3                           4                            12
[1] 2 2
[1] FALSE
D13V4, binary
                               cls
clus                            0 1
  DEL PEAK  2(1P31.1) MUTATED   5 1
  DEL PEAK  2(1P31.1) WILD-TYPE 8 3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED      5    1
  DEL PEAK  2(1P31.1) WILD-TYPE    8    3
   clus
vv  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  0                           5                             8
  1                           1                             3
[1] 2 2
[1] FALSE
D13V5, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P31.1) MUTATED    1  7
  DEL PEAK  2(1P31.1) WILD-TYPE  2 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED      1    7
  DEL PEAK  2(1P31.1) WILD-TYPE    2   21
                        clus
vv                       DEL PEAK  2(1P31.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           7
                        clus
vv                       DEL PEAK  2(1P31.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            21
[1] 2 2
[1] FALSE

Clustering(14) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D14V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  4(2Q37.3) MUTATED         1        1        0        1         0
  DEL PEAK  4(2Q37.3) WILD-TYPE       4        0        2        2         1
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK  4(2Q37.3) MUTATED           0         0          1          0
  DEL PEAK  4(2Q37.3) WILD-TYPE         1         2          1          1
                               vv
clus                            STAGE IS
  DEL PEAK  4(2Q37.3) MUTATED          1
  DEL PEAK  4(2Q37.3) WILD-TYPE       12
D14V2, multiclass
            clus
vv           DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                             1                             0
  STAGE IB                             0                             2
  STAGE II                             1                             2
  STAGE IIA                            0                             1
  STAGE IIC                            0                             1
  STAGE III                            0                             2
  STAGE IIIB                           1                             1
  STAGE IIIC                           0                             1
  STAGE IS                             1                            12
[1] 10  2
[1] 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    3     2
  DEL PEAK  4(2Q37.3) WILD-TYPE 12    14
D14V3, multiclass
       clus
vv      DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  T1                              3                            12
  T2+T3                           2                            14
[1] 2 2
[1] FALSE
D14V4, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.3) MUTATED    2  1
  DEL PEAK  4(2Q37.3) WILD-TYPE 11  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      2    1
  DEL PEAK  4(2Q37.3) WILD-TYPE   11    3
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                           2                            11
  1                           1                             3
[1] 2 2
[1] FALSE
D14V5, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.3) MUTATED    0  5
  DEL PEAK  4(2Q37.3) WILD-TYPE  3 23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      0    5
  DEL PEAK  4(2Q37.3) WILD-TYPE    3   23
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            23
[1] 2 2
[1] FALSE

Clustering(15) Variable = DEL PEAK  5(3P26.2) MUTATION ANALYSIS
D15V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  5(3P26.2) MUTATED         2        1        1        0         0
  DEL PEAK  5(3P26.2) WILD-TYPE       3        0        1        3         1
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK  5(3P26.2) MUTATED           1         1          2          1
  DEL PEAK  5(3P26.2) WILD-TYPE         0         1          0          0
                               vv
clus                            STAGE IS
  DEL PEAK  5(3P26.2) MUTATED          5
  DEL PEAK  5(3P26.2) WILD-TYPE        8
D15V2, multiclass
            clus
vv           DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             1                             0
  STAGE IB                             1                             1
  STAGE II                             0                             3
  STAGE IIA                            0                             1
  STAGE IIC                            1                             0
  STAGE III                            1                             1
  STAGE IIIB                           2                             0
  STAGE IIIC                           1                             0
  STAGE IS                             5                             8
[1] 10  2
[1] 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    5     9
  DEL PEAK  5(3P26.2) WILD-TYPE 10     7
D15V3, multiclass
       clus
vv      DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE
  T1                              5                            10
  T2+T3                           9                             7
[1] 2 2
[1] FALSE
D15V4, binary
                               cls
clus                            0 1
  DEL PEAK  5(3P26.2) MUTATED   6 3
  DEL PEAK  5(3P26.2) WILD-TYPE 7 1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.2) MUTATED      6    3
  DEL PEAK  5(3P26.2) WILD-TYPE    7    1
   clus
vv  DEL PEAK  5(3P26.2) MUTATED DEL PEAK  5(3P26.2) WILD-TYPE
  0                           6                             7
  1                           3                             1
[1] 2 2
[1] FALSE
D15V5, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P26.2) MUTATED    1 13
  DEL PEAK  5(3P26.2) WILD-TYPE  2 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P26.2) MUTATED      1   13
  DEL PEAK  5(3P26.2) WILD-TYPE    2   15
                        clus
vv                       DEL PEAK  5(3P26.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          13
                        clus
vv                       DEL PEAK  5(3P26.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            15
[1] 2 2
[1] FALSE

Clustering(16) Variable = DEL PEAK  6(4Q22.2) MUTATION ANALYSIS
D16V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(4Q22.2) MUTATED         4        1        2        3         1
  DEL PEAK  6(4Q22.2) WILD-TYPE       1        0        0        0         0
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK  6(4Q22.2) MUTATED           0         1          2          1
  DEL PEAK  6(4Q22.2) WILD-TYPE         1         1          0          0
                               vv
clus                            STAGE IS
  DEL PEAK  6(4Q22.2) MUTATED         10
  DEL PEAK  6(4Q22.2) WILD-TYPE        3
D16V2, multiclass
            clus
vv           DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE
  STAGE I                              4                             1
  STAGE IA                             1                             0
  STAGE IB                             2                             0
  STAGE II                             3                             0
  STAGE IIA                            1                             0
  STAGE IIC                            0                             1
  STAGE III                            1                             1
  STAGE IIIB                           2                             0
  STAGE IIIC                           1                             0
  STAGE IS                            10                             3
[1] 10  2
[1] 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   12    13
  DEL PEAK  6(4Q22.2) WILD-TYPE  3     3
D16V3, multiclass
       clus
vv      DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE
  T1                             12                             3
  T2+T3                          13                             3
[1] 2 2
[1] FALSE
D16V4, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q22.2) MUTATED   10  4
  DEL PEAK  6(4Q22.2) WILD-TYPE  3  0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q22.2) MUTATED     10    4
  DEL PEAK  6(4Q22.2) WILD-TYPE    3    0
   clus
vv  DEL PEAK  6(4Q22.2) MUTATED DEL PEAK  6(4Q22.2) WILD-TYPE
  0                          10                             3
  1                           4                             0
[1] 2 2
[1] FALSE
D16V5, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q22.2) MUTATED    3 22
  DEL PEAK  6(4Q22.2) WILD-TYPE  0  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q22.2) MUTATED      3   22
  DEL PEAK  6(4Q22.2) WILD-TYPE    0    6
                        clus
vv                       DEL PEAK  6(4Q22.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          22
                        clus
vv                       DEL PEAK  6(4Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                             6
[1] 2 2
[1] FALSE

Clustering(17) Variable = DEL PEAK  7(5P15.2) MUTATION ANALYSIS
D17V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  7(5P15.2) MUTATED         4        1        1        2         1
  DEL PEAK  7(5P15.2) WILD-TYPE       1        0        1        1         0
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK  7(5P15.2) MUTATED           1         1          1          0
  DEL PEAK  7(5P15.2) WILD-TYPE         0         1          1          1
                               vv
clus                            STAGE IS
  DEL PEAK  7(5P15.2) MUTATED          9
  DEL PEAK  7(5P15.2) WILD-TYPE        4
D17V2, multiclass
            clus
vv           DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE
  STAGE I                              4                             1
  STAGE IA                             1                             0
  STAGE IB                             1                             1
  STAGE II                             2                             1
  STAGE IIA                            1                             0
  STAGE IIC                            1                             0
  STAGE III                            1                             1
  STAGE IIIB                           1                             1
  STAGE IIIC                           0                             1
  STAGE IS                             9                             4
[1] 10  2
[1] 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   12     9
  DEL PEAK  7(5P15.2) WILD-TYPE  3     7
D17V3, multiclass
       clus
vv      DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE
  T1                             12                             3
  T2+T3                           9                             7
[1] 2 2
[1] FALSE
D17V4, binary
                               cls
clus                            0 1
  DEL PEAK  7(5P15.2) MUTATED   8 2
  DEL PEAK  7(5P15.2) WILD-TYPE 5 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5P15.2) MUTATED      8    2
  DEL PEAK  7(5P15.2) WILD-TYPE    5    2
   clus
vv  DEL PEAK  7(5P15.2) MUTATED DEL PEAK  7(5P15.2) WILD-TYPE
  0                           8                             5
  1                           2                             2
[1] 2 2
[1] FALSE
D17V5, binary
                               cls
clus                             0  1
  DEL PEAK  7(5P15.2) MUTATED    2 19
  DEL PEAK  7(5P15.2) WILD-TYPE  1  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5P15.2) MUTATED      2   19
  DEL PEAK  7(5P15.2) WILD-TYPE    1    9
                        clus
vv                       DEL PEAK  7(5P15.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          19
                        clus
vv                       DEL PEAK  7(5P15.2) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                             9
[1] 2 2
[1] FALSE

Clustering(18) Variable = DEL PEAK  8(5P14.3) MUTATION ANALYSIS
D18V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(5P14.3) MUTATED         4        1        1        3         1
  DEL PEAK  8(5P14.3) WILD-TYPE       1        0        1        0         0
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK  8(5P14.3) MUTATED           1         1          1          0
  DEL PEAK  8(5P14.3) WILD-TYPE         0         1          1          1
                               vv
clus                            STAGE IS
  DEL PEAK  8(5P14.3) MUTATED          9
  DEL PEAK  8(5P14.3) WILD-TYPE        4
D18V2, multiclass
            clus
vv           DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE
  STAGE I                              4                             1
  STAGE IA                             1                             0
  STAGE IB                             1                             1
  STAGE II                             3                             0
  STAGE IIA                            1                             0
  STAGE IIC                            1                             0
  STAGE III                            1                             1
  STAGE IIIB                           1                             1
  STAGE IIIC                           0                             1
  STAGE IS                             9                             4
[1] 10  2
[1] 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   13     9
  DEL PEAK  8(5P14.3) WILD-TYPE  2     7
D18V3, multiclass
       clus
vv      DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE
  T1                             13                             2
  T2+T3                           9                             7
[1] 2 2
[1] FALSE
D18V4, binary
                               cls
clus                            0 1
  DEL PEAK  8(5P14.3) MUTATED   8 2
  DEL PEAK  8(5P14.3) WILD-TYPE 5 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P14.3) MUTATED      8    2
  DEL PEAK  8(5P14.3) WILD-TYPE    5    2
   clus
vv  DEL PEAK  8(5P14.3) MUTATED DEL PEAK  8(5P14.3) WILD-TYPE
  0                           8                             5
  1                           2                             2
[1] 2 2
[1] FALSE
D18V5, binary
                               cls
clus                             0  1
  DEL PEAK  8(5P14.3) MUTATED    2 20
  DEL PEAK  8(5P14.3) WILD-TYPE  1  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P14.3) MUTATED      2   20
  DEL PEAK  8(5P14.3) WILD-TYPE    1    8
                        clus
vv                       DEL PEAK  8(5P14.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          20
                        clus
vv                       DEL PEAK  8(5P14.3) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                             8
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEL PEAK  9(5Q12.1) MUTATION ANALYSIS
D19V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  9(5Q12.1) MUTATED         4        1        1        3         1
  DEL PEAK  9(5Q12.1) WILD-TYPE       1        0        1        0         0
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK  9(5Q12.1) MUTATED           1         0          1          0
  DEL PEAK  9(5Q12.1) WILD-TYPE         0         2          1          1
                               vv
clus                            STAGE IS
  DEL PEAK  9(5Q12.1) MUTATED          9
  DEL PEAK  9(5Q12.1) WILD-TYPE        4
D19V2, multiclass
            clus
vv           DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  STAGE I                              4                             1
  STAGE IA                             1                             0
  STAGE IB                             1                             1
  STAGE II                             3                             0
  STAGE IIA                            1                             0
  STAGE IIC                            1                             0
  STAGE III                            0                             2
  STAGE IIIB                           1                             1
  STAGE IIIC                           0                             1
  STAGE IS                             9                             4
[1] 10  2
[1] 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   13     8
  DEL PEAK  9(5Q12.1) WILD-TYPE  2     8
D19V3, multiclass
       clus
vv      DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  T1                             13                             2
  T2+T3                           8                             8
[1] 2 2
[1] FALSE
D19V4, binary
                               cls
clus                            0 1
  DEL PEAK  9(5Q12.1) MUTATED   8 2
  DEL PEAK  9(5Q12.1) WILD-TYPE 5 2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED      8    2
  DEL PEAK  9(5Q12.1) WILD-TYPE    5    2
   clus
vv  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  0                           8                             5
  1                           2                             2
[1] 2 2
[1] FALSE
D19V5, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q12.1) MUTATED    2 19
  DEL PEAK  9(5Q12.1) WILD-TYPE  1  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED      2   19
  DEL PEAK  9(5Q12.1) WILD-TYPE    1    9
                        clus
vv                       DEL PEAK  9(5Q12.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          19
                        clus
vv                       DEL PEAK  9(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                             9
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK 10(6P22.3) MUTATION ANALYSIS
D20V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 10(6P22.3) MUTATED         0        0        1        1         0
  DEL PEAK 10(6P22.3) WILD-TYPE       5        1        1        2         1
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 10(6P22.3) MUTATED           0         0          0          0
  DEL PEAK 10(6P22.3) WILD-TYPE         1         2          2          1
                               vv
clus                            STAGE IS
  DEL PEAK 10(6P22.3) MUTATED          5
  DEL PEAK 10(6P22.3) WILD-TYPE        8
D20V2, multiclass
            clus
vv           DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             0                             1
  STAGE IB                             1                             1
  STAGE II                             1                             2
  STAGE IIA                            0                             1
  STAGE IIC                            0                             1
  STAGE III                            0                             2
  STAGE IIIB                           0                             2
  STAGE IIIC                           0                             1
  STAGE IS                             5                             8
[1] 10  2
[1] 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    3     4
  DEL PEAK 10(6P22.3) WILD-TYPE 12    12
D20V3, multiclass
       clus
vv      DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE
  T1                              3                            12
  T2+T3                           4                            12
[1] 2 2
[1] FALSE
D20V4, binary
                               cls
clus                            0 1
  DEL PEAK 10(6P22.3) MUTATED   4 0
  DEL PEAK 10(6P22.3) WILD-TYPE 9 4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P22.3) MUTATED      4    0
  DEL PEAK 10(6P22.3) WILD-TYPE    9    4
   clus
vv  DEL PEAK 10(6P22.3) MUTATED DEL PEAK 10(6P22.3) WILD-TYPE
  0                           4                             9
  1                           0                             4
[1] 2 2
[1] FALSE
D20V5, binary
                               cls
clus                             0  1
  DEL PEAK 10(6P22.3) MUTATED    1  6
  DEL PEAK 10(6P22.3) WILD-TYPE  2 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P22.3) MUTATED      1    6
  DEL PEAK 10(6P22.3) WILD-TYPE    2   22
                        clus
vv                       DEL PEAK 10(6P22.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           6
                        clus
vv                       DEL PEAK 10(6P22.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            22
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK 11(6Q26) MUTATION ANALYSIS
D21V1, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 11(6Q26) MUTATED         1        1        0        1         1
  DEL PEAK 11(6Q26) WILD-TYPE       4        0        2        2         0
                             vv
clus                          STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 11(6Q26) MUTATED           0         0          0          0
  DEL PEAK 11(6Q26) WILD-TYPE         1         2          2          1
                             vv
clus                          STAGE IS
  DEL PEAK 11(6Q26) MUTATED          4
  DEL PEAK 11(6Q26) WILD-TYPE        9
D21V2, multiclass
            clus
vv           DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  STAGE I                            1                           4
  STAGE IA                           1                           0
  STAGE IB                           0                           2
  STAGE II                           1                           2
  STAGE IIA                          1                           0
  STAGE IIC                          0                           1
  STAGE III                          0                           2
  STAGE IIIB                         0                           2
  STAGE IIIC                         0                           1
  STAGE IS                           4                           9
[1] 10  2
[1] 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    5     3
  DEL PEAK 11(6Q26) WILD-TYPE 10    13
D21V3, multiclass
       clus
vv      DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  T1                            5                          10
  T2+T3                         3                          13
[1] 2 2
[1] FALSE
D21V4, binary
                             cls
clus                          0 1
  DEL PEAK 11(6Q26) MUTATED   5 1
  DEL PEAK 11(6Q26) WILD-TYPE 8 3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED      5    1
  DEL PEAK 11(6Q26) WILD-TYPE    8    3
   clus
vv  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  0                         5                           8
  1                         1                           3
[1] 2 2
[1] FALSE
D21V5, binary
                             cls
clus                           0  1
  DEL PEAK 11(6Q26) MUTATED    1  7
  DEL PEAK 11(6Q26) WILD-TYPE  2 21
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED      1    7
  DEL PEAK 11(6Q26) WILD-TYPE    2   21
                        clus
vv                       DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             1                           2
  NOT HISPANIC OR LATINO                         7                          21
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK 12(7Q11.22) MUTATION ANALYSIS
D22V1, 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       5        1        2        3         1
                                vv
clus                             STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 12(7Q11.22) MUTATED           0         0          0          0
  DEL PEAK 12(7Q11.22) WILD-TYPE         1         2          2          1
                                vv
clus                             STAGE IS
  DEL PEAK 12(7Q11.22) MUTATED          3
  DEL PEAK 12(7Q11.22) WILD-TYPE       10
D22V2, multiclass
            clus
vv           DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                              0                              1
  STAGE IB                              0                              2
  STAGE II                              0                              3
  STAGE IIA                             0                              1
  STAGE IIC                             0                              1
  STAGE III                             0                              2
  STAGE IIIB                            0                              2
  STAGE IIIC                            0                              1
  STAGE IS                              3                             10
[1] 10  2
[1] 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
  DEL PEAK 12(7Q11.22) WILD-TYPE 13    15
D22V3, multiclass
       clus
vv      DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE
  T1                               2                             13
  T2+T3                            1                             15
[1] 2 2
[1] FALSE
D22V4, binary
                                cls
clus                              0  1
  DEL PEAK 12(7Q11.22) MUTATED    2  0
  DEL PEAK 12(7Q11.22) WILD-TYPE 11  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(7Q11.22) MUTATED      2    0
  DEL PEAK 12(7Q11.22) WILD-TYPE   11    4
   clus
vv  DEL PEAK 12(7Q11.22) MUTATED DEL PEAK 12(7Q11.22) WILD-TYPE
  0                            2                             11
  1                            0                              4
[1] 2 2
[1] FALSE
D22V5, binary
                                cls
clus                              0  1
  DEL PEAK 12(7Q11.22) MUTATED    1  2
  DEL PEAK 12(7Q11.22) WILD-TYPE  2 26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(7Q11.22) MUTATED      1    2
  DEL PEAK 12(7Q11.22) WILD-TYPE    2   26
                        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                                  2
  NOT HISPANIC OR LATINO                             26
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK 13(7Q36.1) MUTATION ANALYSIS
D23V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 13(7Q36.1) MUTATED         0        0        0        0         0
  DEL PEAK 13(7Q36.1) WILD-TYPE       5        1        2        3         1
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 13(7Q36.1) MUTATED           0         0          0          0
  DEL PEAK 13(7Q36.1) WILD-TYPE         1         2          2          1
                               vv
clus                            STAGE IS
  DEL PEAK 13(7Q36.1) MUTATED          4
  DEL PEAK 13(7Q36.1) WILD-TYPE        9
D23V2, multiclass
            clus
vv           DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             0                             1
  STAGE IB                             0                             2
  STAGE II                             0                             3
  STAGE IIA                            0                             1
  STAGE IIC                            0                             1
  STAGE III                            0                             2
  STAGE IIIB                           0                             2
  STAGE IIIC                           0                             1
  STAGE IS                             4                             9
[1] 10  2
[1] 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    3     1
  DEL PEAK 13(7Q36.1) WILD-TYPE 12    15
D23V3, multiclass
       clus
vv      DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE
  T1                              3                            12
  T2+T3                           1                            15
[1] 2 2
[1] FALSE
D23V4, binary
                               cls
clus                             0  1
  DEL PEAK 13(7Q36.1) MUTATED    3  0
  DEL PEAK 13(7Q36.1) WILD-TYPE 10  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.1) MUTATED      3    0
  DEL PEAK 13(7Q36.1) WILD-TYPE   10    4
   clus
vv  DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE
  0                           3                            10
  1                           0                             4
[1] 2 2
[1] FALSE
D23V5, binary
                               cls
clus                             0  1
  DEL PEAK 13(7Q36.1) MUTATED    1  3
  DEL PEAK 13(7Q36.1) WILD-TYPE  2 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.1) MUTATED      1    3
  DEL PEAK 13(7Q36.1) WILD-TYPE    2   25
                        clus
vv                       DEL PEAK 13(7Q36.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       DEL PEAK 13(7Q36.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            25
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK 14(9P24.3) MUTATION ANALYSIS
D24V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(9P24.3) MUTATED         2        0        1        2         1
  DEL PEAK 14(9P24.3) WILD-TYPE       3        1        1        1         0
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 14(9P24.3) MUTATED           1         0          2          1
  DEL PEAK 14(9P24.3) WILD-TYPE         0         2          0          0
                               vv
clus                            STAGE IS
  DEL PEAK 14(9P24.3) MUTATED          9
  DEL PEAK 14(9P24.3) WILD-TYPE        4
D24V2, multiclass
            clus
vv           DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             0                             1
  STAGE IB                             1                             1
  STAGE II                             2                             1
  STAGE IIA                            1                             0
  STAGE IIC                            1                             0
  STAGE III                            0                             2
  STAGE IIIB                           2                             0
  STAGE IIIC                           1                             0
  STAGE IS                             9                             4
[1] 10  2
[1] 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    8    11
  DEL PEAK 14(9P24.3) WILD-TYPE  7     5
D24V3, multiclass
       clus
vv      DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE
  T1                              8                             7
  T2+T3                          11                             5
[1] 2 2
[1] FALSE
D24V4, binary
                               cls
clus                            0 1
  DEL PEAK 14(9P24.3) MUTATED   8 4
  DEL PEAK 14(9P24.3) WILD-TYPE 5 0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P24.3) MUTATED      8    4
  DEL PEAK 14(9P24.3) WILD-TYPE    5    0
   clus
vv  DEL PEAK 14(9P24.3) MUTATED DEL PEAK 14(9P24.3) WILD-TYPE
  0                           8                             5
  1                           4                             0
[1] 2 2
[1] FALSE
D24V5, binary
                               cls
clus                             0  1
  DEL PEAK 14(9P24.3) MUTATED    2 17
  DEL PEAK 14(9P24.3) WILD-TYPE  1 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P24.3) MUTATED      2   17
  DEL PEAK 14(9P24.3) WILD-TYPE    1   11
                        clus
vv                       DEL PEAK 14(9P24.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          17
                        clus
vv                       DEL PEAK 14(9P24.3) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            11
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK 15(9P23) MUTATION ANALYSIS
D25V1, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(9P23) MUTATED         2        0        1        2         1
  DEL PEAK 15(9P23) WILD-TYPE       3        1        1        1         0
                             vv
clus                          STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 15(9P23) MUTATED           1         0          2          1
  DEL PEAK 15(9P23) WILD-TYPE         0         2          0          0
                             vv
clus                          STAGE IS
  DEL PEAK 15(9P23) MUTATED          9
  DEL PEAK 15(9P23) WILD-TYPE        4
D25V2, multiclass
            clus
vv           DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  STAGE I                            2                           3
  STAGE IA                           0                           1
  STAGE IB                           1                           1
  STAGE II                           2                           1
  STAGE IIA                          1                           0
  STAGE IIC                          1                           0
  STAGE III                          0                           2
  STAGE IIIB                         2                           0
  STAGE IIIC                         1                           0
  STAGE IS                           9                           4
[1] 10  2
[1] 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    8    11
  DEL PEAK 15(9P23) WILD-TYPE  7     5
D25V3, multiclass
       clus
vv      DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  T1                            8                           7
  T2+T3                        11                           5
[1] 2 2
[1] FALSE
D25V4, binary
                             cls
clus                          0 1
  DEL PEAK 15(9P23) MUTATED   8 4
  DEL PEAK 15(9P23) WILD-TYPE 5 0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED      8    4
  DEL PEAK 15(9P23) WILD-TYPE    5    0
   clus
vv  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  0                         8                           5
  1                         4                           0
[1] 2 2
[1] FALSE
D25V5, binary
                             cls
clus                           0  1
  DEL PEAK 15(9P23) MUTATED    2 17
  DEL PEAK 15(9P23) WILD-TYPE  1 11
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED      2   17
  DEL PEAK 15(9P23) WILD-TYPE    1   11
                        clus
vv                       DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  HISPANIC OR LATINO                             2                           1
  NOT HISPANIC OR LATINO                        17                          11
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK 16(9Q33.3) MUTATION ANALYSIS
D26V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(9Q33.3) MUTATED         2        1        1        2         1
  DEL PEAK 16(9Q33.3) WILD-TYPE       3        0        1        1         0
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 16(9Q33.3) MUTATED           0         0          2          1
  DEL PEAK 16(9Q33.3) WILD-TYPE         1         2          0          0
                               vv
clus                            STAGE IS
  DEL PEAK 16(9Q33.3) MUTATED          6
  DEL PEAK 16(9Q33.3) WILD-TYPE        7
D26V2, multiclass
            clus
vv           DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             1                             0
  STAGE IB                             1                             1
  STAGE II                             2                             1
  STAGE IIA                            1                             0
  STAGE IIC                            0                             1
  STAGE III                            0                             2
  STAGE IIIB                           2                             0
  STAGE IIIC                           1                             0
  STAGE IS                             6                             7
[1] 10  2
[1] 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    7     9
  DEL PEAK 16(9Q33.3) WILD-TYPE  8     7
D26V3, multiclass
       clus
vv      DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE
  T1                              7                             8
  T2+T3                           9                             7
[1] 2 2
[1] FALSE
D26V4, binary
                               cls
clus                            0 1
  DEL PEAK 16(9Q33.3) MUTATED   7 4
  DEL PEAK 16(9Q33.3) WILD-TYPE 6 0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9Q33.3) MUTATED      7    4
  DEL PEAK 16(9Q33.3) WILD-TYPE    6    0
   clus
vv  DEL PEAK 16(9Q33.3) MUTATED DEL PEAK 16(9Q33.3) WILD-TYPE
  0                           7                             6
  1                           4                             0
[1] 2 2
[1] FALSE
D26V5, binary
                               cls
clus                             0  1
  DEL PEAK 16(9Q33.3) MUTATED    1 15
  DEL PEAK 16(9Q33.3) WILD-TYPE  2 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9Q33.3) MUTATED      1   15
  DEL PEAK 16(9Q33.3) WILD-TYPE    2   13
                        clus
vv                       DEL PEAK 16(9Q33.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          15
                        clus
vv                       DEL PEAK 16(9Q33.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            13
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK 17(9Q34.2) MUTATION ANALYSIS
D27V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 17(9Q34.2) MUTATED         2        1        1        2         1
  DEL PEAK 17(9Q34.2) WILD-TYPE       3        0        1        1         0
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 17(9Q34.2) MUTATED           0         0          2          1
  DEL PEAK 17(9Q34.2) WILD-TYPE         1         2          0          0
                               vv
clus                            STAGE IS
  DEL PEAK 17(9Q34.2) MUTATED          4
  DEL PEAK 17(9Q34.2) WILD-TYPE        9
D27V2, multiclass
            clus
vv           DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             1                             0
  STAGE IB                             1                             1
  STAGE II                             2                             1
  STAGE IIA                            1                             0
  STAGE IIC                            0                             1
  STAGE III                            0                             2
  STAGE IIIB                           2                             0
  STAGE IIIC                           1                             0
  STAGE IS                             4                             9
[1] 10  2
[1] 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    6     8
  DEL PEAK 17(9Q34.2) WILD-TYPE  9     8
D27V3, multiclass
       clus
vv      DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE
  T1                              6                             9
  T2+T3                           8                             8
[1] 2 2
[1] FALSE
D27V4, binary
                               cls
clus                            0 1
  DEL PEAK 17(9Q34.2) MUTATED   6 4
  DEL PEAK 17(9Q34.2) WILD-TYPE 7 0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9Q34.2) MUTATED      6    4
  DEL PEAK 17(9Q34.2) WILD-TYPE    7    0
   clus
vv  DEL PEAK 17(9Q34.2) MUTATED DEL PEAK 17(9Q34.2) WILD-TYPE
  0                           6                             7
  1                           4                             0
[1] 2 2
[1] FALSE
D27V5, binary
                               cls
clus                             0  1
  DEL PEAK 17(9Q34.2) MUTATED    0 14
  DEL PEAK 17(9Q34.2) WILD-TYPE  3 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9Q34.2) MUTATED      0   14
  DEL PEAK 17(9Q34.2) WILD-TYPE    3   14
                        clus
vv                       DEL PEAK 17(9Q34.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          14
                        clus
vv                       DEL PEAK 17(9Q34.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            14
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK 18(10P15.3) MUTATION ANALYSIS
D28V1, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(10P15.3) MUTATED         2        0        1        3         1
  DEL PEAK 18(10P15.3) WILD-TYPE       3        1        1        0         0
                                vv
clus                             STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 18(10P15.3) MUTATED           0         2          2          1
  DEL PEAK 18(10P15.3) WILD-TYPE         1         0          0          0
                                vv
clus                             STAGE IS
  DEL PEAK 18(10P15.3) MUTATED         10
  DEL PEAK 18(10P15.3) WILD-TYPE        3
D28V2, multiclass
            clus
vv           DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                              0                              1
  STAGE IB                              1                              1
  STAGE II                              3                              0
  STAGE IIA                             1                              0
  STAGE IIC                             0                              1
  STAGE III                             2                              0
  STAGE IIIB                            2                              0
  STAGE IIIC                            1                              0
  STAGE IS                             10                              3
[1] 10  2
[1] 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   10    12
  DEL PEAK 18(10P15.3) WILD-TYPE  5     4
D28V3, multiclass
       clus
vv      DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  T1                              10                              5
  T2+T3                           12                              4
[1] 2 2
[1] FALSE
D28V4, binary
                                cls
clus                             0 1
  DEL PEAK 18(10P15.3) MUTATED   9 4
  DEL PEAK 18(10P15.3) WILD-TYPE 4 0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED      9    4
  DEL PEAK 18(10P15.3) WILD-TYPE    4    0
   clus
vv  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  0                            9                              4
  1                            4                              0
[1] 2 2
[1] FALSE
D28V5, binary
                                cls
clus                              0  1
  DEL PEAK 18(10P15.3) MUTATED    1 21
  DEL PEAK 18(10P15.3) WILD-TYPE  2  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED      1   21
  DEL PEAK 18(10P15.3) WILD-TYPE    2    7
                        clus
vv                       DEL PEAK 18(10P15.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           21
                        clus
vv                       DEL PEAK 18(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                              7
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK 19(10Q23.1) MUTATION ANALYSIS
D29V1, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 19(10Q23.1) MUTATED         3        1        1        3         1
  DEL PEAK 19(10Q23.1) WILD-TYPE       2        0        1        0         0
                                vv
clus                             STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 19(10Q23.1) MUTATED           0         1          2          1
  DEL PEAK 19(10Q23.1) WILD-TYPE         1         1          0          0
                                vv
clus                             STAGE IS
  DEL PEAK 19(10Q23.1) MUTATED          7
  DEL PEAK 19(10Q23.1) WILD-TYPE        6
D29V2, multiclass
            clus
vv           DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                              1                              0
  STAGE IB                              1                              1
  STAGE II                              3                              0
  STAGE IIA                             1                              0
  STAGE IIC                             0                              1
  STAGE III                             1                              1
  STAGE IIIB                            2                              0
  STAGE IIIC                            1                              0
  STAGE IS                              7                              6
[1] 10  2
[1] 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   11     9
  DEL PEAK 19(10Q23.1) WILD-TYPE  4     7
D29V3, multiclass
       clus
vv      DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE
  T1                              11                              4
  T2+T3                            9                              7
[1] 2 2
[1] FALSE
D29V4, binary
                                cls
clus                             0 1
  DEL PEAK 19(10Q23.1) MUTATED   9 4
  DEL PEAK 19(10Q23.1) WILD-TYPE 4 0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q23.1) MUTATED      9    4
  DEL PEAK 19(10Q23.1) WILD-TYPE    4    0
   clus
vv  DEL PEAK 19(10Q23.1) MUTATED DEL PEAK 19(10Q23.1) WILD-TYPE
  0                            9                              4
  1                            4                              0
[1] 2 2
[1] FALSE
D29V5, binary
                                cls
clus                              0  1
  DEL PEAK 19(10Q23.1) MUTATED    0 20
  DEL PEAK 19(10Q23.1) WILD-TYPE  3  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q23.1) MUTATED      0   20
  DEL PEAK 19(10Q23.1) WILD-TYPE    3    8
                        clus
vv                       DEL PEAK 19(10Q23.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           20
                        clus
vv                       DEL PEAK 19(10Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                              8
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK 20(10Q26.3) MUTATION ANALYSIS
D30V1, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(10Q26.3) MUTATED         2        0        1        3         1
  DEL PEAK 20(10Q26.3) WILD-TYPE       3        1        1        0         0
                                vv
clus                             STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 20(10Q26.3) MUTATED           0         1          2          1
  DEL PEAK 20(10Q26.3) WILD-TYPE         1         1          0          0
                                vv
clus                             STAGE IS
  DEL PEAK 20(10Q26.3) MUTATED          7
  DEL PEAK 20(10Q26.3) WILD-TYPE        6
D30V2, multiclass
            clus
vv           DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                              0                              1
  STAGE IB                              1                              1
  STAGE II                              3                              0
  STAGE IIA                             1                              0
  STAGE IIC                             0                              1
  STAGE III                             1                              1
  STAGE IIIB                            2                              0
  STAGE IIIC                            1                              0
  STAGE IS                              7                              6
[1] 10  2
[1] 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    9     9
  DEL PEAK 20(10Q26.3) WILD-TYPE  6     7
D30V3, multiclass
       clus
vv      DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE
  T1                               9                              6
  T2+T3                            9                              7
[1] 2 2
[1] FALSE
D30V4, binary
                                cls
clus                             0 1
  DEL PEAK 20(10Q26.3) MUTATED   8 4
  DEL PEAK 20(10Q26.3) WILD-TYPE 5 0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10Q26.3) MUTATED      8    4
  DEL PEAK 20(10Q26.3) WILD-TYPE    5    0
   clus
vv  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE
  0                            8                              5
  1                            4                              0
[1] 2 2
[1] FALSE
D30V5, binary
                                cls
clus                              0  1
  DEL PEAK 20(10Q26.3) MUTATED    0 18
  DEL PEAK 20(10Q26.3) WILD-TYPE  3 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10Q26.3) MUTATED      0   18
  DEL PEAK 20(10Q26.3) WILD-TYPE    3   10
                        clus
vv                       DEL PEAK 20(10Q26.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           18
                        clus
vv                       DEL PEAK 20(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             10
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK 21(11P15.5) MUTATION ANALYSIS
D31V1, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(11P15.5) MUTATED         2        0        1        2         0
  DEL PEAK 21(11P15.5) WILD-TYPE       3        1        1        1         1
                                vv
clus                             STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 21(11P15.5) MUTATED           1         1          2          1
  DEL PEAK 21(11P15.5) WILD-TYPE         0         1          0          0
                                vv
clus                             STAGE IS
  DEL PEAK 21(11P15.5) MUTATED          8
  DEL PEAK 21(11P15.5) WILD-TYPE        5
D31V2, multiclass
            clus
vv           DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                              0                              1
  STAGE IB                              1                              1
  STAGE II                              2                              1
  STAGE IIA                             0                              1
  STAGE IIC                             1                              0
  STAGE III                             1                              1
  STAGE IIIB                            2                              0
  STAGE IIIC                            1                              0
  STAGE IS                              8                              5
[1] 10  2
[1] 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    8    10
  DEL PEAK 21(11P15.5) WILD-TYPE  7     6
D31V3, multiclass
       clus
vv      DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  T1                               8                              7
  T2+T3                           10                              6
[1] 2 2
[1] FALSE
D31V4, binary
                                cls
clus                             0 1
  DEL PEAK 21(11P15.5) MUTATED   7 3
  DEL PEAK 21(11P15.5) WILD-TYPE 6 1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED      7    3
  DEL PEAK 21(11P15.5) WILD-TYPE    6    1
   clus
vv  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  0                            7                              6
  1                            3                              1
[1] 2 2
[1] FALSE
D31V5, binary
                                cls
clus                              0  1
  DEL PEAK 21(11P15.5) MUTATED    2 16
  DEL PEAK 21(11P15.5) WILD-TYPE  1 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED      2   16
  DEL PEAK 21(11P15.5) WILD-TYPE    1   12
                        clus
vv                       DEL PEAK 21(11P15.5) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           16
                        clus
vv                       DEL PEAK 21(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             12
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK 22(11P12) MUTATION ANALYSIS
D32V1, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(11P12) MUTATED         2        0        1        3         0
  DEL PEAK 22(11P12) WILD-TYPE       3        1        1        0         1
                              vv
clus                           STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 22(11P12) MUTATED           1         1          2          1
  DEL PEAK 22(11P12) WILD-TYPE         0         1          0          0
                              vv
clus                           STAGE IS
  DEL PEAK 22(11P12) MUTATED          8
  DEL PEAK 22(11P12) WILD-TYPE        5
D32V2, multiclass
            clus
vv           DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE
  STAGE I                             2                            3
  STAGE IA                            0                            1
  STAGE IB                            1                            1
  STAGE II                            3                            0
  STAGE IIA                           0                            1
  STAGE IIC                           1                            0
  STAGE III                           1                            1
  STAGE IIIB                          2                            0
  STAGE IIIC                          1                            0
  STAGE IS                            8                            5
[1] 10  2
[1] 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    8    11
  DEL PEAK 22(11P12) WILD-TYPE  7     5
D32V3, multiclass
       clus
vv      DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE
  T1                             8                            7
  T2+T3                         11                            5
[1] 2 2
[1] FALSE
D32V4, binary
                              cls
clus                           0 1
  DEL PEAK 22(11P12) MUTATED   7 3
  DEL PEAK 22(11P12) WILD-TYPE 6 1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(11P12) MUTATED      7    3
  DEL PEAK 22(11P12) WILD-TYPE    6    1
   clus
vv  DEL PEAK 22(11P12) MUTATED DEL PEAK 22(11P12) WILD-TYPE
  0                          7                            6
  1                          3                            1
[1] 2 2
[1] FALSE
D32V5, binary
                              cls
clus                            0  1
  DEL PEAK 22(11P12) MUTATED    2 17
  DEL PEAK 22(11P12) WILD-TYPE  1 11
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(11P12) MUTATED      2   17
  DEL PEAK 22(11P12) WILD-TYPE    1   11
                        clus
vv                       DEL PEAK 22(11P12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         17
                        clus
vv                       DEL PEAK 22(11P12) WILD-TYPE
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           11
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK 23(11Q12.3) MUTATION ANALYSIS
D33V1, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(11Q12.3) MUTATED         4        0        1        3         0
  DEL PEAK 23(11Q12.3) WILD-TYPE       1        1        1        0         1
                                vv
clus                             STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 23(11Q12.3) MUTATED           1         1          2          1
  DEL PEAK 23(11Q12.3) WILD-TYPE         0         1          0          0
                                vv
clus                             STAGE IS
  DEL PEAK 23(11Q12.3) MUTATED         10
  DEL PEAK 23(11Q12.3) WILD-TYPE        3
D33V2, multiclass
            clus
vv           DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                              0                              1
  STAGE IB                              1                              1
  STAGE II                              3                              0
  STAGE IIA                             0                              1
  STAGE IIC                             1                              0
  STAGE III                             1                              1
  STAGE IIIB                            2                              0
  STAGE IIIC                            1                              0
  STAGE IS                             10                              3
[1] 10  2
[1] 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   11    12
  DEL PEAK 23(11Q12.3) WILD-TYPE  4     4
D33V3, multiclass
       clus
vv      DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE
  T1                              11                              4
  T2+T3                           12                              4
[1] 2 2
[1] FALSE
D33V4, binary
                                cls
clus                             0 1
  DEL PEAK 23(11Q12.3) MUTATED   9 3
  DEL PEAK 23(11Q12.3) WILD-TYPE 4 1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q12.3) MUTATED      9    3
  DEL PEAK 23(11Q12.3) WILD-TYPE    4    1
   clus
vv  DEL PEAK 23(11Q12.3) MUTATED DEL PEAK 23(11Q12.3) WILD-TYPE
  0                            9                              4
  1                            3                              1
[1] 2 2
[1] FALSE
D33V5, binary
                                cls
clus                              0  1
  DEL PEAK 23(11Q12.3) MUTATED    2 21
  DEL PEAK 23(11Q12.3) WILD-TYPE  1  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q12.3) MUTATED      2   21
  DEL PEAK 23(11Q12.3) WILD-TYPE    1    7
                        clus
vv                       DEL PEAK 23(11Q12.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           21
                        clus
vv                       DEL PEAK 23(11Q12.3) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                              7
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 24(11Q24.2) MUTATION ANALYSIS
D34V1, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(11Q24.2) MUTATED         4        0        1        3         1
  DEL PEAK 24(11Q24.2) WILD-TYPE       1        1        1        0         0
                                vv
clus                             STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 24(11Q24.2) MUTATED           1         2          2          1
  DEL PEAK 24(11Q24.2) WILD-TYPE         0         0          0          0
                                vv
clus                             STAGE IS
  DEL PEAK 24(11Q24.2) MUTATED         11
  DEL PEAK 24(11Q24.2) WILD-TYPE        2
D34V2, multiclass
            clus
vv           DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                              0                              1
  STAGE IB                              1                              1
  STAGE II                              3                              0
  STAGE IIA                             1                              0
  STAGE IIC                             1                              0
  STAGE III                             2                              0
  STAGE IIIB                            2                              0
  STAGE IIIC                            1                              0
  STAGE IS                             11                              2
[1] 10  2
[1] 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   12    14
  DEL PEAK 24(11Q24.2) WILD-TYPE  3     2
D34V3, multiclass
       clus
vv      DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE
  T1                              12                              3
  T2+T3                           14                              2
[1] 2 2
[1] FALSE
D34V4, binary
                                cls
clus                              0  1
  DEL PEAK 24(11Q24.2) MUTATED   10  4
  DEL PEAK 24(11Q24.2) WILD-TYPE  3  0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(11Q24.2) MUTATED     10    4
  DEL PEAK 24(11Q24.2) WILD-TYPE    3    0
   clus
vv  DEL PEAK 24(11Q24.2) MUTATED DEL PEAK 24(11Q24.2) WILD-TYPE
  0                           10                              3
  1                            4                              0
[1] 2 2
[1] FALSE
D34V5, binary
                                cls
clus                              0  1
  DEL PEAK 24(11Q24.2) MUTATED    2 24
  DEL PEAK 24(11Q24.2) WILD-TYPE  1  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(11Q24.2) MUTATED      2   24
  DEL PEAK 24(11Q24.2) WILD-TYPE    1    4
                        clus
vv                       DEL PEAK 24(11Q24.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           24
                        clus
vv                       DEL PEAK 24(11Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                              4
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 25(13Q34) MUTATION ANALYSIS
D35V1, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(13Q34) MUTATED         4        1        2        2         1
  DEL PEAK 25(13Q34) WILD-TYPE       1        0        0        1         0
                              vv
clus                           STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 25(13Q34) MUTATED           0         1          2          1
  DEL PEAK 25(13Q34) WILD-TYPE         1         1          0          0
                              vv
clus                           STAGE IS
  DEL PEAK 25(13Q34) MUTATED          8
  DEL PEAK 25(13Q34) WILD-TYPE        5
D35V2, multiclass
            clus
vv           DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE
  STAGE I                             4                            1
  STAGE IA                            1                            0
  STAGE IB                            2                            0
  STAGE II                            2                            1
  STAGE IIA                           1                            0
  STAGE IIC                           0                            1
  STAGE III                           1                            1
  STAGE IIIB                          2                            0
  STAGE IIIC                          1                            0
  STAGE IS                            8                            5
[1] 10  2
[1] 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   10    12
  DEL PEAK 25(13Q34) WILD-TYPE  5     4
D35V3, multiclass
       clus
vv      DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE
  T1                            10                            5
  T2+T3                         12                            4
[1] 2 2
[1] FALSE
D35V4, binary
                              cls
clus                           0 1
  DEL PEAK 25(13Q34) MUTATED   8 4
  DEL PEAK 25(13Q34) WILD-TYPE 5 0
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(13Q34) MUTATED      8    4
  DEL PEAK 25(13Q34) WILD-TYPE    5    0
   clus
vv  DEL PEAK 25(13Q34) MUTATED DEL PEAK 25(13Q34) WILD-TYPE
  0                          8                            5
  1                          4                            0
[1] 2 2
[1] FALSE
D35V5, binary
                              cls
clus                            0  1
  DEL PEAK 25(13Q34) MUTATED    3 19
  DEL PEAK 25(13Q34) WILD-TYPE  0  9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(13Q34) MUTATED      3   19
  DEL PEAK 25(13Q34) WILD-TYPE    0    9
                        clus
vv                       DEL PEAK 25(13Q34) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         19
                        clus
vv                       DEL PEAK 25(13Q34) WILD-TYPE
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            9
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 26(16Q23.1) MUTATION ANALYSIS
D36V1, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(16Q23.1) MUTATED         2        1        1        1         1
  DEL PEAK 26(16Q23.1) WILD-TYPE       3        0        1        2         0
                                vv
clus                             STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 26(16Q23.1) MUTATED           0         1          1          0
  DEL PEAK 26(16Q23.1) WILD-TYPE         1         1          1          1
                                vv
clus                             STAGE IS
  DEL PEAK 26(16Q23.1) MUTATED          7
  DEL PEAK 26(16Q23.1) WILD-TYPE        6
D36V2, multiclass
            clus
vv           DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                              1                              0
  STAGE IB                              1                              1
  STAGE II                              1                              2
  STAGE IIA                             1                              0
  STAGE IIC                             0                              1
  STAGE III                             1                              1
  STAGE IIIB                            1                              1
  STAGE IIIC                            0                              1
  STAGE IS                              7                              6
[1] 10  2
[1] 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    7     8
  DEL PEAK 26(16Q23.1) WILD-TYPE  8     8
D36V3, multiclass
       clus
vv      DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  T1                               7                              8
  T2+T3                            8                              8
[1] 2 2
[1] FALSE
D36V4, binary
                                cls
clus                             0 1
  DEL PEAK 26(16Q23.1) MUTATED   8 2
  DEL PEAK 26(16Q23.1) WILD-TYPE 5 2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED      8    2
  DEL PEAK 26(16Q23.1) WILD-TYPE    5    2
   clus
vv  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  0                            8                              5
  1                            2                              2
[1] 2 2
[1] FALSE
D36V5, binary
                                cls
clus                              0  1
  DEL PEAK 26(16Q23.1) MUTATED    3 12
  DEL PEAK 26(16Q23.1) WILD-TYPE  0 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED      3   12
  DEL PEAK 26(16Q23.1) WILD-TYPE    0   16
                        clus
vv                       DEL PEAK 26(16Q23.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           12
                        clus
vv                       DEL PEAK 26(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                             16
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 27(18P11.32) MUTATION ANALYSIS
D37V1, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(18P11.32) MUTATED         4        1        2        3         0
  DEL PEAK 27(18P11.32) WILD-TYPE       1        0        0        0         1
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 27(18P11.32) MUTATED           0         1          2          1
  DEL PEAK 27(18P11.32) WILD-TYPE         1         1          0          0
                                 vv
clus                              STAGE IS
  DEL PEAK 27(18P11.32) MUTATED         12
  DEL PEAK 27(18P11.32) WILD-TYPE        1
D37V2, multiclass
            clus
vv           DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE
  STAGE I                                4                               1
  STAGE IA                               1                               0
  STAGE IB                               2                               0
  STAGE II                               3                               0
  STAGE IIA                              0                               1
  STAGE IIC                              0                               1
  STAGE III                              1                               1
  STAGE IIIB                             2                               0
  STAGE IIIC                             1                               0
  STAGE IS                              12                               1
[1] 10  2
[1] 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   13    13
  DEL PEAK 27(18P11.32) WILD-TYPE  2     3
D37V3, multiclass
       clus
vv      DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE
  T1                               13                               2
  T2+T3                            13                               3
[1] 2 2
[1] FALSE
D37V4, binary
                                 cls
clus                               0  1
  DEL PEAK 27(18P11.32) MUTATED   12  3
  DEL PEAK 27(18P11.32) WILD-TYPE  1  1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(18P11.32) MUTATED     12    3
  DEL PEAK 27(18P11.32) WILD-TYPE    1    1
   clus
vv  DEL PEAK 27(18P11.32) MUTATED DEL PEAK 27(18P11.32) WILD-TYPE
  0                            12                               1
  1                             3                               1
[1] 2 2
[1] FALSE
D37V5, binary
                                 cls
clus                               0  1
  DEL PEAK 27(18P11.32) MUTATED    3 23
  DEL PEAK 27(18P11.32) WILD-TYPE  0  5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(18P11.32) MUTATED      3   23
  DEL PEAK 27(18P11.32) WILD-TYPE    0    5
                        clus
vv                       DEL PEAK 27(18P11.32) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            23
                        clus
vv                       DEL PEAK 27(18P11.32) WILD-TYPE
  HISPANIC OR LATINO                                   0
  NOT HISPANIC OR LATINO                               5
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 28(18Q22.2) MUTATION ANALYSIS
D38V1, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(18Q22.2) MUTATED         4        1        2        3         0
  DEL PEAK 28(18Q22.2) WILD-TYPE       1        0        0        0         1
                                vv
clus                             STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 28(18Q22.2) MUTATED           0         1          2          1
  DEL PEAK 28(18Q22.2) WILD-TYPE         1         1          0          0
                                vv
clus                             STAGE IS
  DEL PEAK 28(18Q22.2) MUTATED         13
  DEL PEAK 28(18Q22.2) WILD-TYPE        0
D38V2, multiclass
            clus
vv           DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                              1                              0
  STAGE IB                              2                              0
  STAGE II                              3                              0
  STAGE IIA                             0                              1
  STAGE IIC                             0                              1
  STAGE III                             1                              1
  STAGE IIIB                            2                              0
  STAGE IIIC                            1                              0
  STAGE IS                             13                              0
[1] 10  2
[1] 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   14    13
  DEL PEAK 28(18Q22.2) WILD-TYPE  1     3
D38V3, multiclass
       clus
vv      DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE
  T1                              14                              1
  T2+T3                           13                              3
[1] 2 2
[1] FALSE
D38V4, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q22.2) MUTATED   13  3
  DEL PEAK 28(18Q22.2) WILD-TYPE  0  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q22.2) MUTATED     13    3
  DEL PEAK 28(18Q22.2) WILD-TYPE    0    1
   clus
vv  DEL PEAK 28(18Q22.2) MUTATED DEL PEAK 28(18Q22.2) WILD-TYPE
  0                           13                              0
  1                            3                              1
[1] 2 2
[1] FALSE
D38V5, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q22.2) MUTATED    3 24
  DEL PEAK 28(18Q22.2) WILD-TYPE  0  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q22.2) MUTATED      3   24
  DEL PEAK 28(18Q22.2) WILD-TYPE    0    4
                        clus
vv                       DEL PEAK 28(18Q22.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           24
                        clus
vv                       DEL PEAK 28(18Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                              4
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 29(19Q13.41) MUTATION ANALYSIS
D39V1, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 29(19Q13.41) MUTATED         0        1        0        3         1
  DEL PEAK 29(19Q13.41) WILD-TYPE       5        0        2        0         0
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 29(19Q13.41) MUTATED           0         1          1          1
  DEL PEAK 29(19Q13.41) WILD-TYPE         1         1          1          0
                                 vv
clus                              STAGE IS
  DEL PEAK 29(19Q13.41) MUTATED         10
  DEL PEAK 29(19Q13.41) WILD-TYPE        3
D39V2, multiclass
            clus
vv           DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE
  STAGE I                                0                               5
  STAGE IA                               1                               0
  STAGE IB                               0                               2
  STAGE II                               3                               0
  STAGE IIA                              1                               0
  STAGE IIC                              0                               1
  STAGE III                              1                               1
  STAGE IIIB                             1                               1
  STAGE IIIC                             1                               0
  STAGE IS                              10                               3
[1] 10  2
[1] 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    8    10
  DEL PEAK 29(19Q13.41) WILD-TYPE  7     6
D39V3, multiclass
       clus
vv      DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE
  T1                                8                               7
  T2+T3                            10                               6
[1] 2 2
[1] FALSE
D39V4, binary
                                 cls
clus                              0 1
  DEL PEAK 29(19Q13.41) MUTATED   8 3
  DEL PEAK 29(19Q13.41) WILD-TYPE 5 1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.41) MUTATED      8    3
  DEL PEAK 29(19Q13.41) WILD-TYPE    5    1
   clus
vv  DEL PEAK 29(19Q13.41) MUTATED DEL PEAK 29(19Q13.41) WILD-TYPE
  0                             8                               5
  1                             3                               1
[1] 2 2
[1] FALSE
D39V5, binary
                                 cls
clus                               0  1
  DEL PEAK 29(19Q13.41) MUTATED    2 16
  DEL PEAK 29(19Q13.41) WILD-TYPE  1 12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(19Q13.41) MUTATED      2   16
  DEL PEAK 29(19Q13.41) WILD-TYPE    1   12
                        clus
vv                       DEL PEAK 29(19Q13.41) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            16
                        clus
vv                       DEL PEAK 29(19Q13.41) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                              12
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 30(20P12.1) MUTATION ANALYSIS
D40V1, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(20P12.1) MUTATED         0        1        0        1         1
  DEL PEAK 30(20P12.1) WILD-TYPE       5        0        2        2         0
                                vv
clus                             STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 30(20P12.1) MUTATED           0         0          1          0
  DEL PEAK 30(20P12.1) WILD-TYPE         1         2          1          1
                                vv
clus                             STAGE IS
  DEL PEAK 30(20P12.1) MUTATED          3
  DEL PEAK 30(20P12.1) WILD-TYPE       10
D40V2, multiclass
            clus
vv           DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                              1                              0
  STAGE IB                              0                              2
  STAGE II                              1                              2
  STAGE IIA                             1                              0
  STAGE IIC                             0                              1
  STAGE III                             0                              2
  STAGE IIIB                            1                              1
  STAGE IIIC                            0                              1
  STAGE IS                              3                             10
[1] 10  2
[1] 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    3     4
  DEL PEAK 30(20P12.1) WILD-TYPE 12    12
D40V3, multiclass
       clus
vv      DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  T1                               3                             12
  T2+T3                            4                             12
[1] 2 2
[1] FALSE
D40V4, binary
                                cls
clus                              0  1
  DEL PEAK 30(20P12.1) MUTATED    2  2
  DEL PEAK 30(20P12.1) WILD-TYPE 11  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED      2    2
  DEL PEAK 30(20P12.1) WILD-TYPE   11    2
   clus
vv  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  0                            2                             11
  1                            2                              2
[1] 2 2
[1] FALSE
D40V5, binary
                                cls
clus                              0  1
  DEL PEAK 30(20P12.1) MUTATED    1  6
  DEL PEAK 30(20P12.1) WILD-TYPE  2 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED      1    6
  DEL PEAK 30(20P12.1) WILD-TYPE    2   22
                        clus
vv                       DEL PEAK 30(20P12.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       DEL PEAK 30(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             22
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 31(XP21.1) MUTATION ANALYSIS
D41V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 31(XP21.1) MUTATED         2        1        0        2         0
  DEL PEAK 31(XP21.1) WILD-TYPE       3        0        2        1         1
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 31(XP21.1) MUTATED           0         0          0          0
  DEL PEAK 31(XP21.1) WILD-TYPE         1         2          2          1
                               vv
clus                            STAGE IS
  DEL PEAK 31(XP21.1) MUTATED          2
  DEL PEAK 31(XP21.1) WILD-TYPE       11
D41V2, multiclass
            clus
vv           DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                             1                             0
  STAGE IB                             0                             2
  STAGE II                             2                             1
  STAGE IIA                            0                             1
  STAGE IIC                            0                             1
  STAGE III                            0                             2
  STAGE IIIB                           0                             2
  STAGE IIIC                           0                             1
  STAGE IS                             2                            11
[1] 10  2
[1] 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    6     1
  DEL PEAK 31(XP21.1) WILD-TYPE  9    15
D41V3, multiclass
       clus
vv      DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE
  T1                              6                             9
  T2+T3                           1                            15
[1] 2 2
[1] FALSE
D41V4, binary
                               cls
clus                            0 1
  DEL PEAK 31(XP21.1) MUTATED   4 0
  DEL PEAK 31(XP21.1) WILD-TYPE 9 4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 31(XP21.1) MUTATED      4    0
  DEL PEAK 31(XP21.1) WILD-TYPE    9    4
   clus
vv  DEL PEAK 31(XP21.1) MUTATED DEL PEAK 31(XP21.1) WILD-TYPE
  0                           4                             9
  1                           0                             4
[1] 2 2
[1] FALSE
D41V5, binary
                               cls
clus                             0  1
  DEL PEAK 31(XP21.1) MUTATED    1  6
  DEL PEAK 31(XP21.1) WILD-TYPE  2 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 31(XP21.1) MUTATED      1    6
  DEL PEAK 31(XP21.1) WILD-TYPE    2   22
                        clus
vv                       DEL PEAK 31(XP21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           6
                        clus
vv                       DEL PEAK 31(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            22
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 32(XQ27.3) MUTATION ANALYSIS
D42V1, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(XQ27.3) MUTATED         1        0        0        2         0
  DEL PEAK 32(XQ27.3) WILD-TYPE       4        1        2        1         1
                               vv
clus                            STAGE IIC STAGE III STAGE IIIB STAGE IIIC
  DEL PEAK 32(XQ27.3) MUTATED           0         0          0          0
  DEL PEAK 32(XQ27.3) WILD-TYPE         1         2          2          1
                               vv
clus                            STAGE IS
  DEL PEAK 32(XQ27.3) MUTATED          4
  DEL PEAK 32(XQ27.3) WILD-TYPE        9
D42V2, multiclass
            clus
vv           DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                             0                             1
  STAGE IB                             0                             2
  STAGE II                             2                             1
  STAGE IIA                            0                             1
  STAGE IIC                            0                             1
  STAGE III                            0                             2
  STAGE IIIB                           0                             2
  STAGE IIIC                           0                             1
  STAGE IS                             4                             9
[1] 10  2
[1] 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    6     1
  DEL PEAK 32(XQ27.3) WILD-TYPE  9    15
D42V3, multiclass
       clus
vv      DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE
  T1                              6                             9
  T2+T3                           1                            15
[1] 2 2
[1] FALSE
D42V4, binary
                               cls
clus                             0  1
  DEL PEAK 32(XQ27.3) MUTATED    3  0
  DEL PEAK 32(XQ27.3) WILD-TYPE 10  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 32(XQ27.3) MUTATED      3    0
  DEL PEAK 32(XQ27.3) WILD-TYPE   10    4
   clus
vv  DEL PEAK 32(XQ27.3) MUTATED DEL PEAK 32(XQ27.3) WILD-TYPE
  0                           3                            10
  1                           0                             4
[1] 2 2
[1] FALSE
D42V5, binary
                               cls
clus                             0  1
  DEL PEAK 32(XQ27.3) MUTATED    1  6
  DEL PEAK 32(XQ27.3) WILD-TYPE  2 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 32(XQ27.3) MUTATED      1    6
  DEL PEAK 32(XQ27.3) WILD-TYPE    2   22
                        clus
vv                       DEL PEAK 32(XQ27.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           6
                        clus
vv                       DEL PEAK 32(XQ27.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            22
[1] 2 2
[1] FALSE
