[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"        "-oTLUSC-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/LUSC-TP/10006043/LUSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUSC-TP/10686857/transformed.cor.cli.txt"

nPatients in clinical file=422, in cluster file=178, common to both=178
[1]  17 178
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           141             37 
  TP53 MUTATED TP53 WILD-TYPE 
           141             37 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              27              151 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              27              151 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              26              152 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              26              152 
[1] "KEAP1 MUTATION ANALYSIS"
[1] 3
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             156 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             156 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            14            164 
  PTEN MUTATED PTEN WILD-TYPE 
            14            164 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              27              151 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              27              151 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            35            143 
  MLL2 MUTATED MLL2 WILD-TYPE 
            35            143 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           12           166 
  RB1 MUTATED RB1 WILD-TYPE 
           12           166 
[1] "IBTK MUTATION ANALYSIS"
[1] 3
  IBTK MUTATED IBTK WILD-TYPE 
             5            173 
  IBTK MUTATED IBTK WILD-TYPE 
             5            173 
[1] "CYP11B1 MUTATION ANALYSIS"
[1] 3
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
               15               163 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
               15               163 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              14              164 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              14              164 
[1] "SLC28A1 MUTATION ANALYSIS"
[1] 3
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
                9               169 
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
                9               169 
[1] "ASB5 MUTATION ANALYSIS"
[1] 3
  ASB5 MUTATED ASB5 WILD-TYPE 
             9            169 
  ASB5 MUTATED ASB5 WILD-TYPE 
             9            169 
[1] "CPS1 MUTATION ANALYSIS"
[1] 3
  CPS1 MUTATED CPS1 WILD-TYPE 
            25            153 
  CPS1 MUTATED CPS1 WILD-TYPE 
            25            153 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
              8             170 
  EP300 MUTATED EP300 WILD-TYPE 
              8             170 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              166 
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              166 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             10             168 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             10             168 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "COMPLETENESS.OF.RESECTION"             
[21] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCHNUMBER"                           

Input Data has 23 rows and 178 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
        1331          187           85         2754           92          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 
        3636         1426         1852         1058          474          284 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 
         962         1268         1032          329          223          131 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 
          53          429          822          623         1067          734 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 
        1161         1057          399          587          358          965 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 
        1975         1933          445         1346           24         2170 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 
         357          916         1912         1713          506         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        3469         2979         1311         5287         3149         4299 
TCGA-33-4586 TCGA-33-6737 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 
         428           NA           80         1874         1000         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        2062         1715           NA          707          365          428 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 
         941          552           NA          120           13          238 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
         207           12          103         2253         1361         2086 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
          NA         2130         1849           52          740           59 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2578 
         833          474         1084         1086          544          684 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
         822         1007          349          376          757          310 
TCGA-43-6771 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
          NA           NA           NA           NA           NA           NA 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-56-1622 
         324          423           12           12          911          881 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-60-2698 TCGA-60-2707 
           3          555           62           26          311          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        2447         1505         2024         1260          274         1731 
TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        1075         1297           97          983          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-5128 TCGA-63-5131 TCGA-63-6202 
         717          816          358           NA           NA           NA 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 
          NA         1311          641           30           61           28 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
          30           30          639          762           30           61 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
          31           61           61          700          578           NA 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
          61          578           NA          121           NA          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 
          60          790         1217          699           NA           NA 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-70-6722 
         913           NA         1645          122         1492           NA 
TCGA-70-6723 TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
          NA           NA          364          395 
Variable 1:'AGE':	nDistinctValues=37,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=76,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=141,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=100,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=40,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "KARNOFSKY.PERFORMANCE.SCORE"           
 [8] "HISTOLOGICAL.TYPE"                     
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "NUMBERPACKYEARSSMOKED"                 
[11] "COMPLETENESS.OF.RESECTION"             
[12] "RACE"                                  
[13] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 178 columns, 1 survival variables, and 13 non-survival variables.
AGE, nv=37, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=7, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 37 115  14  12 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 37 115  14  12 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 37 115  14  12 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 37 115  14  12 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
116  39  17   5 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
116  39  17   5 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
116  39  17   5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
116  39  17   5 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=56, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   83 49
  TP53 WILD-TYPE 11 22
  TP53 MUTATED TP53 WILD-TYPE 
           132             33 
  TP53 MUTATED TP53 WILD-TYPE 
            49             22 
$`TP53 MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
         396         1810          862           50         1331          187 
TCGA-18-4086 TCGA-18-5592 TCGA-21-1076 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
          85           92         1852          962         1268         1032 
TCGA-21-5787 TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 
         329          223           53          429          822         1067 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 
         734         1161         1057          399          587          358 
TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 
         965         1933          445         1346           24         1952 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 
         357          916         1912         1713          506         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        1940         2979         1311         5287         1966         1941 
TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 TCGA-34-5239 
         428           80         1874         1000         2062          707 
TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 
         365          941          552          120           13          238 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
         207           12          103         2253         1361         1947 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5035 
        1964         1849           52          740          833          474 
TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 
        1084         1086          822         1007          349          376 
TCGA-43-6770 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
         310          324          423           12           12          911 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-60-2698 
         881            3          555           62           26          311 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2719 
         661         1963         1963         1260         1731         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-63-6202 
          97          983          908         1092          717         1973 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 
        1967         1311          641           30           61           28 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
          30           30          639          762           30           61 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2777 TCGA-66-2782 
          31           61           61          700           61         1954 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 
         759          790         1217          699         1977          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-85-6560 TCGA-85-6561 
        1952         1645          122         1492          364          395 

$`TP53 WILD-TYPE`
TCGA-18-3412 TCGA-18-3417 TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
         345          758         2754          827         3636         1426 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 TCGA-22-1002 TCGA-22-4591 TCGA-22-5472 
        1058          474          284          131          623         1964 
TCGA-34-5231 TCGA-34-5234 TCGA-34-5241 TCGA-39-5022 TCGA-39-5030 TCGA-39-5039 
        1528         1715          428         1996           59          544 
TCGA-43-2578 TCGA-43-6647 TCGA-43-6771 TCGA-60-2709 TCGA-60-2712 TCGA-60-2715 
         684          757         1936         1505          274         1075 
TCGA-60-2725 TCGA-60-2726 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 
         816          358          578         1946          578         1956 
TCGA-66-2781 TCGA-66-2785 TCGA-66-2789 
         121           60         1955 

  TP53 MUTATED TP53 WILD-TYPE 
             3             59 
  TP53 MUTATED TP53 WILD-TYPE 
          5287           3636 
  TP53 MUTATED TP53 WILD-TYPE 
           737            758 
[1] "3.0 - 5287.0 (737.0)"  "59.0 - 3636.0 (758.0)"
[1] "hr=" "1.5"
D1V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  TP53 MUTATED         20       56        11        20         19         12
  TP53 WILD-TYPE        8       14         2         6          4          2
                vv
clus             STAGE IV
  TP53 MUTATED          2
  TP53 WILD-TYPE        1
D1V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE IA             20              8
  STAGE IB             56             14
  STAGE IIA            11              2
  STAGE IIB            20              6
  STAGE IIIA           19              4
  STAGE IIIB           12              2
  STAGE IV              2              1
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  TP53 MUTATED   28 91 10 12
  TP53 WILD-TYPE  9 24  4  0
D1V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1           28              9
  T2           91             24
  T3           10              4
  T4           12              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TP53 MUTATED   91 31 15  3
  TP53 WILD-TYPE 25  8  2  2
D1V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           91             25
  N1           31              8
  N2           15              2
  N3            3              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  TP53 MUTATED   132   2   3
  TP53 WILD-TYPE  33   1   3
D1V6, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  M0          132             33
  M1            2              1
  MX            3              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                cls
clus               0   1
  TP53 MUTATED    37 104
  TP53 WILD-TYPE  10  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     37  104
  TP53 WILD-TYPE   10   27
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           37             10
  MALE            104             27
[1] 2 2
[1] FALSE
D1V8, continuous
                vv
clus             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  TP53 MUTATED                                       5
  TP53 WILD-TYPE                                     0
                vv
clus             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  TP53 MUTATED                                        1
  TP53 WILD-TYPE                                      0
                vv
clus             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TP53 MUTATED                                                           135
  TP53 WILD-TYPE                                                          37
D1V9, multiclass
                                                             clus
vv                                                            TP53 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                  5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          135
                                                             clus
vv                                                            TP53 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
                cls
clus               0   1
  TP53 MUTATED     5 136
  TP53 WILD-TYPE   0  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      5  136
  TP53 WILD-TYPE    0   37
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO             5              0
  YES          136             37
[1] 2 2
[1] FALSE
D1V11, continuous
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED   117   2   3   6
  TP53 WILD-TYPE  30   0   1   4
D1V12, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0          117             30
  R1            2              0
  R2            3              1
  RX            6              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       3                         7    87
  TP53 WILD-TYPE     2                         2    24
D1V13, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                3              2
  BLACK OR AFRICAN AMERICAN            7              2
  WHITE                               87             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                cls
clus              0  1
  TP53 MUTATED    3 76
  TP53 WILD-TYPE  0 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      3   76
  TP53 WILD-TYPE    0   24
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                3              0
  NOT HISPANIC OR LATINO           76             24
[1] 2 2
[1] FALSE

Clustering(2) Variable = NFE2L2 MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2               0  1
  NFE2L2 MUTATED   14 10
  NFE2L2 WILD-TYPE 80 61
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              24              141 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              10               61 
$`NFE2L2 MUTATED`
TCGA-18-3411 TCGA-18-3415 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-22-5473 
        1415         1810         2754           92         1426         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5482 TCGA-33-4586 TCGA-34-2596 TCGA-34-2608 
         445         1346          357          428           80         1000 
TCGA-34-5240 TCGA-37-4135 TCGA-39-5022 TCGA-51-4079 TCGA-51-4081 TCGA-56-5897 
         365          207         1996           12          911            3 
TCGA-60-2709 TCGA-66-2766 TCGA-66-2770 TCGA-66-2783 TCGA-66-2787 TCGA-66-2795 
        1505           31          700          759         1217          122 

$`NFE2L2 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 
         370          136         2464         2417          146          345 
TCGA-18-3414 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
         396          862          758           50         1331          187 
TCGA-18-4086 TCGA-18-5595 TCGA-21-1070 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
          85          827         3636         1852         1058          474 
TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 
         284          962         1268         1032          329          223 
TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
         131           53          429          822          623         1067 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 
         734         1161         1057          399          587          358 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5478 TCGA-22-5480 TCGA-22-5485 TCGA-22-5489 
         965         1964           24         1952          916         1912 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
        1713          506         2524         1940         2979         1311 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-34-2600 TCGA-34-5231 TCGA-34-5232 
        5287         1966         1941         1874         1528         2062 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-37-3783 
        1715          707          428          941          552          120 
TCGA-37-3789 TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
          13          238           12          103         2253         1361 
TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
        1947         1964         1849           52          740           59 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2578 
         833          474         1084         1086          544          684 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
         822         1007          349          376          757          310 
TCGA-43-6771 TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-56-1622 TCGA-56-5898 
        1936          324          423           12          881          555 
TCGA-56-6545 TCGA-56-6546 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 
          62           26          311          661         1963         1963 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 
        1260          274         1731         1075         1297           97 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
         983          908         1092          717          816          358 
TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 
        1973         1967         1311          641           30           61 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
          28           30           30          639          762           30 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          61           61           61          578         1946           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 
         578         1956          121         1954           60          790 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
         699         1955         1977          913         1952         1645 
TCGA-66-2800 TCGA-85-6560 TCGA-85-6561 
        1492          364          395 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               3               12 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            2754             5287 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           729.5            757.0 
[1] "3.0 - 2754.0 (729.5)"  "12.0 - 5287.0 (757.0)"
[1] "hr=" "1.1"
D2V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  NFE2L2 MUTATED          5       10         0         5          4          3
  NFE2L2 WILD-TYPE       23       60        13        21         19         11
                  vv
clus               STAGE IV
  NFE2L2 MUTATED          0
  NFE2L2 WILD-TYPE        3
D2V3, multiclass
            clus
vv           NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE IA                5               23
  STAGE IB               10               60
  STAGE IIA               0               13
  STAGE IIB               5               21
  STAGE IIIA              4               19
  STAGE IIIB              3               11
  STAGE IV                0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  NFE2L2 MUTATED    5 17  4  1
  NFE2L2 WILD-TYPE 32 98 10 11
D2V4, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T1              5               32
  T2             17               98
  T3              4               10
  T4              1               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  NFE2L2 MUTATED   18  5  3  1
  NFE2L2 WILD-TYPE 98 34 14  4
D2V5, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0             18               98
  N1              5               34
  N2              3               14
  N3              1                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1  MX
  NFE2L2 MUTATED    24   0   2
  NFE2L2 WILD-TYPE 141   3   4
D2V6, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  M0             24              141
  M1              0                3
  MX              2                4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     4  23
  NFE2L2 WILD-TYPE  43 108
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      4   23
  NFE2L2 WILD-TYPE   43  108
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE              4               43
  MALE               23              108
[1] 2 2
[1] FALSE
D2V8, continuous
                  vv
clus               LUNG BASALOID SQUAMOUS CELL CARCINOMA
  NFE2L2 MUTATED                                       1
  NFE2L2 WILD-TYPE                                     4
                  vv
clus               LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  NFE2L2 MUTATED                                        0
  NFE2L2 WILD-TYPE                                      1
                  vv
clus               LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NFE2L2 MUTATED                                                            26
  NFE2L2 WILD-TYPE                                                         146
D2V9, multiclass
                                                             clus
vv                                                            NFE2L2 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             26
                                                             clus
vv                                                            NFE2L2 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     0  27
  NFE2L2 WILD-TYPE   5 146
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      0   27
  NFE2L2 WILD-TYPE    5  146
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO               0                5
  YES             27              146
[1] 2 2
[1] FALSE
D2V11, continuous
                  vv
clus                R0  R1  R2  RX
  NFE2L2 MUTATED    22   0   1   0
  NFE2L2 WILD-TYPE 125   2   3  10
D2V12, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  R0             22              125
  R1              0                2
  R2              1                3
  RX              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFE2L2 MUTATED       0                         2    17
  NFE2L2 WILD-TYPE     5                         7    94
D2V13, multiclass
                           clus
vv                          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              2                7
  WHITE                                 17               94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    0 16
  NFE2L2 WILD-TYPE  3 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      0   16
  NFE2L2 WILD-TYPE    3   84
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             16               84
[1] 2 2
[1] FALSE

Clustering(3) Variable = CDKN2A MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2               0  1
  CDKN2A MUTATED   10 15
  CDKN2A WILD-TYPE 84 56
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              25              140 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              15               56 
$`CDKN2A MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3416 TCGA-21-5786 TCGA-21-5787 
         136         1415          345          862         1032          329 
TCGA-22-1012 TCGA-22-4593 TCGA-22-4599 TCGA-22-5477 TCGA-22-5492 TCGA-33-4538 
         429         1067         1161         1346          506         2979 
TCGA-34-2596 TCGA-34-5231 TCGA-37-4135 TCGA-39-5027 TCGA-39-5028 TCGA-43-3394 
          80         1528          207         1849           52          822 
TCGA-51-4080 TCGA-60-2698 TCGA-60-2725 TCGA-60-2726 TCGA-66-2786 TCGA-66-2787 
          12          311          816          358          790         1217 
TCGA-66-2792 
         913 

$`CDKN2A WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 
         370         2464         2417          146          396         1810 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
         758           50         1331          187           85         2754 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 
          92          827         3636         1426         1852         1058 
TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-22-0944 TCGA-22-1002 
         474          284          962         1268          223          131 
TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4595 TCGA-22-4601 TCGA-22-4604 
          53          822          623          734         1057          399 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
          24         1952          357          916         1912         1713 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        2524         1940         1311         5287         1966         1941 
TCGA-33-4586 TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
         428         1874         1000         2062         1715          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-37-3783 TCGA-37-3789 
         365          428          941          552          120           13 
TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
         238           12          103         2253         1361         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 
        1996         1964          740           59          833          474 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2578 TCGA-43-3920 TCGA-43-5668 
        1084         1086          544          684         1007          349 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-46-6025 TCGA-46-6026 
         376          757          310         1936          324          423 
TCGA-51-4079 TCGA-51-4081 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
          12          911          881            3          555           62 
TCGA-56-6546 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
          26          661         1963         1505         1963         1260 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
         274         1731         1075         1297           97          983 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 
         908         1092          717         1973         1967         1311 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
         641           30           61           28           30           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
         639          762           30           61           31           61 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
          61          700          578         1946           61          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 
        1956          121         1954          759           60          699 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        1955         1977         1952         1645          122         1492 
TCGA-85-6560 TCGA-85-6561 
         364          395 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
              12                3 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
            2979             5287 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
             816              737 
[1] "12.0 - 2979.0 (816.0)" "3.0 - 5287.0 (737.0)" 
[1] "hr=" "1.9"
D3V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  CDKN2A MUTATED          5        8         2         4          5          2
  CDKN2A WILD-TYPE       23       62        11        22         18         12
                  vv
clus               STAGE IV
  CDKN2A MUTATED          0
  CDKN2A WILD-TYPE        3
D3V3, multiclass
            clus
vv           CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE IA                5               23
  STAGE IB                8               62
  STAGE IIA               2               11
  STAGE IIB               4               22
  STAGE IIIA              5               18
  STAGE IIIB              2               12
  STAGE IV                0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  CDKN2A MUTATED    5 19  0  2
  CDKN2A WILD-TYPE 32 96 14 10
D3V4, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  T1              5               32
  T2             19               96
  T3              0               14
  T4              2               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CDKN2A MUTATED    15   7   4   0
  CDKN2A WILD-TYPE 101  32  13   5
D3V5, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  N0             15              101
  N1              7               32
  N2              4               13
  N3              0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1  MX
  CDKN2A MUTATED    25   0   0
  CDKN2A WILD-TYPE 140   3   6
D3V6, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  M0             25              140
  M1              0                3
  MX              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     6  20
  CDKN2A WILD-TYPE  41 111
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      6   20
  CDKN2A WILD-TYPE   41  111
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              6               41
  MALE               20              111
[1] 2 2
[1] FALSE
D3V8, continuous
                  vv
clus               LUNG BASALOID SQUAMOUS CELL CARCINOMA
  CDKN2A MUTATED                                       1
  CDKN2A WILD-TYPE                                     4
                  vv
clus               LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  CDKN2A MUTATED                                        0
  CDKN2A WILD-TYPE                                      1
                  vv
clus               LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CDKN2A MUTATED                                                            25
  CDKN2A WILD-TYPE                                                         147
D3V9, multiclass
                                                             clus
vv                                                            CDKN2A MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             25
                                                             clus
vv                                                            CDKN2A WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     1  25
  CDKN2A WILD-TYPE   4 148
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      1   25
  CDKN2A WILD-TYPE    4  148
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO               1                4
  YES             25              148
[1] 2 2
[1] FALSE
D3V11, continuous
                  vv
clus                R0  R1  R2  RX
  CDKN2A MUTATED    23   0   0   2
  CDKN2A WILD-TYPE 124   2   4   8
D3V12, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  R0             23              124
  R1              0                2
  R2              0                4
  RX              2                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED       1                         3    15
  CDKN2A WILD-TYPE     4                         6    96
D3V13, multiclass
                           clus
vv                          CDKN2A MUTATED CDKN2A WILD-TYPE
  ASIAN                                  1                4
  BLACK OR AFRICAN AMERICAN              3                6
  WHITE                                 15               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                  cls
clus                0  1
  CDKN2A MUTATED    1 15
  CDKN2A WILD-TYPE  2 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      1   15
  CDKN2A WILD-TYPE    2   85
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO             15               85
[1] 2 2
[1] FALSE

Clustering(4) Variable = KEAP1 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2              0  1
  KEAP1 MUTATED   15  7
  KEAP1 WILD-TYPE 79 64
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             143 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
              7              64 
$`KEAP1 MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-5595 TCGA-21-1077 TCGA-22-4599 TCGA-33-4532 
         136         2417          827         1058         1161         2524 
TCGA-33-4538 TCGA-37-4133 TCGA-37-5819 TCGA-39-5031 TCGA-39-5036 TCGA-43-2578 
        2979          238          103          833         1084          684 
TCGA-43-6143 TCGA-46-6025 TCGA-51-4081 TCGA-60-2710 TCGA-60-2722 TCGA-60-2723 
         376          324          911         1963          908         1092 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2773 TCGA-66-2777 
          61           30         1946           61 

$`KEAP1 WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         370         2464          146         1415          345          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
        1810          862          758           50         1331          187 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 
          85         2754           92         3636         1426         1852 
TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
         474          284          962         1268         1032          329 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
         223          131           53          429          822          623 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 
        1067          734         1057          399          587          358 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
         965         1964         1933          445         1346           24 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
        1952          357          916         1912         1713          506 
TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
        1940         1311         5287         1966         1941          428 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
          80         1874         1000         1528         2062         1715 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-37-3783 
         707          365          428          941          552          120 
TCGA-37-3789 TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
          13          207           12         2253         1361         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
        1996         1964         1849           52          740           59 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
         474         1086          544          822         1007          349 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
         757          310         1936          423           12           12 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-60-2698 
         881            3          555           62           26          311 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
         661         1963         1505         1260          274         1731 
TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 
        1075         1297           97          983          717          816 
TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 
         358         1973         1967         1311          641           30 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
          28           30          639          762           30           61 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2778 
          31           61           61          700          578          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
        1956          121         1954          759           60          790 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
        1217          699         1955         1977          913         1952 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-85-6560 TCGA-85-6561 
        1645          122         1492          364          395 

  KEAP1 MUTATED KEAP1 WILD-TYPE 
             30               3 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
           2979            5287 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
          870.5           734.0 
[1] "30.0 - 2979.0 (870.5)" "3.0 - 5287.0 (734.0)" 
[1] "hr=" "1.6"
D4V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  KEAP1 MUTATED          2        9         1         4          3          2
  KEAP1 WILD-TYPE       26       61        12        22         20         12
                 vv
clus              STAGE IV
  KEAP1 MUTATED          0
  KEAP1 WILD-TYPE        3
D4V3, multiclass
            clus
vv           KEAP1 MUTATED KEAP1 WILD-TYPE
  STAGE IA               2              26
  STAGE IB               9              61
  STAGE IIA              1              12
  STAGE IIB              4              22
  STAGE IIIA             3              20
  STAGE IIIB             2              12
  STAGE IV               0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  KEAP1 MUTATED    4 16  0  2
  KEAP1 WILD-TYPE 33 99 14 10
D4V4, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  T1             4              33
  T2            16              99
  T3             0              14
  T4             2              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KEAP1 MUTATED    14   5   3   0
  KEAP1 WILD-TYPE 102  34  14   5
D4V5, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  N0            14             102
  N1             5              34
  N2             3              14
  N3             0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1  MX
  KEAP1 MUTATED    22   0   0
  KEAP1 WILD-TYPE 143   3   6
D4V6, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  M0            22             143
  M1             0               3
  MX             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                 cls
clus                0   1
  KEAP1 MUTATED     5  17
  KEAP1 WILD-TYPE  42 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      5   17
  KEAP1 WILD-TYPE   42  114
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  FEMALE             5              42
  MALE              17             114
[1] 2 2
[1] FALSE
D4V8, continuous
                 vv
clus              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  KEAP1 MUTATED                                       2
  KEAP1 WILD-TYPE                                     3
                 vv
clus              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  KEAP1 MUTATED                                        0
  KEAP1 WILD-TYPE                                      1
                 vv
clus              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KEAP1 MUTATED                                                            20
  KEAP1 WILD-TYPE                                                         152
D4V9, multiclass
                                                             clus
vv                                                            KEAP1 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                   2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            20
                                                             clus
vv                                                            KEAP1 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
                 cls
clus                0   1
  KEAP1 MUTATED     0  22
  KEAP1 WILD-TYPE   5 151
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      0   22
  KEAP1 WILD-TYPE    5  151
     clus
vv    KEAP1 MUTATED KEAP1 WILD-TYPE
  NO              0               5
  YES            22             151
[1] 2 2
[1] FALSE
D4V11, continuous
                 vv
clus               R0  R1  R2  RX
  KEAP1 MUTATED    19   0   0   2
  KEAP1 WILD-TYPE 128   2   4   8
D4V12, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  R0            19             128
  R1             0               2
  R2             0               4
  RX             2               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KEAP1 MUTATED       1                         0    13
  KEAP1 WILD-TYPE     4                         9    98
D4V13, multiclass
                           clus
vv                          KEAP1 MUTATED KEAP1 WILD-TYPE
  ASIAN                                 1               4
  BLACK OR AFRICAN AMERICAN             0               9
  WHITE                                13              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                 cls
clus               0  1
  KEAP1 MUTATED    1 12
  KEAP1 WILD-TYPE  2 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      1   12
  KEAP1 WILD-TYPE    2   88
                        clus
vv                       KEAP1 MUTATED KEAP1 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            12              88
[1] 2 2
[1] FALSE

Clustering(5) Variable = PTEN MUTATION ANALYSIS
D5V1, survival
                sevent
clus2             0  1
  PTEN MUTATED   10  4
  PTEN WILD-TYPE 84 67
  PTEN MUTATED PTEN WILD-TYPE 
            14            151 
  PTEN MUTATED PTEN WILD-TYPE 
             4             67 
$`PTEN MUTATED`
TCGA-18-3417 TCGA-18-3421 TCGA-22-4599 TCGA-22-5489 TCGA-33-4583 TCGA-39-5024 
         758         1331         1161         1912         1941         1964 
TCGA-39-5027 TCGA-43-2578 TCGA-43-3920 TCGA-56-5897 TCGA-56-6546 TCGA-60-2707 
        1849          684         1007            3           26          661 
TCGA-66-2783 TCGA-66-2788 
         759          699 

$`PTEN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-4083 
         345          396         1810          862           50          187 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
          85         2754           92          827         3636         1426 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 
        1852         1058          474          284          962         1268 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
        1032          329          223          131           53          429 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4601 TCGA-22-4604 
         822          623         1067          734         1057          399 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5491 
        1346           24         1952          357          916         1713 
TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
         506         2524         1940         2979         1311         5287 
TCGA-33-4582 TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 
        1966          428           80         1874         1000         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
        2062         1715          707          365          428          941 
TCGA-34-5928 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
         552          120           13          238          207           12 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5028 
         103         2253         1361         1947         1996           52 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
         740           59          833          474         1084         1086 
TCGA-39-5039 TCGA-43-3394 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
         544          822          349          376          757          310 
TCGA-43-6771 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        1936          324          423           12           12          911 
TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-60-2698 TCGA-60-2708 TCGA-60-2709 
         881          555           62          311         1963         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2719 
        1963         1260          274         1731         1075         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
          97          983          908         1092          717          816 
TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 
         358         1973         1967         1311          641           30 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
          61           28           30           30          639          762 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 
          30           61           31           61           61          700 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
         578         1946           61          578         1956          121 
TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2789 TCGA-66-2791 
        1954           60          790         1217         1955         1977 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-85-6560 
         913         1952         1645          122         1492          364 
TCGA-85-6561 
         395 

  PTEN MUTATED PTEN WILD-TYPE 
             3             12 
  PTEN MUTATED PTEN WILD-TYPE 
          1964           5287 
  PTEN MUTATED PTEN WILD-TYPE 
           883            734 
[1] "3.0 - 1964.0 (883.0)"  "12.0 - 5287.0 (734.0)"
[1] "hr=" "1.6"
D5V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  PTEN MUTATED          4        6         1         0          1          1
  PTEN WILD-TYPE       24       64        12        26         22         13
                vv
clus             STAGE IV
  PTEN MUTATED          1
  PTEN WILD-TYPE        2
D5V3, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  STAGE IA              4             24
  STAGE IB              6             64
  STAGE IIA             1             12
  STAGE IIB             0             26
  STAGE IIIA            1             22
  STAGE IIIB            1             13
  STAGE IV              1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PTEN MUTATED     4  10   0   0
  PTEN WILD-TYPE  33 105  14  12
D5V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1            4             33
  T2           10            105
  T3            0             14
  T4            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PTEN MUTATED    11   1   1   1
  PTEN WILD-TYPE 105  38  16   4
D5V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0           11            105
  N1            1             38
  N2            1             16
  N3            1              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  PTEN MUTATED    11   1   2
  PTEN WILD-TYPE 154   2   4
D5V6, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  M0           11            154
  M1            1              2
  MX            2              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                cls
clus               0   1
  PTEN MUTATED     3  11
  PTEN WILD-TYPE  44 120
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      3   11
  PTEN WILD-TYPE   44  120
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            3             44
  MALE             11            120
[1] 2 2
[1] FALSE
D5V8, continuous
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             2             34 
    TCGA-18-3406     TCGA-18-3407     TCGA-18-3410     TCGA-18-3414 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-18-3419     TCGA-21-5782     TCGA-21-5787     TCGA-22-4591 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-22-4593     TCGA-22-4595     TCGA-22-4601     TCGA-22-4604 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-22-4613     TCGA-22-5472     TCGA-22-5473     TCGA-22-5474 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-22-5477     TCGA-22-5478     TCGA-22-5480     TCGA-22-5482 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-22-5485     TCGA-22-5491     TCGA-22-5492     TCGA-34-5234 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-37-4133     TCGA-37-4135     TCGA-37-5819     TCGA-60-2698 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-60-2712     TCGA-60-2715     TCGA-60-2725     TCGA-60-2726 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-70-6722     TCGA-70-6723 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" 
                vv
clus             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  PTEN MUTATED                                       0
  PTEN WILD-TYPE                                     5
                vv
clus             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  PTEN MUTATED                                        0
  PTEN WILD-TYPE                                      1
                vv
clus             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PTEN MUTATED                                                            14
  PTEN WILD-TYPE                                                         158
D5V9, multiclass
                                                             clus
vv                                                            PTEN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           14
                                                             clus
vv                                                            PTEN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
                cls
clus               0   1
  PTEN MUTATED     0  14
  PTEN WILD-TYPE   5 159
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0   14
  PTEN WILD-TYPE    5  159
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             0              5
  YES           14            159
[1] 2 2
[1] FALSE
D5V11, continuous
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED    10   0   1   1
  PTEN WILD-TYPE 137   2   3   9
D5V12, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0           10            137
  R1            0              2
  R2            1              3
  RX            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       0                         0    10
  PTEN WILD-TYPE     5                         9   101
D5V13, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              9
  WHITE                               10            101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                cls
clus              0  1
  PTEN MUTATED    1  8
  PTEN WILD-TYPE  2 92
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1    8
  PTEN WILD-TYPE    2   92
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO            8             92
[1] 2 2
[1] FALSE

Clustering(6) Variable = PIK3CA MUTATION ANALYSIS
D6V1, survival
                  sevent
clus2               0  1
  PIK3CA MUTATED   11 14
  PIK3CA WILD-TYPE 83 57
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              25              140 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              14               57 
$`PIK3CA MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3414 TCGA-18-5595 TCGA-21-1071 TCGA-21-1078 
         136          146          396          827         1426          474 
TCGA-21-5782 TCGA-22-4613 TCGA-22-5473 TCGA-22-5489 TCGA-22-5491 TCGA-33-4547 
         962          358         1933         1912         1713         1311 
TCGA-33-4583 TCGA-34-5232 TCGA-37-3783 TCGA-37-5819 TCGA-51-4079 TCGA-60-2724 
        1941         2062          120          103           12          717 
TCGA-60-2726 TCGA-66-2755 TCGA-66-2759 TCGA-66-2766 TCGA-66-2773 TCGA-66-2785 
         358           28          762           31         1946           60 
TCGA-85-6560 
         364 

$`PIK3CA WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 
         370         2464         2417         1415          345         1810 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
         862          758           50         1331          187           85 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1076 TCGA-21-1077 TCGA-21-1081 
        2754           92         3636         1852         1058          284 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 
        1268         1032          329          223          131           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 
         429          822          623         1067          734         1161 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 
        1057          399          587          965         1964          445 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5492 
        1346           24         1952          357          916          506 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 
        2524         1940         2979         5287         1966          428 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5234 TCGA-34-5239 
          80         1874         1000         1528         1715          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-37-3789 TCGA-37-4133 
         365          428          941          552           13          238 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
         207           12         2253         1361         1947         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1964         1849           52          740           59          833 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2578 TCGA-43-3394 
         474         1084         1086          544          684          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
        1007          349          376          757          310         1936 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-56-1622 TCGA-56-5897 
         324          423           12          911          881            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 
         555           62           26          311          661         1963 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 
        1505         1963         1260          274         1731         1075 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
        1297           97          983          908         1092          816 
TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 
        1973         1967         1311          641           30           61 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
          30           30          639           30           61           61 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
          61          700          578           61          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
         121         1954          759          790         1217          699 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
        1955         1977          913         1952         1645          122 
TCGA-66-2800 TCGA-85-6561 
        1492          395 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
              12                3 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
            2062             5287 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           474.0            758.5 
[1] "12.0 - 2062.0 (474.0)" "3.0 - 5287.0 (758.5)" 
[1] "hr=" "1.8"
D6V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  PIK3CA MUTATED          5       11         3         0          7          0
  PIK3CA WILD-TYPE       23       59        10        26         16         14
                  vv
clus               STAGE IV
  PIK3CA MUTATED          1
  PIK3CA WILD-TYPE        2
D6V3, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE IA                5               23
  STAGE IB               11               59
  STAGE IIA               3               10
  STAGE IIB               0               26
  STAGE IIIA              7               16
  STAGE IIIB              0               14
  STAGE IV                1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3CA MUTATED     7  14   5   1
  PIK3CA WILD-TYPE  30 101   9  11
D6V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              7               30
  T2             14              101
  T3              5                9
  T4              1               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PIK3CA MUTATED   17  6  4  0
  PIK3CA WILD-TYPE 99 33 13  5
D6V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             17               99
  N1              6               33
  N2              4               13
  N3              0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1  MX
  PIK3CA MUTATED    25   1   0
  PIK3CA WILD-TYPE 140   2   6
D6V6, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  M0             25              140
  M1              1                2
  MX              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     4  23
  PIK3CA WILD-TYPE  43 108
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      4   23
  PIK3CA WILD-TYPE   43  108
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE              4               43
  MALE               23              108
[1] 2 2
[1] FALSE
D6V8, continuous
                  vv
clus               LUNG BASALOID SQUAMOUS CELL CARCINOMA
  PIK3CA MUTATED                                       0
  PIK3CA WILD-TYPE                                     5
                  vv
clus               LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  PIK3CA MUTATED                                        0
  PIK3CA WILD-TYPE                                      1
                  vv
clus               LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PIK3CA MUTATED                                                            27
  PIK3CA WILD-TYPE                                                         145
D6V9, multiclass
                                                             clus
vv                                                            PIK3CA MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             27
                                                             clus
vv                                                            PIK3CA WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     0  27
  PIK3CA WILD-TYPE   5 146
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      0   27
  PIK3CA WILD-TYPE    5  146
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO               0                5
  YES             27              146
[1] 2 2
[1] FALSE
D6V11, continuous
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED    25   0   0   1
  PIK3CA WILD-TYPE 122   2   4   9
D6V12, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             25              122
  R1              0                2
  R2              0                4
  RX              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED       3                         2    15
  PIK3CA WILD-TYPE     2                         7    96
D6V13, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  3                2
  BLACK OR AFRICAN AMERICAN              2                7
  WHITE                                 15               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
                  cls
clus                0  1
  PIK3CA MUTATED    0 17
  PIK3CA WILD-TYPE  3 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      0   17
  PIK3CA WILD-TYPE    3   83
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             17               83
[1] 2 2
[1] FALSE

Clustering(7) Variable = MLL2 MUTATION ANALYSIS
D7V1, survival
                sevent
clus2             0  1
  MLL2 MUTATED   17 16
  MLL2 WILD-TYPE 77 55
  MLL2 MUTATED MLL2 WILD-TYPE 
            33            132 
  MLL2 MUTATED MLL2 WILD-TYPE 
            16             55 
$`MLL2 MUTATED`
TCGA-18-3411 TCGA-18-3414 TCGA-18-3416 TCGA-18-4083 TCGA-21-1078 TCGA-22-1002 
        1415          396          862          187          474          131 
TCGA-22-1016 TCGA-22-4599 TCGA-22-5473 TCGA-22-5477 TCGA-22-5482 TCGA-33-4538 
         822         1161         1933         1346          357         2979 
TCGA-34-2596 TCGA-34-5927 TCGA-34-5928 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 
          80          941          552           13          238          207 
TCGA-39-5027 TCGA-39-5030 TCGA-39-5036 TCGA-43-3394 TCGA-56-5897 TCGA-56-6545 
        1849           59         1084          822            3           62 
TCGA-60-2698 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 TCGA-66-2744 TCGA-66-2765 
         311          358         1973         1967           30           61 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2773 
          61           61         1946 

$`MLL2 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 
         370          136         2464         2417          146          345 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
        1810          758           50         1331           85         2754 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 
          92          827         3636         1426         1852         1058 
TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 
         284          962         1268         1032          329          223 
TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4601 
          53          429          623         1067          734         1057 
TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 
         399          587          358          965         1964          445 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
          24         1952          916         1912         1713          506 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        2524         1940         1311         5287         1966         1941 
TCGA-33-4586 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
         428         1874         1000         1528         2062         1715 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-37-3783 TCGA-37-4141 TCGA-37-5819 
         707          365          428          120           12          103 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
        2253         1361         1947         1996         1964           52 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-43-2578 
         740          833          474         1086          544          684 
TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
        1007          349          376          757          310         1936 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-56-1622 
         324          423           12           12          911          881 
TCGA-56-5898 TCGA-56-6546 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
         555           26          661         1963         1505         1963 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 
        1260          274         1731         1075         1297           97 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-66-2734 
         983          908         1092          717          816         1311 
TCGA-66-2742 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
         641           61           28           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 
         762           30           31          700          578           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
         578         1956          121         1954          759           60 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 
         790         1217          699         1955         1977          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-85-6560 TCGA-85-6561 
        1952         1645          122         1492          364          395 

  MLL2 MUTATED MLL2 WILD-TYPE 
             3             12 
  MLL2 MUTATED MLL2 WILD-TYPE 
          2979           5287 
  MLL2 MUTATED MLL2 WILD-TYPE 
         396.0          760.5 
[1] "3.0 - 2979.0 (396.0)"  "12.0 - 5287.0 (760.5)"
[1] "hr=" "1.5"
D7V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  MLL2 MUTATED          5       13         2         7          4          3
  MLL2 WILD-TYPE       23       57        11        19         19         11
                vv
clus             STAGE IV
  MLL2 MUTATED          1
  MLL2 WILD-TYPE        2
D7V3, multiclass
            clus
vv           MLL2 MUTATED MLL2 WILD-TYPE
  STAGE IA              5             23
  STAGE IB             13             57
  STAGE IIA             2             11
  STAGE IIB             7             19
  STAGE IIIA            4             19
  STAGE IIIB            3             11
  STAGE IV              1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  MLL2 MUTATED    5 26  2  2
  MLL2 WILD-TYPE 32 89 12 10
D7V4, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  T1            5             32
  T2           26             89
  T3            2             12
  T4            2             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MLL2 MUTATED   21 10  3  1
  MLL2 WILD-TYPE 95 29 14  4
D7V5, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  N0           21             95
  N1           10             29
  N2            3             14
  N3            1              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  MLL2 MUTATED    32   1   1
  MLL2 WILD-TYPE 133   2   5
D7V6, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  M0           32            133
  M1            1              2
  MX            1              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                cls
clus               0   1
  MLL2 MUTATED     8  27
  MLL2 WILD-TYPE  39 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      8   27
  MLL2 WILD-TYPE   39  104
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  FEMALE            8             39
  MALE             27            104
[1] 2 2
[1] FALSE
D7V8, continuous
                vv
clus             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  MLL2 MUTATED                                       0
  MLL2 WILD-TYPE                                     5
                vv
clus             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  MLL2 MUTATED                                        0
  MLL2 WILD-TYPE                                      1
                vv
clus             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MLL2 MUTATED                                                            35
  MLL2 WILD-TYPE                                                         137
D7V9, multiclass
                                                             clus
vv                                                            MLL2 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           35
                                                             clus
vv                                                            MLL2 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
                cls
clus               0   1
  MLL2 MUTATED     0  35
  MLL2 WILD-TYPE   5 138
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      0   35
  MLL2 WILD-TYPE    5  138
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO             0              5
  YES           35            138
[1] 2 2
[1] FALSE
D7V11, continuous
                vv
clus              R0  R1  R2  RX
  MLL2 MUTATED    29   0   0   3
  MLL2 WILD-TYPE 118   2   4   7
D7V12, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  R0           29            118
  R1            0              2
  R2            0              4
  RX            3              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL2 MUTATED       3                         1    21
  MLL2 WILD-TYPE     2                         8    90
D7V13, multiclass
                           clus
vv                          MLL2 MUTATED MLL2 WILD-TYPE
  ASIAN                                3              2
  BLACK OR AFRICAN AMERICAN            1              8
  WHITE                               21             90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
                cls
clus              0  1
  MLL2 MUTATED    1 17
  MLL2 WILD-TYPE  2 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      1   17
  MLL2 WILD-TYPE    2   83
                        clus
vv                       MLL2 MUTATED MLL2 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           17             83
[1] 2 2
[1] FALSE

Clustering(8) Variable = RB1 MUTATION ANALYSIS
D8V1, survival
               sevent
clus2            0  1
  RB1 MUTATED    6  6
  RB1 WILD-TYPE 88 65
  RB1 MUTATED RB1 WILD-TYPE 
           12           153 
  RB1 MUTATED RB1 WILD-TYPE 
            6            65 
$`RB1 MUTATED`
TCGA-18-4086 TCGA-22-4601 TCGA-22-4607 TCGA-33-4533 TCGA-34-5240 TCGA-39-5021 
          85         1057          587         1940          365         1947 
TCGA-39-5031 TCGA-43-2578 TCGA-43-6143 TCGA-56-1622 TCGA-66-2754 TCGA-66-2783 
         833          684          376          881           61          759 

$`RB1 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
        1331          187         2754           92          827         3636 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 
        1426         1852         1058          474          284          962 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 
        1268         1032          329          223          131           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 
         429          822          623         1067          734         1161 
TCGA-22-4604 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         399          358          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
        1346           24         1952          357          916         1912 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
        1713          506         2524         2979         1311         5287 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 
        1966         1941          428           80         1874         1000 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 
        1528         2062         1715          707          428          941 
TCGA-34-5928 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
         552          120           13          238          207           12 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
         103         2253         1361         1996         1964         1849 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
          52          740           59          474         1084         1086 
TCGA-39-5039 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6647 TCGA-43-6770 
         544          822         1007          349          757          310 
TCGA-43-6771 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        1936          324          423           12           12          911 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-60-2698 TCGA-60-2707 
           3          555           62           26          311          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        1963         1505         1963         1260          274         1731 
TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        1075         1297           97          983          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 
         717          816          358         1973         1967         1311 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
         641           30           28           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
         762           30           61           31           61           61 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
         700          578         1946           61          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
         121         1954           60          790         1217          699 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
        1955         1977          913         1952         1645          122 
TCGA-66-2800 TCGA-85-6560 TCGA-85-6561 
        1492          364          395 

  RB1 MUTATED RB1 WILD-TYPE 
           61             3 
  RB1 MUTATED RB1 WILD-TYPE 
         1947          5287 
  RB1 MUTATED RB1 WILD-TYPE 
        721.5         757.0 
[1] "61.0 - 1947.0 (721.5)" "3.0 - 5287.0 (757.0)" 
[1] "hr=" "1.5"
D8V2, continuous
               vv
clus            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  RB1 MUTATED          2        6         0         1          2          1
  RB1 WILD-TYPE       26       64        13        25         21         13
               vv
clus            STAGE IV
  RB1 MUTATED          0
  RB1 WILD-TYPE        3
D8V3, multiclass
            clus
vv           RB1 MUTATED RB1 WILD-TYPE
  STAGE IA             2            26
  STAGE IB             6            64
  STAGE IIA            0            13
  STAGE IIB            1            25
  STAGE IIIA           2            21
  STAGE IIIB           1            13
  STAGE IV             0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  RB1 MUTATED     2   9   0   1
  RB1 WILD-TYPE  35 106  14  11
D8V4, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  T1           2            35
  T2           9           106
  T3           0            14
  T4           1            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  RB1 MUTATED     9   1   1   1
  RB1 WILD-TYPE 107  38  16   4
D8V5, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  N0           9           107
  N1           1            38
  N2           1            16
  N3           1             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1  MX
  RB1 MUTATED    12   0   0
  RB1 WILD-TYPE 153   3   6
D8V6, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  M0          12           153
  M1           0             3
  MX           0             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
               cls
clus              0   1
  RB1 MUTATED     5   7
  RB1 WILD-TYPE  42 124
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      5    7
  RB1 WILD-TYPE   42  124
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE           5            42
  MALE             7           124
[1] 2 2
[1] FALSE
D8V8, continuous
[1] "Remove cluster labels:" "RB1 MUTATED"           
clus
  RB1 MUTATED RB1 WILD-TYPE 
            1            35 
   TCGA-18-3406    TCGA-18-3407    TCGA-18-3410    TCGA-18-3414    TCGA-18-3419 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-21-5782    TCGA-21-5787    TCGA-22-4591    TCGA-22-4593    TCGA-22-4595 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-22-4599    TCGA-22-4604    TCGA-22-4613    TCGA-22-5472    TCGA-22-5473 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-22-5474    TCGA-22-5477    TCGA-22-5478    TCGA-22-5480    TCGA-22-5482 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-22-5485    TCGA-22-5489    TCGA-22-5491    TCGA-22-5492    TCGA-34-5234 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-37-4133    TCGA-37-4135    TCGA-37-5819    TCGA-60-2698    TCGA-60-2712 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-60-2715    TCGA-60-2725    TCGA-60-2726    TCGA-70-6722    TCGA-70-6723 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
               vv
clus            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  RB1 MUTATED                                       2
  RB1 WILD-TYPE                                     3
               vv
clus            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  RB1 MUTATED                                        0
  RB1 WILD-TYPE                                      1
               vv
clus            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RB1 MUTATED                                                            10
  RB1 WILD-TYPE                                                         162
D8V9, multiclass
                                                             clus
vv                                                            RB1 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                 2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          10
                                                             clus
vv                                                            RB1 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                   3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
               cls
clus              0   1
  RB1 MUTATED     0  12
  RB1 WILD-TYPE   5 161
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0   12
  RB1 WILD-TYPE    5  161
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            0             5
  YES          12           161
[1] 2 2
[1] FALSE
D8V11, continuous
               vv
clus             R0  R1  R2  RX
  RB1 MUTATED     9   0   1   1
  RB1 WILD-TYPE 138   2   3   9
D8V12, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0           9           138
  R1           0             2
  R2           1             3
  RX           1             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED       0                         1     7
  RB1 WILD-TYPE     5                         8   104
D8V13, multiclass
                           clus
vv                          RB1 MUTATED RB1 WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           1             8
  WHITE                               7           104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
               cls
clus             0  1
  RB1 MUTATED    0  6
  RB1 WILD-TYPE  3 94
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0    6
  RB1 WILD-TYPE    3   94
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           6            94
[1] 2 2
[1] FALSE

Clustering(9) Variable = IBTK MUTATION ANALYSIS
D9V1, survival
                sevent
clus2             0  1
  IBTK MUTATED    3  1
  IBTK WILD-TYPE 91 70
  IBTK MUTATED IBTK WILD-TYPE 
             4            161 
  IBTK MUTATED IBTK WILD-TYPE 
             1             70 
$`IBTK MUTATED`
TCGA-18-3410 TCGA-37-4133 TCGA-60-2722 TCGA-66-2734 
         146          238          908         1311 

$`IBTK WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
         370          136         2464         2417         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
         396         1810          862          758           50         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
         187           85         2754           92          827         3636 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 
        1426         1852         1058          474          284          962 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 
        1268         1032          329          223          131           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 
         429          822          623         1067          734         1161 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
        1057          399          587          358          965         1964 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 
        1933          445         1346           24         1952          357 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 
         916         1912         1713          506         2524         1940 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
        2979         1311         5287         1966         1941          428 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
          80         1874         1000         1528         2062         1715 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-37-3783 
         707          365          428          941          552          120 
TCGA-37-3789 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
          13          207           12          103         2253         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        1947         1996         1964         1849           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 
          59          833          474         1084         1086          544 
TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 
         684          822         1007          349          376          757 
TCGA-43-6770 TCGA-43-6771 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
         310         1936          324          423           12           12 
TCGA-51-4081 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
         911          881            3          555           62           26 
TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
         311          661         1963         1505         1963         1260 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
         274         1731         1075         1297           97          983 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 
        1092          717          816          358         1973         1967 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
         641           30           61           28           30           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
         639          762           30           61           31           61 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
          61          700          578         1946           61          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
        1956          121         1954          759           60          790 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
        1217          699         1955         1977          913         1952 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-85-6560 TCGA-85-6561 
        1645          122         1492          364          395 

  IBTK MUTATED IBTK WILD-TYPE 
           146              3 
  IBTK MUTATED IBTK WILD-TYPE 
          1311           5287 
  IBTK MUTATED IBTK WILD-TYPE 
           573            757 
[1] "146.0 - 1311.0 (573.0)" "3.0 - 5287.0 (757.0)"  
[1] "hr=" "1"  
D9V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  IBTK MUTATED          0        1         0         1          2          1
  IBTK WILD-TYPE       28       69        13        25         21         13
                vv
clus             STAGE IV
  IBTK MUTATED          0
  IBTK WILD-TYPE        3
D9V3, multiclass
            clus
vv           IBTK MUTATED IBTK WILD-TYPE
  STAGE IA              0             28
  STAGE IB              1             69
  STAGE IIA             0             13
  STAGE IIB             1             25
  STAGE IIIA            2             21
  STAGE IIIB            1             13
  STAGE IV              0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IBTK MUTATED     0   2   2   1
  IBTK WILD-TYPE  37 113  12  11
D9V4, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  T1            0             37
  T2            2            113
  T3            2             12
  T4            1             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  IBTK MUTATED     3   2   0   0
  IBTK WILD-TYPE 113  37  17   5
D9V5, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  N0            3            113
  N1            2             37
  N2            0             17
  N3            0              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  IBTK MUTATED     5   0   0
  IBTK WILD-TYPE 160   3   6
D9V6, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  M0            5            160
  M1            0              3
  MX            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                cls
clus               0   1
  IBTK MUTATED     1   4
  IBTK WILD-TYPE  46 127
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED      1    4
  IBTK WILD-TYPE   46  127
        clus
vv       IBTK MUTATED IBTK WILD-TYPE
  FEMALE            1             46
  MALE              4            127
[1] 2 2
[1] FALSE
D9V8, continuous
[1] "Remove cluster labels:" "IBTK MUTATED"          
clus
  IBTK MUTATED IBTK WILD-TYPE 
             2             34 
    TCGA-18-3406     TCGA-18-3407     TCGA-18-3414     TCGA-18-3419 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-21-5782     TCGA-21-5787     TCGA-22-4591     TCGA-22-4593 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-22-4595     TCGA-22-4599     TCGA-22-4601     TCGA-22-4604 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-22-4613     TCGA-22-5472     TCGA-22-5473     TCGA-22-5474 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-22-5477     TCGA-22-5478     TCGA-22-5480     TCGA-22-5482 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-22-5485     TCGA-22-5489     TCGA-22-5491     TCGA-22-5492 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-34-5234     TCGA-37-4135     TCGA-37-5819     TCGA-60-2698 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-60-2712     TCGA-60-2715     TCGA-60-2725     TCGA-60-2726 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-70-6722     TCGA-70-6723 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" 
                vv
clus             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  IBTK MUTATED                                       0
  IBTK WILD-TYPE                                     5
                vv
clus             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  IBTK MUTATED                                        0
  IBTK WILD-TYPE                                      1
                vv
clus             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  IBTK MUTATED                                                             5
  IBTK WILD-TYPE                                                         167
D9V9, multiclass
                                                             clus
vv                                                            IBTK MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            5
                                                             clus
vv                                                            IBTK WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
                cls
clus               0   1
  IBTK MUTATED     0   5
  IBTK WILD-TYPE   5 168
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED      0    5
  IBTK WILD-TYPE    5  168
     clus
vv    IBTK MUTATED IBTK WILD-TYPE
  NO             0              5
  YES            5            168
[1] 2 2
[1] FALSE
D9V11, continuous
                vv
clus              R0  R1  R2  RX
  IBTK MUTATED     5   0   0   0
  IBTK WILD-TYPE 142   2   4  10
D9V12, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  R0            5            142
  R1            0              2
  R2            0              4
  RX            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IBTK MUTATED       0                         0     3
  IBTK WILD-TYPE     5                         9   108
D9V13, multiclass
                           clus
vv                          IBTK MUTATED IBTK WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              9
  WHITE                                3            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                cls
clus              0  1
  IBTK MUTATED    0  3
  IBTK WILD-TYPE  3 97
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED      0    3
  IBTK WILD-TYPE    3   97
                        clus
vv                       IBTK MUTATED IBTK WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3             97
[1] 2 2
[1] FALSE

Clustering(10) Variable = CYP11B1 MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  CYP11B1 MUTATED    4 11
  CYP11B1 WILD-TYPE 90 60
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
               15               150 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
               11                60 
$`CYP11B1 MUTATED`
TCGA-21-1077 TCGA-21-5787 TCGA-22-1016 TCGA-22-4595 TCGA-22-5491 TCGA-33-4566 
        1058          329          822          734         1713         5287 
TCGA-43-6771 TCGA-51-4079 TCGA-51-4080 TCGA-60-2719 TCGA-60-2726 TCGA-66-2766 
        1936           12           12         1297          358           31 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2789 
         759           60         1955 

$`CYP11B1 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
        1331          187           85         2754           92          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 
        3636         1426         1852          474          284          962 
TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
        1268         1032          223          131           53          429 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 
         623         1067         1161         1057          399          587 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
         358          965         1964         1933          445         1346 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 
          24         1952          357          916         1912          506 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 
        2524         1940         2979         1311         1966         1941 
TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
         428           80         1874         1000         1528         2062 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        1715          707          365          428          941          552 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
         120           13          238          207           12          103 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
        2253         1361         1947         1996         1964         1849 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
          52          740           59          833          474         1084 
TCGA-39-5037 TCGA-39-5039 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
        1086          544          684          822         1007          349 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-46-6025 TCGA-46-6026 TCGA-51-4081 
         376          757          310          324          423          911 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-60-2698 
         881            3          555           62           26          311 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 
         661         1963         1505         1963         1260          274 
TCGA-60-2713 TCGA-60-2715 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        1731         1075           97          983          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 
         717          816         1973         1967         1311          641 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
          30           61           28           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 
         762           30           61           61           61          700 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
         578         1946           61          578         1956          121 
TCGA-66-2782 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 
        1954          790         1217          699         1977          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-85-6560 TCGA-85-6561 
        1952         1645          122         1492          364          395 

  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
               12                 3 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
             5287              3636 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
            759.0             748.5 
[1] "12.0 - 5287.0 (759.0)" "3.0 - 3636.0 (748.5)" 
[1] "hr=" "1.7"
D10V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  CYP11B1 MUTATED          1        6         1         1          3          3
  CYP11B1 WILD-TYPE       27       64        12        25         20         11
                   vv
clus                STAGE IV
  CYP11B1 MUTATED          0
  CYP11B1 WILD-TYPE        3
D10V3, multiclass
            clus
vv           CYP11B1 MUTATED CYP11B1 WILD-TYPE
  STAGE IA                 1                27
  STAGE IB                 6                64
  STAGE IIA                1                12
  STAGE IIB                1                25
  STAGE IIIA               3                20
  STAGE IIIB               3                11
  STAGE IV                 0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CYP11B1 MUTATED     3  10   1   1
  CYP11B1 WILD-TYPE  34 105  13  11
D10V4, multiclass
    clus
vv   CYP11B1 MUTATED CYP11B1 WILD-TYPE
  T1               3                34
  T2              10               105
  T3               1                13
  T4               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CYP11B1 MUTATED     7   3   3   2
  CYP11B1 WILD-TYPE 109  36  14   3
D10V5, multiclass
    clus
vv   CYP11B1 MUTATED CYP11B1 WILD-TYPE
  N0               7               109
  N1               3                36
  N2               3                14
  N3               2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  CYP11B1 MUTATED    11   0   1
  CYP11B1 WILD-TYPE 154   3   5
D10V6, multiclass
    clus
vv   CYP11B1 MUTATED CYP11B1 WILD-TYPE
  M0              11               154
  M1               0                 3
  MX               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                  0   1
  CYP11B1 MUTATED     2  13
  CYP11B1 WILD-TYPE  45 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP11B1 MUTATED      2   13
  CYP11B1 WILD-TYPE   45  118
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  FEMALE               2                45
  MALE                13               118
[1] 2 2
[1] FALSE
D10V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  CYP11B1 MUTATED                                       1
  CYP11B1 WILD-TYPE                                     4
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  CYP11B1 MUTATED                                        0
  CYP11B1 WILD-TYPE                                      1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CYP11B1 MUTATED                                                            14
  CYP11B1 WILD-TYPE                                                         158
D10V9, multiclass
                                                             clus
vv                                                            CYP11B1 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              14
                                                             clus
vv                                                            CYP11B1 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
                   cls
clus                  0   1
  CYP11B1 MUTATED     2  13
  CYP11B1 WILD-TYPE   3 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP11B1 MUTATED      2   13
  CYP11B1 WILD-TYPE    3  160
     clus
vv    CYP11B1 MUTATED CYP11B1 WILD-TYPE
  NO                2                 3
  YES              13               160
[1] 2 2
[1] FALSE
D10V11, continuous
                   vv
clus                 R0  R1  R2  RX
  CYP11B1 MUTATED    13   0   1   1
  CYP11B1 WILD-TYPE 134   2   3   9
D10V12, multiclass
    clus
vv   CYP11B1 MUTATED CYP11B1 WILD-TYPE
  R0              13               134
  R1               0                 2
  R2               1                 3
  RX               1                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CYP11B1 MUTATED       0                         3     8
  CYP11B1 WILD-TYPE     5                         6   103
D10V13, multiclass
                           clus
vv                          CYP11B1 MUTATED CYP11B1 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               3                 6
  WHITE                                   8               103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                   cls
clus                 0  1
  CYP11B1 MUTATED    0  8
  CYP11B1 WILD-TYPE  3 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP11B1 MUTATED      0    8
  CYP11B1 WILD-TYPE    3   92
                        clus
vv                       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               8                92
[1] 2 2
[1] FALSE

Clustering(11) Variable = NOTCH1 MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2               0  1
  NOTCH1 MUTATED    5  9
  NOTCH1 WILD-TYPE 89 62
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              14              151 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
               9               62 
$`NOTCH1 MUTATED`
TCGA-18-5592 TCGA-21-5782 TCGA-22-1016 TCGA-22-5480 TCGA-22-5485 TCGA-22-5491 
          92          962          822         1952          916         1713 
TCGA-22-5492 TCGA-33-4583 TCGA-39-5037 TCGA-51-4079 TCGA-66-2759 TCGA-66-2789 
         506         1941         1086           12          762         1955 
TCGA-66-2793 TCGA-66-2795 
        1952          122 

$`NOTCH1 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 
        1331          187           85         2754          827         3636 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 TCGA-21-5784 
        1426         1852         1058          474          284         1268 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
        1032          329          223          131           53          429 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
         623         1067          734         1161         1057          399 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5482 TCGA-22-5489 TCGA-33-4532 TCGA-33-4533 
        1346           24          357         1912         2524         1940 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-34-2596 
        2979         1311         5287         1966          428           80 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
        1874         1000         1528         2062         1715          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-37-3783 TCGA-37-3789 
         365          428          941          552          120           13 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
         238          207           12          103         2253         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        1947         1996         1964         1849           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-43-2578 
          59          833          474         1084          544          684 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
         822         1007          349          376          757          310 
TCGA-43-6771 TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-56-1622 
        1936          324          423           12          911          881 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-60-2698 TCGA-60-2707 
           3          555           62           26          311          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        1963         1505         1963         1260          274         1731 
TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        1075         1297           97          983          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 
         717          816          358         1973         1967         1311 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
         641           30           61           28           30           30 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
         639           30           61           31           61           61 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
         700          578         1946           61          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
         121         1954          759           60          790         1217 
TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2800 TCGA-85-6560 
         699         1977          913         1645         1492          364 
TCGA-85-6561 
         395 

  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              12                3 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
            1955             5287 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
             939              717 
[1] "12.0 - 1955.0 (939.0)" "3.0 - 5287.0 (717.0)" 
[1] "hr=" "1.5"
D11V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  NOTCH1 MUTATED          4        3         1         1          2          3
  NOTCH1 WILD-TYPE       24       67        12        25         21         11
                  vv
clus               STAGE IV
  NOTCH1 MUTATED          0
  NOTCH1 WILD-TYPE        3
D11V3, multiclass
            clus
vv           NOTCH1 MUTATED NOTCH1 WILD-TYPE
  STAGE IA                4               24
  STAGE IB                3               67
  STAGE IIA               1               12
  STAGE IIB               1               25
  STAGE IIIA              2               21
  STAGE IIIB              3               11
  STAGE IV                0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NOTCH1 MUTATED     6   5   1   2
  NOTCH1 WILD-TYPE  31 110  13  10
D11V4, multiclass
    clus
vv   NOTCH1 MUTATED NOTCH1 WILD-TYPE
  T1              6               31
  T2              5              110
  T3              1               13
  T4              2               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NOTCH1 MUTATED     8   3   2   1
  NOTCH1 WILD-TYPE 108  36  15   4
D11V5, multiclass
    clus
vv   NOTCH1 MUTATED NOTCH1 WILD-TYPE
  N0              8              108
  N1              3               36
  N2              2               15
  N3              1                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1  MX
  NOTCH1 MUTATED    13   0   0
  NOTCH1 WILD-TYPE 152   3   6
D11V6, multiclass
    clus
vv   NOTCH1 MUTATED NOTCH1 WILD-TYPE
  M0             13              152
  M1              0                3
  MX              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED     5   9
  NOTCH1 WILD-TYPE  42 122
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      5    9
  NOTCH1 WILD-TYPE   42  122
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  FEMALE              5               42
  MALE                9              122
[1] 2 2
[1] FALSE
D11V8, continuous
                  vv
clus               LUNG BASALOID SQUAMOUS CELL CARCINOMA
  NOTCH1 MUTATED                                       0
  NOTCH1 WILD-TYPE                                     5
                  vv
clus               LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  NOTCH1 MUTATED                                        0
  NOTCH1 WILD-TYPE                                      1
                  vv
clus               LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NOTCH1 MUTATED                                                            14
  NOTCH1 WILD-TYPE                                                         158
D11V9, multiclass
                                                             clus
vv                                                            NOTCH1 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             14
                                                             clus
vv                                                            NOTCH1 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED     0  14
  NOTCH1 WILD-TYPE   5 159
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      0   14
  NOTCH1 WILD-TYPE    5  159
     clus
vv    NOTCH1 MUTATED NOTCH1 WILD-TYPE
  NO               0                5
  YES             14              159
[1] 2 2
[1] FALSE
D11V11, continuous
                  vv
clus                R0  R1  R2  RX
  NOTCH1 MUTATED    14   0   0   0
  NOTCH1 WILD-TYPE 133   2   4  10
D11V12, multiclass
    clus
vv   NOTCH1 MUTATED NOTCH1 WILD-TYPE
  R0             14              133
  R1              0                2
  R2              0                4
  RX              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NOTCH1 MUTATED       0                         1     7
  NOTCH1 WILD-TYPE     5                         8   104
D11V13, multiclass
                           clus
vv                          NOTCH1 MUTATED NOTCH1 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              1                8
  WHITE                                  7              104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V14, binary
                  cls
clus                0  1
  NOTCH1 MUTATED    0  6
  NOTCH1 WILD-TYPE  3 94
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      0    6
  NOTCH1 WILD-TYPE    3   94
                        clus
vv                       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              6               94
[1] 2 2
[1] FALSE

Clustering(12) Variable = SLC28A1 MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  SLC28A1 MUTATED    5  3
  SLC28A1 WILD-TYPE 89 68
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
                8               157 
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
                3                68 
$`SLC28A1 MUTATED`
TCGA-18-3409 TCGA-18-3412 TCGA-22-5472 TCGA-34-5232 TCGA-34-5239 TCGA-34-5928 
        2417          345         1964         2062          707          552 
TCGA-39-5028 TCGA-66-2785 
          52           60 

$`SLC28A1 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
         370          136         2464          146         1415          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
        1810          862          758           50         1331          187 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
          85         2754           92          827         3636         1426 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 
        1852         1058          474          284          962         1268 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
        1032          329          223          131           53          429 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
         822          623         1067          734         1161         1057 
TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 
         399          587          358          965         1933          445 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
        1346           24         1952          357          916         1912 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
        1713          506         2524         1940         2979         1311 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 
        5287         1966         1941          428           80         1874 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5234 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
        1000         1528         1715          365          428          941 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
         120           13          238          207           12          103 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
        2253         1361         1947         1996         1964         1849 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
         740           59          833          474         1084         1086 
TCGA-39-5039 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 
         544          684          822         1007          349          376 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
         757          310         1936          324          423           12 
TCGA-51-4080 TCGA-51-4081 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
          12          911          881            3          555           62 
TCGA-56-6546 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
          26          311          661         1963         1505         1963 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 
        1260          274         1731         1075         1297           97 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
         983          908         1092          717          816          358 
TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 
        1973         1967         1311          641           30           61 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
          28           30           30          639          762           30 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 
          61           31           61           61          700          578 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        1946           61          578         1956          121         1954 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 
         759          790         1217          699         1955         1977 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-85-6560 
         913         1952         1645          122         1492          364 
TCGA-85-6561 
         395 

  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
               52                 3 
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
             2417              5287 
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
            629.5             758.0 
[1] "52.0 - 2417.0 (629.5)" "3.0 - 5287.0 (758.0)" 
[1] "hr=" "1.7"
D12V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  SLC28A1 MUTATED          1        3         1         1          1          1
  SLC28A1 WILD-TYPE       27       67        12        25         22         13
                   vv
clus                STAGE IV
  SLC28A1 MUTATED          0
  SLC28A1 WILD-TYPE        3
D12V3, multiclass
            clus
vv           SLC28A1 MUTATED SLC28A1 WILD-TYPE
  STAGE IA                 1                27
  STAGE IB                 3                67
  STAGE IIA                1                12
  STAGE IIB                1                25
  STAGE IIIA               1                22
  STAGE IIIB               1                13
  STAGE IV                 0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC28A1 MUTATED     3   4   0   2
  SLC28A1 WILD-TYPE  34 111  14  10
D12V4, multiclass
    clus
vv   SLC28A1 MUTATED SLC28A1 WILD-TYPE
  T1               3                34
  T2               4               111
  T3               0                14
  T4               2                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC28A1 MUTATED     6   3   0   0
  SLC28A1 WILD-TYPE 110  36  17   5
D12V5, multiclass
    clus
vv   SLC28A1 MUTATED SLC28A1 WILD-TYPE
  N0               6               110
  N1               3                36
  N2               0                17
  N3               0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  SLC28A1 MUTATED     9   0   0
  SLC28A1 WILD-TYPE 156   3   6
D12V6, multiclass
    clus
vv   SLC28A1 MUTATED SLC28A1 WILD-TYPE
  M0               9               156
  M1               0                 3
  MX               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                   cls
clus                  0   1
  SLC28A1 MUTATED     2   7
  SLC28A1 WILD-TYPE  45 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A1 MUTATED      2    7
  SLC28A1 WILD-TYPE   45  124
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  FEMALE               2                45
  MALE                 7               124
[1] 2 2
[1] FALSE
D12V8, continuous
[1] "Remove cluster labels:" "SLC28A1 MUTATED"       
clus
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
                1                35 
       TCGA-18-3406        TCGA-18-3407        TCGA-18-3410        TCGA-18-3414 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-18-3419        TCGA-21-5782        TCGA-21-5787        TCGA-22-4591 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-22-4593        TCGA-22-4595        TCGA-22-4599        TCGA-22-4601 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-22-4604        TCGA-22-4613        TCGA-22-5473        TCGA-22-5474 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-22-5477        TCGA-22-5478        TCGA-22-5480        TCGA-22-5482 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-22-5485        TCGA-22-5489        TCGA-22-5491        TCGA-22-5492 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-34-5234        TCGA-37-4133        TCGA-37-4135        TCGA-37-5819 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-60-2698        TCGA-60-2712        TCGA-60-2715        TCGA-60-2725 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
       TCGA-60-2726        TCGA-70-6722        TCGA-70-6723 
"SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" "SLC28A1 WILD-TYPE" 
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  SLC28A1 MUTATED                                       1
  SLC28A1 WILD-TYPE                                     4
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  SLC28A1 MUTATED                                        0
  SLC28A1 WILD-TYPE                                      1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLC28A1 MUTATED                                                             8
  SLC28A1 WILD-TYPE                                                         164
D12V9, multiclass
                                                             clus
vv                                                            SLC28A1 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               8
                                                             clus
vv                                                            SLC28A1 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, binary
                   cls
clus                  0   1
  SLC28A1 MUTATED     0   9
  SLC28A1 WILD-TYPE   5 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A1 MUTATED      0    9
  SLC28A1 WILD-TYPE    5  164
     clus
vv    SLC28A1 MUTATED SLC28A1 WILD-TYPE
  NO                0                 5
  YES               9               164
[1] 2 2
[1] FALSE
D12V11, continuous
                   vv
clus                 R0  R1  R2  RX
  SLC28A1 MUTATED     6   0   0   0
  SLC28A1 WILD-TYPE 141   2   4  10
D12V12, multiclass
    clus
vv   SLC28A1 MUTATED SLC28A1 WILD-TYPE
  R0               6               141
  R1               0                 2
  R2               0                 4
  RX               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC28A1 MUTATED       0                         1     6
  SLC28A1 WILD-TYPE     5                         8   105
D12V13, multiclass
                           clus
vv                          SLC28A1 MUTATED SLC28A1 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               1                 8
  WHITE                                   6               105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                   cls
clus                 0  1
  SLC28A1 MUTATED    0  7
  SLC28A1 WILD-TYPE  3 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A1 MUTATED      0    7
  SLC28A1 WILD-TYPE    3   93
                        clus
vv                       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               7                93
[1] 2 2
[1] FALSE

Clustering(13) Variable = ASB5 MUTATION ANALYSIS
D13V1, survival
                sevent
clus2             0  1
  ASB5 MUTATED    6  3
  ASB5 WILD-TYPE 88 68
  ASB5 MUTATED ASB5 WILD-TYPE 
             9            156 
  ASB5 MUTATED ASB5 WILD-TYPE 
             3             68 
$`ASB5 MUTATED`
TCGA-18-3409 TCGA-18-3412 TCGA-22-4613 TCGA-33-4533 TCGA-33-4538 TCGA-39-5016 
        2417          345          358         1940         2979         2253 
TCGA-66-2755 TCGA-66-2766 TCGA-66-2768 
          28           31           61 

$`ASB5 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
         370          136         2464          146         1415          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
        1810          862          758           50         1331          187 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
          85         2754           92          827         3636         1426 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 
        1852         1058          474          284          962         1268 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
        1032          329          223          131           53          429 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
         822          623         1067          734         1161         1057 
TCGA-22-4604 TCGA-22-4607 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         399          587          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
        1346           24         1952          357          916         1912 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
        1713          506         2524         1311         5287         1966 
TCGA-33-4583 TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 
        1941          428           80         1874         1000         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
        2062         1715          707          365          428          941 
TCGA-34-5928 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
         552          120           13          238          207           12 
TCGA-37-5819 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
         103         1361         1947         1996         1964         1849 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
          52          740           59          833          474         1084 
TCGA-39-5037 TCGA-39-5039 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
        1086          544          684          822         1007          349 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-46-6025 TCGA-46-6026 
         376          757          310         1936          324          423 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
          12           12          911          881            3          555 
TCGA-56-6545 TCGA-56-6546 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
          62           26          311          661         1963         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2719 
        1963         1260          274         1731         1075         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
          97          983          908         1092          717          816 
TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 
         358         1973         1967         1311          641           30 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
          61           30           30          639          762           30 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          61           61          700          578         1946           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
         578         1956          121         1954          759           60 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 
         790         1217          699         1955         1977          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-85-6560 TCGA-85-6561 
        1952         1645          122         1492          364          395 

  ASB5 MUTATED ASB5 WILD-TYPE 
            28              3 
  ASB5 MUTATED ASB5 WILD-TYPE 
          2979           5287 
  ASB5 MUTATED ASB5 WILD-TYPE 
         358.0          757.5 
[1] "28.0 - 2979.0 (358.0)" "3.0 - 5287.0 (757.5)" 
[1] "hr=" "2.1"
D13V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  ASB5 MUTATED          1        3         1         1          2          0
  ASB5 WILD-TYPE       27       67        12        25         21         14
                vv
clus             STAGE IV
  ASB5 MUTATED          0
  ASB5 WILD-TYPE        3
D13V3, multiclass
            clus
vv           ASB5 MUTATED ASB5 WILD-TYPE
  STAGE IA              1             27
  STAGE IB              3             67
  STAGE IIA             1             12
  STAGE IIB             1             25
  STAGE IIIA            2             21
  STAGE IIIB            0             14
  STAGE IV              0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ASB5 MUTATED     2   7   0   0
  ASB5 WILD-TYPE  35 108  14  12
D13V4, multiclass
    clus
vv   ASB5 MUTATED ASB5 WILD-TYPE
  T1            2             35
  T2            7            108
  T3            0             14
  T4            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ASB5 MUTATED     5   2   2   0
  ASB5 WILD-TYPE 111  37  15   5
D13V5, multiclass
    clus
vv   ASB5 MUTATED ASB5 WILD-TYPE
  N0            5            111
  N1            2             37
  N2            2             15
  N3            0              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  ASB5 MUTATED     9   0   0
  ASB5 WILD-TYPE 156   3   6
D13V6, multiclass
    clus
vv   ASB5 MUTATED ASB5 WILD-TYPE
  M0            9            156
  M1            0              3
  MX            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                cls
clus               0   1
  ASB5 MUTATED     2   7
  ASB5 WILD-TYPE  45 124
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASB5 MUTATED      2    7
  ASB5 WILD-TYPE   45  124
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  FEMALE            2             45
  MALE              7            124
[1] 2 2
[1] FALSE
D13V8, continuous
[1] "Remove cluster labels:" "ASB5 MUTATED"          
clus
  ASB5 MUTATED ASB5 WILD-TYPE 
             1             35 
    TCGA-18-3406     TCGA-18-3407     TCGA-18-3410     TCGA-18-3414 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-18-3419     TCGA-21-5782     TCGA-21-5787     TCGA-22-4591 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-22-4593     TCGA-22-4595     TCGA-22-4599     TCGA-22-4601 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-22-4604     TCGA-22-5472     TCGA-22-5473     TCGA-22-5474 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-22-5477     TCGA-22-5478     TCGA-22-5480     TCGA-22-5482 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-22-5485     TCGA-22-5489     TCGA-22-5491     TCGA-22-5492 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-34-5234     TCGA-37-4133     TCGA-37-4135     TCGA-37-5819 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-60-2698     TCGA-60-2712     TCGA-60-2715     TCGA-60-2725 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-60-2726     TCGA-70-6722     TCGA-70-6723 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
                vv
clus             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  ASB5 MUTATED                                       2
  ASB5 WILD-TYPE                                     3
                vv
clus             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  ASB5 MUTATED                                        0
  ASB5 WILD-TYPE                                      1
                vv
clus             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ASB5 MUTATED                                                             7
  ASB5 WILD-TYPE                                                         165
D13V9, multiclass
                                                             clus
vv                                                            ASB5 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                  2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            7
                                                             clus
vv                                                            ASB5 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, binary
                cls
clus               0   1
  ASB5 MUTATED     0   9
  ASB5 WILD-TYPE   5 164
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASB5 MUTATED      0    9
  ASB5 WILD-TYPE    5  164
     clus
vv    ASB5 MUTATED ASB5 WILD-TYPE
  NO             0              5
  YES            9            164
[1] 2 2
[1] FALSE
D13V11, continuous
                vv
clus              R0  R1  R2  RX
  ASB5 MUTATED     8   0   0   1
  ASB5 WILD-TYPE 139   2   4   9
D13V12, multiclass
    clus
vv   ASB5 MUTATED ASB5 WILD-TYPE
  R0            8            139
  R1            0              2
  R2            0              4
  RX            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASB5 MUTATED       0                         1     3
  ASB5 WILD-TYPE     5                         8   108
D13V13, multiclass
                           clus
vv                          ASB5 MUTATED ASB5 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            1              8
  WHITE                                3            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V14, binary
                cls
clus              0  1
  ASB5 MUTATED    1  2
  ASB5 WILD-TYPE  2 98
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASB5 MUTATED      1    2
  ASB5 WILD-TYPE    2   98
                        clus
vv                       ASB5 MUTATED ASB5 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO            2             98
[1] 2 2
[1] FALSE

Clustering(14) Variable = CPS1 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2             0  1
  CPS1 MUTATED   16  8
  CPS1 WILD-TYPE 78 63
  CPS1 MUTATED CPS1 WILD-TYPE 
            24            141 
  CPS1 MUTATED CPS1 WILD-TYPE 
             8             63 
$`CPS1 MUTATED`
TCGA-18-3409 TCGA-18-3415 TCGA-18-3419 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
        2417         1810           50           92         3636         1426 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1081 TCGA-21-5784 TCGA-22-4591 TCGA-22-5482 
        1852         1058          284         1268          623          357 
TCGA-39-5016 TCGA-46-6026 TCGA-51-4080 TCGA-60-2698 TCGA-60-2720 TCGA-60-2722 
        2253          423           12          311           97          908 
TCGA-66-2757 TCGA-66-2759 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 TCGA-85-6560 
          30          762           60          790         1955          364 

$`CPS1 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
         370          136         2464          146         1415          345 
TCGA-18-3414 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
         396          862          758         1331          187           85 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1078 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 
        2754          827          474          962         1032          329 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 
         223          131           53          429          822         1067 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 
         734         1161         1057          399          587          358 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
         965         1964         1933          445         1346           24 
TCGA-22-5480 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 
        1952          916         1912         1713          506         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        1940         2979         1311         5287         1966         1941 
TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
         428           80         1874         1000         1528         2062 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        1715          707          365          428          941          552 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
         120           13          238          207           12          103 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
        1361         1947         1996         1964         1849           52 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
         740           59          833          474         1084         1086 
TCGA-39-5039 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 
         544          684          822         1007          349          376 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-46-6025 TCGA-51-4079 TCGA-51-4081 
         757          310         1936          324           12          911 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-60-2707 
         881            3          555           62           26          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        1963         1505         1963         1260          274         1731 
TCGA-60-2715 TCGA-60-2719 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
        1075         1297          983         1092          717          816 
TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 
         358         1973         1967         1311          641           30 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 
          61           28           30          639           30           61 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
          31           61           61          700          578         1946 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
          61          578         1956          121         1954          759 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
        1217          699         1977          913         1952         1645 
TCGA-66-2795 TCGA-66-2800 TCGA-85-6561 
         122         1492          395 

  CPS1 MUTATED CPS1 WILD-TYPE 
            12              3 
  CPS1 MUTATED CPS1 WILD-TYPE 
          3636           5287 
  CPS1 MUTATED CPS1 WILD-TYPE 
         692.5          757.0 
[1] "12.0 - 3636.0 (692.5)" "3.0 - 5287.0 (757.0)" 
[1] "hr=" "1.4"
D14V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  CPS1 MUTATED          2        7         2         8          3          2
  CPS1 WILD-TYPE       26       63        11        18         20         12
                vv
clus             STAGE IV
  CPS1 MUTATED          0
  CPS1 WILD-TYPE        3
D14V3, multiclass
            clus
vv           CPS1 MUTATED CPS1 WILD-TYPE
  STAGE IA              2             26
  STAGE IB              7             63
  STAGE IIA             2             11
  STAGE IIB             8             18
  STAGE IIIA            3             20
  STAGE IIIB            2             12
  STAGE IV              0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CPS1 MUTATED     5  15   4   1
  CPS1 WILD-TYPE  32 100  10  11
D14V4, multiclass
    clus
vv   CPS1 MUTATED CPS1 WILD-TYPE
  T1            5             32
  T2           15            100
  T3            4             10
  T4            1             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CPS1 MUTATED    13   9   2   1
  CPS1 WILD-TYPE 103  30  15   4
D14V5, multiclass
    clus
vv   CPS1 MUTATED CPS1 WILD-TYPE
  N0           13            103
  N1            9             30
  N2            2             15
  N3            1              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  CPS1 MUTATED    24   0   0
  CPS1 WILD-TYPE 141   3   6
D14V6, multiclass
    clus
vv   CPS1 MUTATED CPS1 WILD-TYPE
  M0           24            141
  M1            0              3
  MX            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                cls
clus               0   1
  CPS1 MUTATED     6  19
  CPS1 WILD-TYPE  41 112
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED      6   19
  CPS1 WILD-TYPE   41  112
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  FEMALE            6             41
  MALE             19            112
[1] 2 2
[1] FALSE
D14V8, continuous
                vv
clus             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  CPS1 MUTATED                                       3
  CPS1 WILD-TYPE                                     2
                vv
clus             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  CPS1 MUTATED                                        0
  CPS1 WILD-TYPE                                      1
                vv
clus             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CPS1 MUTATED                                                            22
  CPS1 WILD-TYPE                                                         150
D14V9, multiclass
                                                             clus
vv                                                            CPS1 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                  3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           22
                                                             clus
vv                                                            CPS1 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, binary
                cls
clus               0   1
  CPS1 MUTATED     1  24
  CPS1 WILD-TYPE   4 149
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED      1   24
  CPS1 WILD-TYPE    4  149
     clus
vv    CPS1 MUTATED CPS1 WILD-TYPE
  NO             1              4
  YES           24            149
[1] 2 2
[1] FALSE
D14V11, continuous
                vv
clus              R0  R1  R2  RX
  CPS1 MUTATED    22   0   1   1
  CPS1 WILD-TYPE 125   2   3   9
D14V12, multiclass
    clus
vv   CPS1 MUTATED CPS1 WILD-TYPE
  R0           22            125
  R1            0              2
  R2            1              3
  RX            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CPS1 MUTATED       0                         2    14
  CPS1 WILD-TYPE     5                         7    97
D14V13, multiclass
                           clus
vv                          CPS1 MUTATED CPS1 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            2              7
  WHITE                               14             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                cls
clus              0  1
  CPS1 MUTATED    0 12
  CPS1 WILD-TYPE  3 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED      0   12
  CPS1 WILD-TYPE    3   88
                        clus
vv                       CPS1 MUTATED CPS1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           12             88
[1] 2 2
[1] FALSE

Clustering(15) Variable = EP300 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2              0  1
  EP300 MUTATED    5  3
  EP300 WILD-TYPE 89 68
  EP300 MUTATED EP300 WILD-TYPE 
              8             157 
  EP300 MUTATED EP300 WILD-TYPE 
              3              68 
$`EP300 MUTATED`
TCGA-18-3419 TCGA-21-5786 TCGA-22-4595 TCGA-37-3783 TCGA-56-1622 TCGA-60-2713 
          50         1032          734          120          881         1731 
TCGA-66-2763 TCGA-66-2773 
          30         1946 

$`EP300 WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 
         345          396         1810          862          758         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
         187           85         2754           92          827         3636 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 
        1426         1852         1058          474          284          962 
TCGA-21-5784 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
        1268          329          223          131           53          429 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
         822          623         1067         1161         1057          399 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
        1346           24         1952          357          916         1912 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
        1713          506         2524         1940         2979         1311 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 
        5287         1966         1941          428           80         1874 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
        1000         1528         2062         1715          707          365 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 
         428          941          552           13          238          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
          12          103         2253         1361         1947         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1964         1849           52          740           59          833 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2578 TCGA-43-3394 
         474         1084         1086          544          684          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
        1007          349          376          757          310         1936 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-56-5897 
         324          423           12           12          911            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 
         555           62           26          311          661         1963 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2719 
        1505         1963         1260          274         1075         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
          97          983          908         1092          717          816 
TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 
         358         1973         1967         1311          641           30 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
          61           28           30           30          639          762 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 
          61           31           61           61          700          578 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
          61          578         1956          121         1954          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 
          60          790         1217          699         1955         1977 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-85-6560 
         913         1952         1645          122         1492          364 
TCGA-85-6561 
         395 

  EP300 MUTATED EP300 WILD-TYPE 
             30               3 
  EP300 MUTATED EP300 WILD-TYPE 
           1946            5287 
  EP300 MUTATED EP300 WILD-TYPE 
          807.5           757.0 
[1] "30.0 - 1946.0 (807.5)" "3.0 - 5287.0 (757.0)" 
[1] "hr=" "1.2"
D15V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  EP300 MUTATED          0        5         0         1          2          0
  EP300 WILD-TYPE       28       65        13        25         21         14
                 vv
clus              STAGE IV
  EP300 MUTATED          0
  EP300 WILD-TYPE        3
D15V3, multiclass
            clus
vv           EP300 MUTATED EP300 WILD-TYPE
  STAGE IA               0              28
  STAGE IB               5              65
  STAGE IIA              0              13
  STAGE IIB              1              25
  STAGE IIIA             2              21
  STAGE IIIB             0              14
  STAGE IV               0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EP300 MUTATED     0   6   2   0
  EP300 WILD-TYPE  37 109  12  12
D15V4, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  T1             0              37
  T2             6             109
  T3             2              12
  T4             0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EP300 MUTATED     5   1   2   0
  EP300 WILD-TYPE 111  38  15   5
D15V5, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  N0             5             111
  N1             1              38
  N2             2              15
  N3             0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1  MX
  EP300 MUTATED     7   0   0
  EP300 WILD-TYPE 158   3   6
D15V6, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  M0             7             158
  M1             0               3
  MX             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                 cls
clus                0   1
  EP300 MUTATED     1   7
  EP300 WILD-TYPE  46 124
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      1    7
  EP300 WILD-TYPE   46  124
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  FEMALE             1              46
  MALE               7             124
[1] 2 2
[1] FALSE
D15V8, continuous
[1] "Remove cluster labels:" "EP300 MUTATED"         
clus
  EP300 MUTATED EP300 WILD-TYPE 
              2              34 
     TCGA-18-3406      TCGA-18-3407      TCGA-18-3410      TCGA-18-3414 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-21-5782      TCGA-21-5787      TCGA-22-4591      TCGA-22-4593 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-4599      TCGA-22-4601      TCGA-22-4604      TCGA-22-4613 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5472      TCGA-22-5473      TCGA-22-5474      TCGA-22-5477 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5478      TCGA-22-5480      TCGA-22-5482      TCGA-22-5485 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5489      TCGA-22-5491      TCGA-22-5492      TCGA-34-5234 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-37-4133      TCGA-37-4135      TCGA-37-5819      TCGA-60-2698 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-60-2712      TCGA-60-2715      TCGA-60-2725      TCGA-60-2726 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-70-6722      TCGA-70-6723 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" 
                 vv
clus              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  EP300 MUTATED                                       0
  EP300 WILD-TYPE                                     5
                 vv
clus              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  EP300 MUTATED                                        0
  EP300 WILD-TYPE                                      1
                 vv
clus              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  EP300 MUTATED                                                             8
  EP300 WILD-TYPE                                                         164
D15V9, multiclass
                                                             clus
vv                                                            EP300 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             8
                                                             clus
vv                                                            EP300 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, binary
                 cls
clus                0   1
  EP300 MUTATED     1   7
  EP300 WILD-TYPE   4 166
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      1    7
  EP300 WILD-TYPE    4  166
     clus
vv    EP300 MUTATED EP300 WILD-TYPE
  NO              1               4
  YES             7             166
[1] 2 2
[1] FALSE
D15V11, continuous
                 vv
clus               R0  R1  R2  RX
  EP300 MUTATED     8   0   0   0
  EP300 WILD-TYPE 139   2   4  10
D15V12, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  R0             8             139
  R1             0               2
  R2             0               4
  RX             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EP300 MUTATED       0                         0     5
  EP300 WILD-TYPE     5                         9   106
D15V13, multiclass
                           clus
vv                          EP300 MUTATED EP300 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               9
  WHITE                                 5             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                 cls
clus               0  1
  EP300 MUTATED    0  4
  EP300 WILD-TYPE  3 96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      0    4
  EP300 WILD-TYPE    3   96
                        clus
vv                       EP300 MUTATED EP300 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4              96
[1] 2 2
[1] FALSE

Clustering(16) Variable = ARID1A MUTATION ANALYSIS
D16V1, survival
                  sevent
clus2               0  1
  ARID1A MUTATED    7  5
  ARID1A WILD-TYPE 87 66
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              153 
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               66 
$`ARID1A MUTATED`
TCGA-18-3409 TCGA-21-1078 TCGA-39-5022 TCGA-39-5037 TCGA-39-5039 TCGA-43-3394 
        2417          474         1996         1086          544          822 
TCGA-51-4080 TCGA-51-4081 TCGA-60-2720 TCGA-63-6202 TCGA-66-2756 TCGA-66-2793 
          12          911           97         1973           30         1952 

$`ARID1A WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
         370          136         2464          146         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
         396         1810          862          758           50         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
         187           85         2754           92          827         3636 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 
        1426         1852         1058          284          962         1268 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
        1032          329          223          131           53          429 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
         822          623         1067          734         1161         1057 
TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
         399          587          358          965         1964         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 
         445         1346           24         1952          357          916 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
        1912         1713          506         2524         1940         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-34-2596 
        1311         5287         1966         1941          428           80 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
        1874         1000         1528         2062         1715          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-37-3783 TCGA-37-3789 
         365          428          941          552          120           13 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
         238          207           12          103         2253         1361 
TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
        1947         1964         1849           52          740           59 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-43-2578 TCGA-43-3920 TCGA-43-5668 
         833          474         1084          684         1007          349 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-46-6025 TCGA-46-6026 
         376          757          310         1936          324          423 
TCGA-51-4079 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
          12          881            3          555           62           26 
TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
         311          661         1963         1505         1963         1260 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 
         274         1731         1075         1297          983          908 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-66-2727 TCGA-66-2734 
        1092          717          816          358         1967         1311 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 
         641           30           61           28           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
         762           30           61           31           61           61 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
         700          578         1946           61          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
         121         1954          759           60          790         1217 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
         699         1955         1977          913         1645          122 
TCGA-66-2800 TCGA-85-6560 TCGA-85-6561 
        1492          364          395 

  ARID1A MUTATED ARID1A WILD-TYPE 
              12                3 
  ARID1A MUTATED ARID1A WILD-TYPE 
            2417             5287 
  ARID1A MUTATED ARID1A WILD-TYPE 
           866.5            740.0 
[1] "12.0 - 2417.0 (866.5)" "3.0 - 5287.0 (740.0)" 
[1] "hr=" "1.4"
D16V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  ARID1A MUTATED          0        4         3         1          0          3
  ARID1A WILD-TYPE       28       66        10        25         23         11
                  vv
clus               STAGE IV
  ARID1A MUTATED          0
  ARID1A WILD-TYPE        3
D16V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE IA                0               28
  STAGE IB                4               66
  STAGE IIA               3               10
  STAGE IIB               1               25
  STAGE IIIA              0               23
  STAGE IIIB              3               11
  STAGE IV                0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID1A MUTATED     2   7   0   3
  ARID1A WILD-TYPE  35 108  14   9
D16V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              2               35
  T2              7              108
  T3              0               14
  T4              3                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ARID1A MUTATED     8   4   0   0
  ARID1A WILD-TYPE 108  35  17   5
D16V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0              8              108
  N1              4               35
  N2              0               17
  N3              0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1  MX
  ARID1A MUTATED    11   0   0
  ARID1A WILD-TYPE 154   3   6
D16V6, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  M0             11              154
  M1              0                3
  MX              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED     1  11
  ARID1A WILD-TYPE  46 120
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      1   11
  ARID1A WILD-TYPE   46  120
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              1               46
  MALE               11              120
[1] 2 2
[1] FALSE
D16V8, continuous
                  vv
clus               LUNG BASALOID SQUAMOUS CELL CARCINOMA
  ARID1A MUTATED                                       2
  ARID1A WILD-TYPE                                     3
                  vv
clus               LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  ARID1A MUTATED                                        0
  ARID1A WILD-TYPE                                      1
                  vv
clus               LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ARID1A MUTATED                                                            10
  ARID1A WILD-TYPE                                                         162
D16V9, multiclass
                                                             clus
vv                                                            ARID1A MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             10
                                                             clus
vv                                                            ARID1A WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, binary
                  cls
clus                 0   1
  ARID1A MUTATED     0  12
  ARID1A WILD-TYPE   5 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      0   12
  ARID1A WILD-TYPE    5  161
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO               0                5
  YES             12              161
[1] 2 2
[1] FALSE
D16V11, continuous
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    12   0   0   0
  ARID1A WILD-TYPE 135   2   4  10
D16V12, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             12              135
  R1              0                2
  R2              0                4
  RX              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       0                         2     6
  ARID1A WILD-TYPE     5                         7   105
D16V13, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              2                7
  WHITE                                  6              105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                  cls
clus                0  1
  ARID1A MUTATED    0  7
  ARID1A WILD-TYPE  3 93
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      0    7
  ARID1A WILD-TYPE    3   93
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              7               93
[1] 2 2
[1] FALSE

Clustering(17) Variable = FBXW7 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2              0  1
  FBXW7 MUTATED    3  7
  FBXW7 WILD-TYPE 91 64
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             10             155 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              7              64 
$`FBXW7 MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-4083 TCGA-18-5595 TCGA-21-1078 TCGA-22-1012 
         370         2417          187          827          474          429 
TCGA-22-4604 TCGA-51-4081 TCGA-60-2698 TCGA-60-2722 
         399          911          311          908 

$`FBXW7 WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         136         2464          146         1415          345          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
        1810          862          758           50         1331           85 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 
        2754           92         3636         1426         1852         1058 
TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 
         284          962         1268         1032          329          223 
TCGA-22-1002 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 
         131           53          822          623         1067          734 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
        1161         1057          587          358          965         1964 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 
        1933          445         1346           24         1952          357 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 
         916         1912         1713          506         2524         1940 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
        2979         1311         5287         1966         1941          428 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
          80         1874         1000         1528         2062         1715 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-37-3783 
         707          365          428          941          552          120 
TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 
          13          238          207           12          103         2253 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
        1361         1947         1996         1964         1849           52 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
         740           59          833          474         1084         1086 
TCGA-39-5039 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 
         544          684          822         1007          349          376 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
         757          310         1936          324          423           12 
TCGA-51-4080 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
          12          881            3          555           62           26 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 
         661         1963         1505         1963         1260          274 
TCGA-60-2713 TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 
        1731         1075         1297           97          983         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 
         717          816          358         1973         1967         1311 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
         641           30           61           28           30           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
         639          762           30           61           31           61 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
          61          700          578         1946           61          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
        1956          121         1954          759           60          790 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
        1217          699         1955         1977          913         1952 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-85-6560 TCGA-85-6561 
        1645          122         1492          364          395 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
            187               3 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
           2417            5287 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          451.5           758.0 
[1] "187.0 - 2417.0 (451.5)" "3.0 - 5287.0 (758.0)"  
[1] "hr=" "2.1"
D17V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  FBXW7 MUTATED          1        3         1         4          0          0
  FBXW7 WILD-TYPE       27       67        12        22         23         14
                 vv
clus              STAGE IV
  FBXW7 MUTATED          0
  FBXW7 WILD-TYPE        3
D17V3, multiclass
            clus
vv           FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE IA               1              27
  STAGE IB               3              67
  STAGE IIA              1              12
  STAGE IIB              4              22
  STAGE IIIA             0              23
  STAGE IIIB             0              14
  STAGE IV               0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FBXW7 MUTATED     2   8   0   0
  FBXW7 WILD-TYPE  35 107  14  12
D17V4, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  T1             2              35
  T2             8             107
  T3             0              14
  T4             0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FBXW7 MUTATED     5   5   0   0
  FBXW7 WILD-TYPE 111  34  17   5
D17V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0             5             111
  N1             5              34
  N2             0              17
  N3             0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1  MX
  FBXW7 MUTATED    10   0   0
  FBXW7 WILD-TYPE 155   3   6
D17V6, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  M0            10             155
  M1             0               3
  MX             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                 cls
clus                0   1
  FBXW7 MUTATED     1   9
  FBXW7 WILD-TYPE  46 122
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      1    9
  FBXW7 WILD-TYPE   46  122
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE             1              46
  MALE               9             122
[1] 2 2
[1] FALSE
D17V8, continuous
                 vv
clus              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  FBXW7 MUTATED                                       1
  FBXW7 WILD-TYPE                                     4
                 vv
clus              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  FBXW7 MUTATED                                        0
  FBXW7 WILD-TYPE                                      1
                 vv
clus              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FBXW7 MUTATED                                                             9
  FBXW7 WILD-TYPE                                                         163
D17V9, multiclass
                                                             clus
vv                                                            FBXW7 MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                   1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             9
                                                             clus
vv                                                            FBXW7 WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, binary
                 cls
clus                0   1
  FBXW7 MUTATED     0  10
  FBXW7 WILD-TYPE   5 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      0   10
  FBXW7 WILD-TYPE    5  163
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO              0               5
  YES            10             163
[1] 2 2
[1] FALSE
D17V11, continuous
                 vv
clus               R0  R1  R2  RX
  FBXW7 MUTATED     9   0   0   1
  FBXW7 WILD-TYPE 138   2   4   9
D17V12, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0             9             138
  R1             0               2
  R2             0               4
  RX             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FBXW7 MUTATED       0                         0     8
  FBXW7 WILD-TYPE     5                         9   103
D17V13, multiclass
                           clus
vv                          FBXW7 MUTATED FBXW7 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               9
  WHITE                                 8             103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V14, binary
                 cls
clus               0  1
  FBXW7 MUTATED    0  6
  FBXW7 WILD-TYPE  3 94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      0    6
  FBXW7 WILD-TYPE    3   94
                        clus
vv                       FBXW7 MUTATED FBXW7 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6              94
[1] 2 2
[1] FALSE
