[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"        "-oTLUAD-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/LUAD-TP/10006018/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUAD-TP/10686947/transformed.cor.cli.txt"

nPatients in clinical file=474, in cluster file=229, common to both=172
[1] "Reduce the number of clustering variables from 21 to 20."
[1]  20 172
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            86             86 
  TP53 MUTATED TP53 WILD-TYPE 
            86             86 
[1] "STK11 MUTATION ANALYSIS"
[1] 3
  STK11 MUTATED STK11 WILD-TYPE 
             20             152 
  STK11 MUTATED STK11 WILD-TYPE 
             20             152 
[1] "KEAP1 MUTATION ANALYSIS"
[1] 3
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             31             141 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             31             141 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            47            125 
  KRAS MUTATED KRAS WILD-TYPE 
            47            125 
[1] "SMARCA4 MUTATION ANALYSIS"
[1] 3
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               15               157 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               15               157 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              161 
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              161 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           22           150 
  NF1 MUTATED NF1 WILD-TYPE 
           22           150 
[1] "U2AF1 MUTATION ANALYSIS"
[1] 3
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              6             166 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              6             166 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
            23            149 
  EGFR MUTATED EGFR WILD-TYPE 
            23            149 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             15             157 
  SETD2 MUTATED SETD2 WILD-TYPE 
             15             157 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               8              164 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               8              164 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
           11           161 
  MET MUTATED MET WILD-TYPE 
           11           161 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              8             164 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              8             164 
[1] "CHRND MUTATION ANALYSIS"
[1] 3
  CHRND MUTATED CHRND WILD-TYPE 
              9             163 
  CHRND MUTATED CHRND WILD-TYPE 
              9             163 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            16            156 
  BRAF MUTATED BRAF WILD-TYPE 
            16            156 
[1] "GEN1 MUTATION ANALYSIS"
[1] 3
  GEN1 MUTATED GEN1 WILD-TYPE 
             4            168 
  GEN1 MUTATED GEN1 WILD-TYPE 
             4            168 
[1] "STX2 MUTATION ANALYSIS"
[1] 3
  STX2 MUTATED STX2 WILD-TYPE 
             4            168 
  STX2 MUTATED STX2 WILD-TYPE 
             4            168 
[1] "MGA MUTATION ANALYSIS"
[1] 3
  MGA MUTATED MGA WILD-TYPE 
           15           157 
  MGA MUTATED MGA WILD-TYPE 
           15           157 
[1] "GALC MUTATION ANALYSIS"
[1] 3
  GALC MUTATED GALC WILD-TYPE 
             5            167 
  GALC MUTATED GALC WILD-TYPE 
             5            167 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               9              163 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               9              163 
[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 172 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-05-4244 TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 
          NA         1523           NA          607          426         1369 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
        1126           NA           NA           NA         1431           NA 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 
         578          610           NA           NA          455           NA 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         912          365          913          669          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
         761          761          730           NA          457          151 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         882          670           30           62           14          225 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         182          264         2973         3674         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 
         864         1073          354         1357          448         1324 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        1429          400         1367          741         1280         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
          97          246         1130         1163         1036          190 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
         722         1013          383          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         845          704          658          705         1938           NA 
TCGA-44-6778 TCGA-44-6779 TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
        1864           NA         2318           NA           NA           NA 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
        1081         1421          428          999          268          896 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         157         1700          445          369          890          522 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
          NA           NA         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         944         1499          246          282          267         1091 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        2370          653           NA           NA          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
         764          686           NA           NA           NA           NA 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
          NA           NA         1015          701         1178         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-64-1676 
        1375           87            2          993           24         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
         628         1189         1126         2676           62         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
         864         1559          866           31          610          573 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         427          385           NA          174          141          422 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
          61         1600          711          912          800          467 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-5122 TCGA-75-5125 
         131           40          164           38           NA           NA 
TCGA-75-5126 TCGA-75-5146 TCGA-75-5147 TCGA-75-6203 TCGA-75-6205 TCGA-75-6206 
          NA           NA           NA           NA           NA           NA 
TCGA-75-6207 TCGA-75-6211 TCGA-75-6212 TCGA-80-5611 TCGA-86-6562 TCGA-91-6828 
          NA           NA           NA           NA           NA          323 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
          NA          310           79          417 
Variable 1:'AGE':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=124,	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=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=8,	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"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 172 columns, 1 survival variables, and 12 non-survival variables.
AGE, nv=44, 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 
 41 109  14   8 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 41 109  14   8 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 41 109  14   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 41 109  14   8 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
95 37 34  1 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
   95    37    35 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 N3 
95 37 34  1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
   95    37    35 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=11, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=47, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   52 16
  TP53 WILD-TYPE 48 22
  TP53 MUTATED TP53 WILD-TYPE 
            68             70 
  TP53 MUTATED TP53 WILD-TYPE 
            16             22 
$`TP53 MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 
         607          426         1947         1431          610         1958 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         912          913          791          791          761          761 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
         730          151          670          225          182          264 
TCGA-38-4625 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 
        1952          864         1073         1357          448         1429 
TCGA-44-2659 TCGA-44-2662 TCGA-44-2668 TCGA-44-3396 TCGA-44-3918 TCGA-44-5643 
        1367         1280          246         1130         1036         1013 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 
         383          723          328          845          658          705 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-49-4505 TCGA-49-4514 TCGA-50-5045 
        1942         1864         1978          428         1700         2174 
TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 
        2146          944         1499          267         2370          567 
TCGA-50-5944 TCGA-50-5946 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
         764          686          701         1178         1375           87 
TCGA-55-6712 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-5775 TCGA-64-5778 
          24         1728          628         1189           62         1305 
TCGA-67-3770 TCGA-67-3771 TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-91-6829 
          31          610          800          131          164         1940 
TCGA-91-6831 TCGA-91-6836 
         310          417 

$`TP53 WILD-TYPE`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        1523         1369         1126          578         1997          455 
TCGA-05-4422 TCGA-05-4425 TCGA-05-5420 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 
         365          669          457          882           30           62 
TCGA-35-3615 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4631 TCGA-44-2655 
          14         1962         1147         1492          354         1324 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-3398 TCGA-44-3919 
         400          741         1301           97         1163          190 
TCGA-44-4112 TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-49-4486 TCGA-49-4494 
         722          302          704         1938         1932         1081 
TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 
        1421          999          268          896          157          445 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 
         369          890          522          455          785          246 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5935 TCGA-50-5942 TCGA-50-6597 TCGA-55-1595 
         282         1091          653          883         1015         1479 
TCGA-55-6543 TCGA-55-6642 TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 
           2          993         1126         1959          864         1559 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         866          573          427          385          174          141 
TCGA-67-6217 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 
         422           61         1600          711          912          467 
TCGA-73-4675 TCGA-73-4677 TCGA-91-6828 TCGA-91-6835 
          40           38          323           79 

  TP53 MUTATED TP53 WILD-TYPE 
            24              2 
  TP53 MUTATED TP53 WILD-TYPE 
          2370           1997 
  TP53 MUTATED TP53 WILD-TYPE 
         777.5          686.5 
[1] "24.0 - 2370.0 (777.5)" "2.0 - 1997.0 (686.5)" 
[1] "hr=" "2.1"
D1V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  TP53 MUTATED         19       26         4        13         15          4
  TP53 WILD-TYPE       18       27         7        10         18          2
                vv
clus             STAGE IV
  TP53 MUTATED          5
  TP53 WILD-TYPE        4
D1V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE IA             19             18
  STAGE IB             26             27
  STAGE IIA             4              7
  STAGE IIB            13             10
  STAGE IIIA           15             18
  STAGE IIIB            4              2
  STAGE IV              5              4
[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   21 55  5  5
  TP53 WILD-TYPE 20 54  9  3
D1V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1           21             20
  T2           55             54
  T3            5              9
  T4            5              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             N0 N1 N2+N3
  TP53 MUTATED   48 17    17
  TP53 WILD-TYPE 47 20    18
D1V5, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  N0              48             47
  N1              17             20
  N2+N3           17             18
[1] 3 2
[1] 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   68  5 11
  TP53 WILD-TYPE 75  4  7
D1V6, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  M0           68             75
  M1            5              4
  MX           11              7
[1] 3 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   43 43
  TP53 WILD-TYPE 50 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     43   43
  TP53 WILD-TYPE   50   36
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           43             50
  MALE             43             36
[1] 2 2
[1] FALSE
D1V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TP53 MUTATED                            1                                22
  TP53 WILD-TYPE                          1                                17
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TP53 MUTATED                                                   59
  TP53 WILD-TYPE                                                 56
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TP53 MUTATED                                            0
  TP53 WILD-TYPE                                          1
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TP53 MUTATED                                               2
  TP53 WILD-TYPE                                             0
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  TP53 MUTATED                                0
  TP53 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  TP53 MUTATED                                    0
  TP53 WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TP53 MUTATED                              0                             2
  TP53 WILD-TYPE                            2                             2
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TP53 MUTATED                                               0
  TP53 WILD-TYPE                                             1
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  TP53 MUTATED                              0
  TP53 WILD-TYPE                            2
D1V9, multiclass
                                                    clus
vv                                                   TP53 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           59
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 2
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   TP53 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              17
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             56
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                   2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    2
[1] 11  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    8 78
  TP53 WILD-TYPE  7 79
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      8   78
  TP53 WILD-TYPE    7   79
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO             8              7
  YES           78             79
[1] 2 2
[1] FALSE
D1V11, continuous
                vv
clus             R0 R1 R2 RX
  TP53 MUTATED   53  3  1  4
  TP53 WILD-TYPE 62  3  3  5
D1V12, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           53             62
  R1            3              3
  R2            1              3
  RX            4              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             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  0     1
  TP53 WILD-TYPE                                1     2
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                           8    54
  TP53 WILD-TYPE                         1    59
D1V13, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              2
  BLACK OR AFRICAN AMERICAN                   8              1
  WHITE                                      54             59
[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"

Clustering(2) Variable = STK11 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2              0  1
  STK11 MUTATED    9  7
  STK11 WILD-TYPE 91 31
  STK11 MUTATED STK11 WILD-TYPE 
             16             122 
  STK11 MUTATED STK11 WILD-TYPE 
              7              31 
$`STK11 MUTATED`
TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4432 TCGA-35-3615 TCGA-44-6144 
        1997          455          365          761           14          723 
TCGA-44-6776 TCGA-44-6779 TCGA-49-4486 TCGA-49-4507 TCGA-50-5072 TCGA-50-5932 
        1938         1978         1932          268          246         1091 
TCGA-55-1596 TCGA-67-3774 TCGA-73-4670 TCGA-73-4677 
        1375          385          131           38 

$`STK11 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4420 TCGA-05-4424 
        1431          578          610         1958          912          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 
         669          791          791          761          730          457 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
         151          882          670           30           62          225 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         182          264         1952         1962         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 
         864         1073          354         1357          448         1324 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        1429          400         1367          741         1280         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
          97          246         1130         1163         1036          190 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
         722         1013          383          328          302          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-49-4494 
         704          658          705         1942         1864         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
        1421          428          999          896          157         1700 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 
         445          369          890          522         2174         2146 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 
         455          785          944         1499          282          267 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        2370          653          567          883          764          686 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
        1015          701         1178         1479           87            2 
TCGA-55-6642 TCGA-55-6712 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 
         993           24         1728          628         1189         1126 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1959           62         1305          864         1559          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
          31          610          573          427          174          141 
TCGA-67-6217 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         422           61         1600          711          912          800 
TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 
         467           40          164          323         1940          310 
TCGA-91-6835 TCGA-91-6836 
          79          417 

  STK11 MUTATED STK11 WILD-TYPE 
             14               2 
  STK11 MUTATED STK11 WILD-TYPE 
           1997            2370 
  STK11 MUTATED STK11 WILD-TYPE 
            589             751 
[1] "14.0 - 1997.0 (589.0)" "2.0 - 2370.0 (751.0)" 
[1] "hr=" "1.5"
D2V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  STK11 MUTATED          5        6         0         4          2          2
  STK11 WILD-TYPE       32       47        11        19         31          4
                 vv
clus              STAGE IV
  STK11 MUTATED          1
  STK11 WILD-TYPE        8
D2V3, multiclass
            clus
vv           STK11 MUTATED STK11 WILD-TYPE
  STAGE IA               5              32
  STAGE IB               6              47
  STAGE IIA              0              11
  STAGE IIB              4              19
  STAGE IIIA             2              31
  STAGE IIIB             2               4
  STAGE IV               1               8
[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
  STK11 MUTATED    4 13  1  2
  STK11 WILD-TYPE 37 96 13  6
D2V4, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  T1             4              37
  T2            13              96
  T3             1              13
  T4             2               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2+N3
  STK11 MUTATED   12  5     3
  STK11 WILD-TYPE 83 32    32
D2V5, multiclass
       clus
vv      STK11 MUTATED STK11 WILD-TYPE
  N0               12              83
  N1                5              32
  N2+N3             3              32
[1] 3 2
[1] 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
  STK11 MUTATED    17   1   2
  STK11 WILD-TYPE 126   8  16
D2V6, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  M0            17             126
  M1             1               8
  MX             2              16
[1] 3 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
  STK11 MUTATED    7 13
  STK11 WILD-TYPE 86 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED      7   13
  STK11 WILD-TYPE   86   66
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  FEMALE             7              86
  MALE              13              66
[1] 2 2
[1] FALSE
D2V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  STK11 MUTATED                            0                                 6
  STK11 WILD-TYPE                          2                                33
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  STK11 MUTATED                                                   14
  STK11 WILD-TYPE                                                101
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  STK11 MUTATED                                            0
  STK11 WILD-TYPE                                          1
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  STK11 MUTATED                                               0
  STK11 WILD-TYPE                                             2
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  STK11 MUTATED                                0
  STK11 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  STK11 MUTATED                                    0
  STK11 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  STK11 MUTATED                              0                             0
  STK11 WILD-TYPE                            2                             4
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  STK11 MUTATED                                               0
  STK11 WILD-TYPE                                             1
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  STK11 MUTATED                              0
  STK11 WILD-TYPE                            2
D2V9, multiclass
                                                    clus
vv                                                   STK11 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            14
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   STK11 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             101
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                    4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     2
[1] 11  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
  STK11 MUTATED     2  18
  STK11 WILD-TYPE  13 139
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED      2   18
  STK11 WILD-TYPE   13  139
     clus
vv    STK11 MUTATED STK11 WILD-TYPE
  NO              2              13
  YES            18             139
[1] 2 2
[1] FALSE
D2V11, continuous
                 vv
clus               R0  R1  R2  RX
  STK11 MUTATED    13   0   0   2
  STK11 WILD-TYPE 102   6   4   7
D2V12, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  R0            13             102
  R1             0               6
  R2             0               4
  RX             2               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              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK11 MUTATED                                  0     1
  STK11 WILD-TYPE                                1     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STK11 MUTATED                           0    13
  STK11 WILD-TYPE                         9   100
D2V13, multiclass
                                  clus
vv                                 STK11 MUTATED STK11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               2
  BLACK OR AFRICAN AMERICAN                    0               9
  WHITE                                       13             100
[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"

Clustering(3) Variable = KEAP1 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2              0  1
  KEAP1 MUTATED   16  8
  KEAP1 WILD-TYPE 84 30
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             24             114 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
              8              30 
$`KEAP1 MUTATED`
TCGA-05-4384 TCGA-05-4389 TCGA-35-3615 TCGA-35-5375 TCGA-38-4631 TCGA-44-2655 
         426         1369           14          264          354         1324 
TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-49-4486 TCGA-49-4506 TCGA-49-4507 
        1938         1864         1978         1932          999          268 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-50-5051 TCGA-50-5068 TCGA-55-5899 
        1700          445          369          455         1499           87 
TCGA-64-5781 TCGA-67-3771 TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 
        1559          610          800          131          164           38 

$`KEAP1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
        1523          607         1126         1947         1431          578 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
         610         1958         1997          455          912          365 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         913          669          791          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         730          457          151          882          670           30 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
          62          225          182         1952         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 
        1492          864         1073         1357          448         1429 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
         400         1367          741         1280         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
        1013          383          723          328          302          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-49-4494 TCGA-49-4501 
         704          658          705         1942         1081         1421 
TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 
         428          896          157          890          522         2174 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
        2146          785          944          246          282          267 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        1091         2370          653          567          883          764 
TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
         686         1015          701         1178         1479         1375 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
           2          993           24         1728          628         1189 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 
        1126         1959           62         1305          864          866 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
          31          573          427          385          174          141 
TCGA-67-6217 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 
         422           61         1600          711          912          467 
TCGA-73-4675 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
          40          323         1940          310           79          417 

  KEAP1 MUTATED KEAP1 WILD-TYPE 
             14               2 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
           1978            2370 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
          532.5           751.0 
[1] "14.0 - 1978.0 (532.5)" "2.0 - 2370.0 (751.0)" 
[1] "hr=" "1.3"
D3V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  KEAP1 MUTATED         10        6         1         4          7          1
  KEAP1 WILD-TYPE       27       47        10        19         26          5
                 vv
clus              STAGE IV
  KEAP1 MUTATED          2
  KEAP1 WILD-TYPE        7
D3V3, multiclass
            clus
vv           KEAP1 MUTATED KEAP1 WILD-TYPE
  STAGE IA              10              27
  STAGE IB               6              47
  STAGE IIA              1              10
  STAGE IIB              4              19
  STAGE IIIA             7              26
  STAGE IIIB             1               5
  STAGE IV               2               7
[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   11 17  2  1
  KEAP1 WILD-TYPE 30 92 12  7
D3V4, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  T1            11              30
  T2            17              92
  T3             2              12
  T4             1               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              N0 N1 N2+N3
  KEAP1 MUTATED   17  7     7
  KEAP1 WILD-TYPE 78 30    28
D3V5, multiclass
       clus
vv      KEAP1 MUTATED KEAP1 WILD-TYPE
  N0               17              78
  N1                7              30
  N2+N3             7              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1  MX
  KEAP1 MUTATED    23   2   6
  KEAP1 WILD-TYPE 120   7  12
D3V6, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  M0            23             120
  M1             2               7
  MX             6              12
[1] 3 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
  KEAP1 MUTATED   16 15
  KEAP1 WILD-TYPE 77 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED     16   15
  KEAP1 WILD-TYPE   77   64
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  FEMALE            16              77
  MALE              15              64
[1] 2 2
[1] FALSE
D3V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KEAP1 MUTATED                            0                                 6
  KEAP1 WILD-TYPE                          2                                33
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KEAP1 MUTATED                                                   21
  KEAP1 WILD-TYPE                                                 94
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KEAP1 MUTATED                                            0
  KEAP1 WILD-TYPE                                          1
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KEAP1 MUTATED                                               0
  KEAP1 WILD-TYPE                                             2
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  KEAP1 MUTATED                                1
  KEAP1 WILD-TYPE                              1
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  KEAP1 MUTATED                                    0
  KEAP1 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KEAP1 MUTATED                              0                             1
  KEAP1 WILD-TYPE                            2                             3
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KEAP1 MUTATED                                               0
  KEAP1 WILD-TYPE                                             1
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  KEAP1 MUTATED                              2
  KEAP1 WILD-TYPE                            0
D3V9, multiclass
                                                    clus
vv                                                   KEAP1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            21
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   2
                                                    clus
vv                                                   KEAP1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              94
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                    3
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
[1] 11  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
  KEAP1 MUTATED     3  28
  KEAP1 WILD-TYPE  12 129
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      3   28
  KEAP1 WILD-TYPE   12  129
     clus
vv    KEAP1 MUTATED KEAP1 WILD-TYPE
  NO              3              12
  YES            28             129
[1] 2 2
[1] FALSE
D3V11, continuous
                 vv
clus              R0 R1 R2 RX
  KEAP1 MUTATED   22  1  0  1
  KEAP1 WILD-TYPE 93  5  4  8
D3V12, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  R0            22              93
  R1             1               5
  R2             0               4
  RX             1               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              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KEAP1 MUTATED                                  0     0
  KEAP1 WILD-TYPE                                1     3
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KEAP1 MUTATED                           2    23
  KEAP1 WILD-TYPE                         7    90
D3V13, multiclass
                                  clus
vv                                 KEAP1 MUTATED KEAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               3
  BLACK OR AFRICAN AMERICAN                    2               7
  WHITE                                       23              90
[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"

Clustering(4) Variable = KRAS MUTATION ANALYSIS
D4V1, survival
                sevent
clus2             0  1
  KRAS MUTATED   27 12
  KRAS WILD-TYPE 73 26
  KRAS MUTATED KRAS WILD-TYPE 
            39             99 
  KRAS MUTATED KRAS WILD-TYPE 
            12             26 
$`KRAS MUTATED`
TCGA-05-4249 TCGA-05-4390 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
        1523         1126          578          610         1997          455 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-35-3615 TCGA-38-4626 TCGA-44-2668 
         791          761          730           14         1962          246 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6776 TCGA-44-6777 TCGA-49-4505 
         723          328          302         1938         1942          428 
TCGA-49-4510 TCGA-49-6744 TCGA-50-5051 TCGA-50-5932 TCGA-50-5933 TCGA-50-5941 
         896          890          455         1091         2370          567 
TCGA-55-1595 TCGA-55-6642 TCGA-64-1677 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
        1479          993          628         1959           62         1305 
TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 
         866          427          385          711          912          131 
TCGA-73-4677 TCGA-91-6828 TCGA-91-6836 
          38          323          417 

$`KRAS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4410 
         607          426         1369         1947         1431         1958 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4432 
         912          365          913          669          791          761 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         457          151          882          670           30           62 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 
         225          182          264         1952         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 
         864         1073          354         1357          448         1324 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        1429          400         1367          741         1280         1301 
TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
          97         1130         1163         1036          190          722 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
        1013          383          845          704          658          705 
TCGA-44-6778 TCGA-44-6779 TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 
        1864         1978         1932         1081         1421          999 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 
         268          157         1700          445          369          522 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        2174         2146          785          944         1499          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
         282          267          653          883          764          686 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
        1015          701         1178         1375           87            2 
TCGA-55-6712 TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 TCGA-64-5779 TCGA-64-5781 
          24         1728         1189         1126          864         1559 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
          31          610          573          174          141          422 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
          61         1600          800          467           40          164 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 
        1940          310           79 

  KRAS MUTATED KRAS WILD-TYPE 
            14              2 
  KRAS MUTATED KRAS WILD-TYPE 
          2370           2174 
  KRAS MUTATED KRAS WILD-TYPE 
           723            761 
[1] "14.0 - 2370.0 (723.0)" "2.0 - 2174.0 (761.0)" 
[1] "hr=" "1.1"
D4V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  KRAS MUTATED          7       18         2         6          9          3
  KRAS WILD-TYPE       30       35         9        17         24          3
                vv
clus             STAGE IV
  KRAS MUTATED          2
  KRAS WILD-TYPE        7
D4V3, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE IA              7             30
  STAGE IB             18             35
  STAGE IIA             2              9
  STAGE IIB             6             17
  STAGE IIIA            9             24
  STAGE IIIB            3              3
  STAGE IV              2              7
[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
  KRAS MUTATED    6 32  5  4
  KRAS WILD-TYPE 35 77  9  4
D4V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            6             35
  T2           32             77
  T3            5              9
  T4            4              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             N0 N1 N2+N3
  KRAS MUTATED   28  7    11
  KRAS WILD-TYPE 67 30    24
D4V5, multiclass
       clus
vv      KRAS MUTATED KRAS WILD-TYPE
  N0              28             67
  N1               7             30
  N2+N3           11             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"
                vv
clus              M0  M1  MX
  KRAS MUTATED    40   2   5
  KRAS WILD-TYPE 103   7  13
D4V6, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  M0           40            103
  M1            2              7
  MX            5             13
[1] 3 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
  KRAS MUTATED   23 24
  KRAS WILD-TYPE 70 55
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     23   24
  KRAS WILD-TYPE   70   55
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           23             70
  MALE             24             55
[1] 2 2
[1] FALSE
D4V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KRAS MUTATED                            0                                12
  KRAS WILD-TYPE                          2                                27
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KRAS MUTATED                                                   30
  KRAS WILD-TYPE                                                 85
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KRAS MUTATED                                            0
  KRAS WILD-TYPE                                          1
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KRAS MUTATED                                               1
  KRAS WILD-TYPE                                             1
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  KRAS MUTATED                                1
  KRAS WILD-TYPE                              1
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  KRAS MUTATED                                    0
  KRAS WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KRAS MUTATED                              1                             1
  KRAS WILD-TYPE                            1                             3
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KRAS MUTATED                                               0
  KRAS WILD-TYPE                                             1
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  KRAS MUTATED                              1
  KRAS WILD-TYPE                            1
D4V9, multiclass
                                                    clus
vv                                                   KRAS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            12
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           30
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  1
                                                    clus
vv                                                   KRAS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              27
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             85
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    1
  LUNG PAPILLARY ADENOCARCINOMA                                   3
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    1
[1] 11  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
  KRAS MUTATED     2  45
  KRAS WILD-TYPE  13 112
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      2   45
  KRAS WILD-TYPE   13  112
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             2             13
  YES           45            112
[1] 2 2
[1] FALSE
D4V11, continuous
                vv
clus             R0 R1 R2 RX
  KRAS MUTATED   32  0  2  3
  KRAS WILD-TYPE 83  6  2  6
D4V12, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           32             83
  R1            0              6
  R2            2              2
  RX            3              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRAS MUTATED                                  0     1
  KRAS WILD-TYPE                                1     2
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED                           1    30
  KRAS WILD-TYPE                         8    83
D4V13, multiclass
                                  clus
vv                                 KRAS MUTATED KRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              2
  BLACK OR AFRICAN AMERICAN                   1              8
  WHITE                                      30             83
[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"

Clustering(5) Variable = SMARCA4 MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  SMARCA4 MUTATED    9  2
  SMARCA4 WILD-TYPE 91 36
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               11               127 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
                2                36 
$`SMARCA4 MUTATED`
TCGA-05-4432 TCGA-05-5420 TCGA-35-5375 TCGA-38-4631 TCGA-44-2656 TCGA-49-6742 
         761          457          264          354         1429          445 
TCGA-50-5072 TCGA-50-5941 TCGA-55-1596 TCGA-55-6543 TCGA-67-3771 
         246          567         1375            2          610 

$`SMARCA4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1431          578          610         1958         1997          455 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         912          365          913          669          791          791 
TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         761          730          151          882          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 
          62           14          225          182         1952         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
        1147         1492          864         1073         1357          448 
TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        1324          400         1367          741         1280         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
          97          246         1130         1163         1036          190 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
         722         1013          383          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         845          704          658          705         1938         1942 
TCGA-44-6778 TCGA-44-6779 TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
        1864         1978         1932         1081         1421          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
         999          268          896          157         1700          369 
TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         890          522         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
         944         1499          282          267         1091         2370 
TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 
         653          883          764          686         1015          701 
TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-64-1676 
        1178         1479           87          993           24         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
         628         1189         1126         1959           62         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 
         864         1559          866           31          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-71-6725 TCGA-73-4658 
         385          174          141          422           61         1600 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
         711          912          800          467          131           40 
TCGA-73-4676 TCGA-73-4677 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 
         164           38          323         1940          310           79 
TCGA-91-6836 
         417 

  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
                2                14 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
             1429              2370 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
              457               764 
[1] "2.0 - 1429.0 (457.0)"  "14.0 - 2370.0 (764.0)"
[1] "hr=" "1.3"
D5V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  SMARCA4 MUTATED          2        4         0         4          5          0
  SMARCA4 WILD-TYPE       35       49        11        19         28          6
                   vv
clus                STAGE IV
  SMARCA4 MUTATED          0
  SMARCA4 WILD-TYPE        9
D5V3, multiclass
            clus
vv           SMARCA4 MUTATED SMARCA4 WILD-TYPE
  STAGE IA                 2                35
  STAGE IB                 4                49
  STAGE IIA                0                11
  STAGE IIB                4                19
  STAGE IIIA               5                28
  STAGE IIIB               0                 6
  STAGE IV                 0                 9
[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
  SMARCA4 MUTATED    2 12  1  0
  SMARCA4 WILD-TYPE 39 97 13  8
D5V4, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  T1               2                39
  T2              12                97
  T3               1                13
  T4               0                 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                N0 N1 N2+N3
  SMARCA4 MUTATED    7  3     5
  SMARCA4 WILD-TYPE 88 34    30
D5V5, multiclass
       clus
vv      SMARCA4 MUTATED SMARCA4 WILD-TYPE
  N0                  7                88
  N1                  3                34
  N2+N3               5                30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  SMARCA4 MUTATED    13   0   2
  SMARCA4 WILD-TYPE 130   9  16
D5V6, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  M0              13               130
  M1               0                 9
  MX               2                16
[1] 3 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
  SMARCA4 MUTATED    6  9
  SMARCA4 WILD-TYPE 87 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      6    9
  SMARCA4 WILD-TYPE   87   70
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  FEMALE               6                87
  MALE                 9                70
[1] 2 2
[1] FALSE
D5V8, continuous
[1] "Remove cluster labels:" "SMARCA4 MUTATED"       
clus
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
                1                11 
       TCGA-35-4122        TCGA-35-4123        TCGA-64-1677        TCGA-64-5778 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-71-6725        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4676        TCGA-75-5122 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  SMARCA4 MUTATED                            0
  SMARCA4 WILD-TYPE                          2
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  SMARCA4 MUTATED                                   1
  SMARCA4 WILD-TYPE                                38
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SMARCA4 MUTATED                                                   10
  SMARCA4 WILD-TYPE                                                105
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SMARCA4 MUTATED                                            1
  SMARCA4 WILD-TYPE                                          0
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SMARCA4 MUTATED                                               0
  SMARCA4 WILD-TYPE                                             2
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  SMARCA4 MUTATED                                0
  SMARCA4 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  SMARCA4 MUTATED                                    0
  SMARCA4 WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SMARCA4 MUTATED                              0                             0
  SMARCA4 WILD-TYPE                            2                             4
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SMARCA4 MUTATED                                               1
  SMARCA4 WILD-TYPE                                             0
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  SMARCA4 MUTATED                              2
  SMARCA4 WILD-TYPE                            0
D5V9, multiclass
                                                    clus
vv                                                   SMARCA4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   SMARCA4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               105
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      2
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                      4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      0
  MUCINOUS (COLLOID) CARCINOMA                                       0
[1] 11  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
  SMARCA4 MUTATED     1  14
  SMARCA4 WILD-TYPE  14 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      1   14
  SMARCA4 WILD-TYPE   14  143
     clus
vv    SMARCA4 MUTATED SMARCA4 WILD-TYPE
  NO                1                14
  YES              14               143
[1] 2 2
[1] FALSE
D5V11, continuous
                   vv
clus                 R0  R1  R2  RX
  SMARCA4 MUTATED     9   0   0   0
  SMARCA4 WILD-TYPE 106   6   4   9
D5V12, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  R0               9               106
  R1               0                 6
  R2               0                 4
  RX               0                 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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCA4 MUTATED                                  0     1
  SMARCA4 WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCA4 MUTATED                           1    10
  SMARCA4 WILD-TYPE                         8   103
D5V13, multiclass
                                  clus
vv                                 SMARCA4 MUTATED SMARCA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 2
  BLACK OR AFRICAN AMERICAN                      1                 8
  WHITE                                         10               103
[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"

Clustering(6) Variable = ARID1A MUTATION ANALYSIS
D6V1, survival
                  sevent
clus2               0  1
  ARID1A MUTATED    9  1
  ARID1A WILD-TYPE 91 37
  ARID1A MUTATED ARID1A WILD-TYPE 
              10              128 
  ARID1A MUTATED ARID1A WILD-TYPE 
               1               37 
$`ARID1A MUTATED`
TCGA-05-4382 TCGA-05-4425 TCGA-05-4427 TCGA-05-5715 TCGA-38-4631 TCGA-44-6147 
         607          669          791           62          354          845 
TCGA-55-5899 TCGA-64-1678 TCGA-67-3771 TCGA-91-6831 
          87         1189          610          310 

$`ARID1A WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
        1523          426         1369         1126         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         578          610         1958         1997          455          912 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
         365          913          791          761          761          730 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 
         457          151          882          670           30           14 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
         225          182          264         1952         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 
        1492          864         1073         1357          448         1324 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        1429          400         1367          741         1280         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
          97          246         1130         1163         1036          190 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
         722         1013          383          723          328          302 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
         704          658          705         1938         1942         1864 
TCGA-44-6779 TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
        1978         1932         1081         1421          428          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
         268          896          157         1700          445          369 
TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         890          522         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         944         1499          246          282          267         1091 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        2370          653          567          883          764          686 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 
        1015          701         1178         1479         1375            2 
TCGA-55-6642 TCGA-55-6712 TCGA-64-1676 TCGA-64-1677 TCGA-64-1680 TCGA-64-5774 
         993           24         1728          628         1126         1959 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
          62         1305          864         1559          866           31 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         573          427          385          174          141          422 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
          61         1600          711          912          800          467 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-91-6828 TCGA-91-6829 
         131           40          164           38          323         1940 
TCGA-91-6835 TCGA-91-6836 
          79          417 

  ARID1A MUTATED ARID1A WILD-TYPE 
              62                2 
  ARID1A MUTATED ARID1A WILD-TYPE 
            1189             2370 
  ARID1A MUTATED ARID1A WILD-TYPE 
           608.5            761.0 
[1] "62.0 - 1189.0 (608.5)" "2.0 - 2370.0 (761.0)" 
[1] "hr=" "1.3"
D6V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  ARID1A MUTATED          3        4         1         1          1          0
  ARID1A WILD-TYPE       34       49        10        22         32          6
                  vv
clus               STAGE IV
  ARID1A MUTATED          1
  ARID1A WILD-TYPE        8
D6V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE IA                3               34
  STAGE IB                4               49
  STAGE IIA               1               10
  STAGE IIB               1               22
  STAGE IIIA              1               32
  STAGE IIIB              0                6
  STAGE IV                1                8
[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     3   8   0   0
  ARID1A WILD-TYPE  38 101  14   8
D6V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              3               38
  T2              8              101
  T3              0               14
  T4              0                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               N0 N1 N2+N3
  ARID1A MUTATED    7  2     1
  ARID1A WILD-TYPE 88 35    34
D6V5, multiclass
       clus
vv      ARID1A MUTATED ARID1A WILD-TYPE
  N0                 7               88
  N1                 2               35
  N2+N3              1               34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1  MX
  ARID1A MUTATED     9   1   1
  ARID1A WILD-TYPE 134   8  17
D6V6, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  M0              9              134
  M1              1                8
  MX              1               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                  cls
clus                0  1
  ARID1A MUTATED    7  4
  ARID1A WILD-TYPE 86 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      7    4
  ARID1A WILD-TYPE   86   75
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              7               86
  MALE                4               75
[1] 2 2
[1] FALSE
D6V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ARID1A MUTATED                            0                                 4
  ARID1A WILD-TYPE                          2                                35
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ARID1A MUTATED                                                    7
  ARID1A WILD-TYPE                                                108
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ARID1A MUTATED                                            0
  ARID1A WILD-TYPE                                          1
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ARID1A MUTATED                                               0
  ARID1A WILD-TYPE                                             2
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ARID1A MUTATED                                0
  ARID1A WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ARID1A MUTATED                                    0
  ARID1A WILD-TYPE                                  2
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ARID1A MUTATED                              0                             0
  ARID1A WILD-TYPE                            2                             4
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ARID1A MUTATED                                               0
  ARID1A WILD-TYPE                                             1
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ARID1A MUTATED                              0
  ARID1A WILD-TYPE                            2
D6V9, multiclass
                                                    clus
vv                                                   ARID1A MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ARID1A WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                35
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              108
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     2
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                     4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      2
[1] 11  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
  ARID1A MUTATED     0  11
  ARID1A WILD-TYPE  15 146
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      0   11
  ARID1A WILD-TYPE   15  146
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO               0               15
  YES             11              146
[1] 2 2
[1] FALSE
D6V11, continuous
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED     8   1   0   0
  ARID1A WILD-TYPE 107   5   4   9
D6V12, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0              8              107
  R1              1                5
  R2              0                4
  RX              0                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               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID1A MUTATED                                  0     0
  ARID1A WILD-TYPE                                1     3
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED                           1     5
  ARID1A WILD-TYPE                         8   108
D6V13, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                3
  BLACK OR AFRICAN AMERICAN                     1                8
  WHITE                                         5              108
[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"

Clustering(7) Variable = NF1 MUTATION ANALYSIS
D7V1, survival
               sevent
clus2            0  1
  NF1 MUTATED   10  8
  NF1 WILD-TYPE 90 30
  NF1 MUTATED NF1 WILD-TYPE 
           18           120 
  NF1 MUTATED NF1 WILD-TYPE 
            8            30 
$`NF1 MUTATED`
TCGA-05-4424 TCGA-05-5428 TCGA-38-4629 TCGA-38-4631 TCGA-44-2656 TCGA-44-2657 
         913          670          864          354         1429          400 
TCGA-44-2659 TCGA-44-3918 TCGA-44-6144 TCGA-44-6775 TCGA-50-5045 TCGA-50-5068 
        1367         1036          723          705         2174         1499 
TCGA-50-5072 TCGA-50-5946 TCGA-55-1592 TCGA-73-4658 TCGA-73-4676 TCGA-91-6829 
         246          686          701         1600          164         1940 

$`NF1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1431          578          610         1958         1997          455 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         912          365          669          791          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 
         761          730          457          151          882           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          62           14          225          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
        1962         1147         1492         1073         1357          448 
TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        1324          741         1280         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
        1130         1163          190          722         1013          383 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 
         328          302          845          704          658         1938 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 
        1942         1864         1978         1932         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
         428          999          268          896          157         1700 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-50-5049 TCGA-50-5051 
         445          369          890          522         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
         785          944          282          267         1091         2370 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-55-1594 
         653          567          883          764         1015         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        1479         1375           87            2          993           24 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 
        1728          628         1189         1126         1959           62 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        1305          864         1559          866           31          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         573          427          385          174          141          422 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
          61          711          912          800          467          131 
TCGA-73-4675 TCGA-73-4677 TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
          40           38          323          310           79          417 

  NF1 MUTATED NF1 WILD-TYPE 
          164             2 
  NF1 MUTATED NF1 WILD-TYPE 
         2174          2370 
  NF1 MUTATED NF1 WILD-TYPE 
        793.5         735.5 
[1] "164.0 - 2174.0 (793.5)" "2.0 - 2370.0 (735.5)"  
[1] "hr=" "1.4"
D7V2, continuous
               vv
clus            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  NF1 MUTATED          6        7         2         5          2          0
  NF1 WILD-TYPE       31       46         9        18         31          6
               vv
clus            STAGE IV
  NF1 MUTATED          0
  NF1 WILD-TYPE        9
D7V3, multiclass
            clus
vv           NF1 MUTATED NF1 WILD-TYPE
  STAGE IA             6            31
  STAGE IB             7            46
  STAGE IIA            2             9
  STAGE IIB            5            18
  STAGE IIIA           2            31
  STAGE IIIB           0             6
  STAGE IV             0             9
[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
  NF1 MUTATED    7 12  3  0
  NF1 WILD-TYPE 34 97 11  8
D7V4, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  T1           7            34
  T2          12            97
  T3           3            11
  T4           0             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            N0 N1 N2+N3
  NF1 MUTATED   14  5     2
  NF1 WILD-TYPE 81 32    33
D7V5, multiclass
       clus
vv      NF1 MUTATED NF1 WILD-TYPE
  N0             14            81
  N1              5            32
  N2+N3           2            33
[1] 3 2
[1] 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
  NF1 MUTATED    16   0   6
  NF1 WILD-TYPE 127   9  12
D7V6, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  M0          16           127
  M1           0             9
  MX           6            12
[1] 3 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
  NF1 MUTATED   12 10
  NF1 WILD-TYPE 81 69
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     12   10
  NF1 WILD-TYPE   81   69
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE          12            81
  MALE            10            69
[1] 2 2
[1] FALSE
D7V8, continuous
[1] "Remove cluster labels:" "NF1 MUTATED"           
clus
  NF1 MUTATED NF1 WILD-TYPE 
            1            11 
   TCGA-35-4122    TCGA-35-4123    TCGA-35-5375    TCGA-64-1677    TCGA-64-5778 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-71-6725    TCGA-73-4659    TCGA-73-4662    TCGA-73-4666    TCGA-73-4668 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-75-5122 
"NF1 WILD-TYPE" 
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NF1 MUTATED                            0                                 4
  NF1 WILD-TYPE                          2                                35
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NF1 MUTATED                                                   17
  NF1 WILD-TYPE                                                 98
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NF1 MUTATED                                            0
  NF1 WILD-TYPE                                          1
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NF1 MUTATED                                               1
  NF1 WILD-TYPE                                             1
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  NF1 MUTATED                                0
  NF1 WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  NF1 MUTATED                                    0                            0
  NF1 WILD-TYPE                                  2                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  NF1 MUTATED                               0
  NF1 WILD-TYPE                             4
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NF1 MUTATED                                               0
  NF1 WILD-TYPE                                             1
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  NF1 MUTATED                              0
  NF1 WILD-TYPE                            2
D7V9, multiclass
                                                    clus
vv                                                   NF1 MUTATED NF1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0             2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            4            35
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          17            98
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                1             1
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             2
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0             4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             1
  MUCINOUS (COLLOID) CARCINOMA                                 0             2
[1] 11  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
  NF1 MUTATED     3  19
  NF1 WILD-TYPE  12 138
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      3   19
  NF1 WILD-TYPE   12  138
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO            3            12
  YES          19           138
[1] 2 2
[1] FALSE
D7V11, continuous
               vv
clus             R0  R1  R2  RX
  NF1 MUTATED    14   1   0   2
  NF1 WILD-TYPE 101   5   4   7
D7V12, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  R0          14           101
  R1           1             5
  R2           0             4
  RX           2             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            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF1 MUTATED                                  0     0
  NF1 WILD-TYPE                                1     3
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED                           1    18
  NF1 WILD-TYPE                         8    95
D7V13, multiclass
                                  clus
vv                                 NF1 MUTATED NF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             3
  BLACK OR AFRICAN AMERICAN                  1             8
  WHITE                                     18            95
[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"

Clustering(8) Variable = U2AF1 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2              0  1
  U2AF1 MUTATED    5  1
  U2AF1 WILD-TYPE 95 37
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              6             132 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              1              37 
$`U2AF1 MUTATED`
TCGA-49-4505 TCGA-49-6743 TCGA-49-6744 TCGA-50-5941 TCGA-55-1595 TCGA-64-1680 
         428          369          890          567         1479         1126 

$`U2AF1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1431          578          610         1958         1997          455 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         912          365          913          669          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
         761          761          730          457          151          882 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 
         670           30           62           14          225          182 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
         264         1952         1962         1147         1492          864 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 TCGA-44-2656 
        1073          354         1357          448         1324         1429 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
         400         1367          741         1280         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
        1013          383          723          328          302          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
         704          658          705         1938         1942         1864 
TCGA-44-6779 TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 
        1978         1932         1081         1421          999          268 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6745 TCGA-50-5045 
         896          157         1700          445          522         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        2146          455          785          944         1499          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 
         282          267         1091         2370          653          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
         764          686         1015          701         1178         1375 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-64-1676 TCGA-64-1677 
          87            2          993           24         1728          628 
TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
        1189         1959           62         1305          864         1559 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
         866           31          610          573          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
         174          141          422           61         1600          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
         912          800          467          131           40          164 
TCGA-73-4677 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
          38          323         1940          310           79          417 

  U2AF1 MUTATED U2AF1 WILD-TYPE 
            369               2 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
           1479            2370 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
          728.5           735.5 
[1] "369.0 - 1479.0 (728.5)" "2.0 - 2370.0 (735.5)"  
[1] "hr=" "1.2"
D8V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  U2AF1 MUTATED          1        0         1         1          2          0
  U2AF1 WILD-TYPE       36       53        10        22         31          6
                 vv
clus              STAGE IV
  U2AF1 MUTATED          1
  U2AF1 WILD-TYPE        8
D8V3, multiclass
            clus
vv           U2AF1 MUTATED U2AF1 WILD-TYPE
  STAGE IA               1              36
  STAGE IB               0              53
  STAGE IIA              1              10
  STAGE IIB              1              22
  STAGE IIIA             2              31
  STAGE IIIB             0               6
  STAGE IV               1               8
[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
  U2AF1 MUTATED     2   4   0   0
  U2AF1 WILD-TYPE  39 105  14   8
D8V4, multiclass
    clus
vv   U2AF1 MUTATED U2AF1 WILD-TYPE
  T1             2              39
  T2             4             105
  T3             0              14
  T4             0               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              N0 N1 N2+N3
  U2AF1 MUTATED    1  2     3
  U2AF1 WILD-TYPE 94 35    32
D8V5, multiclass
       clus
vv      U2AF1 MUTATED U2AF1 WILD-TYPE
  N0                1              94
  N1                2              35
  N2+N3             3              32
[1] 3 2
[1] 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
  U2AF1 MUTATED     3   1   2
  U2AF1 WILD-TYPE 140   8  16
D8V6, multiclass
    clus
vv   U2AF1 MUTATED U2AF1 WILD-TYPE
  M0             3             140
  M1             1               8
  MX             2              16
[1] 3 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
  U2AF1 MUTATED    5  1
  U2AF1 WILD-TYPE 88 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      5    1
  U2AF1 WILD-TYPE   88   78
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  FEMALE             5              88
  MALE               1              78
[1] 2 2
[1] FALSE
D8V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  U2AF1 MUTATED                            0                                 2
  U2AF1 WILD-TYPE                          2                                37
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  U2AF1 MUTATED                                                    2
  U2AF1 WILD-TYPE                                                113
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  U2AF1 MUTATED                                            0
  U2AF1 WILD-TYPE                                          1
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  U2AF1 MUTATED                                               0
  U2AF1 WILD-TYPE                                             2
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  U2AF1 MUTATED                                2
  U2AF1 WILD-TYPE                              0
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  U2AF1 MUTATED                                    0
  U2AF1 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  U2AF1 MUTATED                              0                             0
  U2AF1 WILD-TYPE                            2                             4
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  U2AF1 MUTATED                                               0
  U2AF1 WILD-TYPE                                             1
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  U2AF1 MUTATED                              0
  U2AF1 WILD-TYPE                            2
D8V9, multiclass
                                                    clus
vv                                                   U2AF1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   U2AF1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             113
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                    4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     2
[1] 11  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
  U2AF1 MUTATED     1   5
  U2AF1 WILD-TYPE  14 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      1    5
  U2AF1 WILD-TYPE   14  152
     clus
vv    U2AF1 MUTATED U2AF1 WILD-TYPE
  NO              1              14
  YES             5             152
[1] 2 2
[1] FALSE
D8V11, continuous
                 vv
clus               R0  R1  R2  RX
  U2AF1 MUTATED     3   0   0   0
  U2AF1 WILD-TYPE 112   6   4   9
D8V12, multiclass
    clus
vv   U2AF1 MUTATED U2AF1 WILD-TYPE
  R0             3             112
  R1             0               6
  R2             0               4
  RX             0               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              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  U2AF1 MUTATED                                  0     1
  U2AF1 WILD-TYPE                                1     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  U2AF1 MUTATED                           0     5
  U2AF1 WILD-TYPE                         9   108
D8V13, multiclass
                                  clus
vv                                 U2AF1 MUTATED U2AF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               2
  BLACK OR AFRICAN AMERICAN                    0               9
  WHITE                                        5             108
[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"

Clustering(9) Variable = EGFR MUTATION ANALYSIS
D9V1, survival
                sevent
clus2             0  1
  EGFR MUTATED   11  6
  EGFR WILD-TYPE 89 32
  EGFR MUTATED EGFR WILD-TYPE 
            17            121 
  EGFR MUTATED EGFR WILD-TYPE 
             6             32 
$`EGFR MUTATED`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4410 TCGA-05-5423 TCGA-38-4627 TCGA-38-4628 
         607         1947         1958          151         1147         1492 
TCGA-38-4629 TCGA-38-6178 TCGA-44-2657 TCGA-44-6147 TCGA-49-4494 TCGA-49-4501 
         864          448          400          845         1081         1421 
TCGA-50-5944 TCGA-67-3770 TCGA-67-3772 TCGA-67-6217 TCGA-91-6835 
         764           31          573          422           79 

$`EGFR WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4403 
        1523          426         1369         1126         1431          578 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
         610         1997          455          912          365          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
         669          791          791          761          761          730 
TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         457          882          670           30           62           14 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4630 
         225          182          264         1952         1962         1073 
TCGA-38-4631 TCGA-38-4632 TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 
         354         1357         1324         1429         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 
        1036          190          722         1013          383          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         328          302          704          658          705         1938 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-49-4486 TCGA-49-4505 TCGA-49-4506 
        1942         1864         1978         1932          428          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
         268          896          157         1700          445          369 
TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         890          522         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         944         1499          246          282          267         1091 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6597 
        2370          653          567          883          686         1015 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
         701         1178         1479         1375           87            2 
TCGA-55-6642 TCGA-55-6712 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 
         993           24         1728          628         1189         1126 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1959           62         1305          864         1559          866 
TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-71-6725 
         610          427          385          174          141           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        1600          711          912          800          467          131 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 
          40          164           38          323         1940          310 
TCGA-91-6836 
         417 

  EGFR MUTATED EGFR WILD-TYPE 
            31              2 
  EGFR MUTATED EGFR WILD-TYPE 
          1958           2370 
  EGFR MUTATED EGFR WILD-TYPE 
           764            730 
[1] "31.0 - 1958.0 (764.0)" "2.0 - 2370.0 (730.0)" 
[1] "hr=" "1.4"
D9V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  EGFR MUTATED          4        5         3         3          5          1
  EGFR WILD-TYPE       33       48         8        20         28          5
                vv
clus             STAGE IV
  EGFR MUTATED          2
  EGFR WILD-TYPE        7
D9V3, multiclass
            clus
vv           EGFR MUTATED EGFR WILD-TYPE
  STAGE IA              4             33
  STAGE IB              5             48
  STAGE IIA             3              8
  STAGE IIB             3             20
  STAGE IIIA            5             28
  STAGE IIIB            1              5
  STAGE IV              2              7
[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
  EGFR MUTATED    5 14  3  1
  EGFR WILD-TYPE 36 95 11  7
D9V4, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  T1            5             36
  T2           14             95
  T3            3             11
  T4            1              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             N0 N1 N2+N3
  EGFR MUTATED    9  6     5
  EGFR WILD-TYPE 86 31    30
D9V5, multiclass
       clus
vv      EGFR MUTATED EGFR WILD-TYPE
  N0               9             86
  N1               6             31
  N2+N3            5             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  EGFR MUTATED    20   2   0
  EGFR WILD-TYPE 123   7  18
D9V6, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  M0           20            123
  M1            2              7
  MX            0             18
[1] 3 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
  EGFR MUTATED   16  7
  EGFR WILD-TYPE 77 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     16    7
  EGFR WILD-TYPE   77   72
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  FEMALE           16             77
  MALE              7             72
[1] 2 2
[1] FALSE
D9V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  EGFR MUTATED                            1                                 5
  EGFR WILD-TYPE                          1                                34
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  EGFR MUTATED                                                   16
  EGFR WILD-TYPE                                                 99
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  EGFR MUTATED                                            0
  EGFR WILD-TYPE                                          1
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  EGFR MUTATED                                               0
  EGFR WILD-TYPE                                             2
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  EGFR MUTATED                                0
  EGFR WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  EGFR MUTATED                                    1
  EGFR WILD-TYPE                                  1
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  EGFR MUTATED                              0                             0
  EGFR WILD-TYPE                            2                             4
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  EGFR MUTATED                                               0
  EGFR WILD-TYPE                                             1
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  EGFR MUTATED                              0
  EGFR WILD-TYPE                            2
D9V9, multiclass
                                                    clus
vv                                                   EGFR MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           16
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            1
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   EGFR WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              34
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             99
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   2
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              1
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                   4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    2
[1] 11  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
  EGFR MUTATED     0  23
  EGFR WILD-TYPE  15 134
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      0   23
  EGFR WILD-TYPE   15  134
     clus
vv    EGFR MUTATED EGFR WILD-TYPE
  NO             0             15
  YES           23            134
[1] 2 2
[1] FALSE
D9V11, continuous
                vv
clus              R0  R1  R2  RX
  EGFR MUTATED    15   1   1   1
  EGFR WILD-TYPE 100   5   3   8
D9V12, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  R0           15            100
  R1            1              5
  R2            1              3
  RX            1              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             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EGFR MUTATED                                  0     0
  EGFR WILD-TYPE                                1     3
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EGFR MUTATED                           0    16
  EGFR WILD-TYPE                         9    97
D9V13, multiclass
                                  clus
vv                                 EGFR MUTATED EGFR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              3
  BLACK OR AFRICAN AMERICAN                   0              9
  WHITE                                      16             97
[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"

Clustering(10) Variable = SETD2 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2              0  1
  SETD2 MUTATED    8  5
  SETD2 WILD-TYPE 92 33
  SETD2 MUTATED SETD2 WILD-TYPE 
             13             125 
  SETD2 MUTATED SETD2 WILD-TYPE 
              5              33 
$`SETD2 MUTATED`
TCGA-05-4396 TCGA-05-4425 TCGA-05-4427 TCGA-38-4631 TCGA-44-2666 TCGA-49-6744 
        1947          669          791          354           97          890 
TCGA-50-5941 TCGA-50-5942 TCGA-64-5775 TCGA-67-6216 TCGA-73-4658 TCGA-73-4666 
         567          883           62          141         1600          800 
TCGA-73-4676 
         164 

$`SETD2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 
        1523          607          426         1369         1126         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         578          610         1958         1997          455          912 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
         365          913          791          761          761          730 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         457          151          882          670           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
          14          225          182          264         1952         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
        1147         1492          864         1073         1357          448 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
        1324         1429          400         1367          741         1280 
TCGA-44-2665 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
        1301          246         1130         1163         1036          190 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
         722         1013          383          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         845          704          658          705         1938         1942 
TCGA-44-6778 TCGA-44-6779 TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
        1864         1978         1932         1081         1421          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
         999          268          896          157         1700          445 
TCGA-49-6743 TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         369          522         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         944         1499          246          282          267         1091 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 
        2370          653          764          686         1015          701 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        1178         1479         1375           87            2          993 
TCGA-55-6712 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 
          24         1728          628         1189         1126         1959 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        1305          864         1559          866           31          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6217 TCGA-71-6725 
         573          427          385          174          422           61 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
         711          912          467          131           40           38 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
         323         1940          310           79          417 

  SETD2 MUTATED SETD2 WILD-TYPE 
             62               2 
  SETD2 MUTATED SETD2 WILD-TYPE 
           1947            2370 
  SETD2 MUTATED SETD2 WILD-TYPE 
            669             741 
[1] "62.0 - 1947.0 (669.0)" "2.0 - 2370.0 (741.0)" 
[1] "hr=" "2"  
D10V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  SETD2 MUTATED          3        3         2         1          3          1
  SETD2 WILD-TYPE       34       50         9        22         30          5
                 vv
clus              STAGE IV
  SETD2 MUTATED          2
  SETD2 WILD-TYPE        7
D10V3, multiclass
            clus
vv           SETD2 MUTATED SETD2 WILD-TYPE
  STAGE IA               3              34
  STAGE IB               3              50
  STAGE IIA              2               9
  STAGE IIB              1              22
  STAGE IIIA             3              30
  STAGE IIIB             1               5
  STAGE IV               2               7
[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
  SETD2 MUTATED     4   8   1   2
  SETD2 WILD-TYPE  37 101  13   6
D10V4, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  T1             4              37
  T2             8             101
  T3             1              13
  T4             2               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2+N3
  SETD2 MUTATED    9  4     2
  SETD2 WILD-TYPE 86 33    33
D10V5, multiclass
       clus
vv      SETD2 MUTATED SETD2 WILD-TYPE
  N0                9              86
  N1                4              33
  N2+N3             2              33
[1] 3 2
[1] 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
  SETD2 MUTATED    12   2   1
  SETD2 WILD-TYPE 131   7  17
D10V6, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  M0            12             131
  M1             2               7
  MX             1              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                 cls
clus               0  1
  SETD2 MUTATED   11  4
  SETD2 WILD-TYPE 82 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     11    4
  SETD2 WILD-TYPE   82   75
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE            11              82
  MALE               4              75
[1] 2 2
[1] FALSE
D10V8, continuous
[1] "Remove cluster labels:" "SETD2 MUTATED"         
clus
  SETD2 MUTATED SETD2 WILD-TYPE 
              2              10 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-64-1677 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-64-5778      TCGA-71-6725      TCGA-73-4659      TCGA-73-4662 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-73-4668      TCGA-75-5122 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SETD2 MUTATED                            0                                 4
  SETD2 WILD-TYPE                          2                                35
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SETD2 MUTATED                                                   10
  SETD2 WILD-TYPE                                                105
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SETD2 MUTATED                                            0
  SETD2 WILD-TYPE                                          1
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SETD2 MUTATED                                               0
  SETD2 WILD-TYPE                                             2
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  SETD2 MUTATED                                0
  SETD2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  SETD2 MUTATED                                    0
  SETD2 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SETD2 MUTATED                              0                             1
  SETD2 WILD-TYPE                            2                             3
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SETD2 MUTATED                                               0
  SETD2 WILD-TYPE                                             1
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  SETD2 MUTATED                              0
  SETD2 WILD-TYPE                            2
D10V9, multiclass
                                                    clus
vv                                                   SETD2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   SETD2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               35
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             105
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                    3
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     2
[1] 11  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
  SETD2 MUTATED     3  12
  SETD2 WILD-TYPE  12 145
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      3   12
  SETD2 WILD-TYPE   12  145
     clus
vv    SETD2 MUTATED SETD2 WILD-TYPE
  NO              3              12
  YES            12             145
[1] 2 2
[1] FALSE
D10V11, continuous
                 vv
clus               R0  R1  R2  RX
  SETD2 MUTATED    12   1   1   0
  SETD2 WILD-TYPE 103   5   3   9
D10V12, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  R0            12             103
  R1             1               5
  R2             1               3
  RX             0               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              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETD2 MUTATED                                  0     0
  SETD2 WILD-TYPE                                1     3
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED                           0    11
  SETD2 WILD-TYPE                         9   102
D10V13, multiclass
                                  clus
vv                                 SETD2 MUTATED SETD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               3
  BLACK OR AFRICAN AMERICAN                    0               9
  WHITE                                       11             102
[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"

Clustering(11) Variable = CDKN2A MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2               0  1
  CDKN2A MUTATED    6  1
  CDKN2A WILD-TYPE 94 37
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               7              131 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               1               37 
$`CDKN2A MUTATED`
TCGA-05-4426 TCGA-05-4433 TCGA-38-4625 TCGA-44-5645 TCGA-49-4505 TCGA-55-1594 
         791          730         1952          383          428         1178 
TCGA-67-3771 
         610 

$`CDKN2A WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1431          578          610         1958         1997          455 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 
         912          365          913          669          791          761 
TCGA-05-4432 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         761          457          151          882          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 
          62           14          225          182          264         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
        1147         1492          864         1073          354         1357 
TCGA-38-6178 TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         448         1324         1429          400         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-6144 TCGA-44-6145 
        1036          190          722         1013          723          328 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         302          845          704          658          705         1938 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 
        1942         1864         1978         1932         1081         1421 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
         999          268          896          157         1700          445 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         369          890          522         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
         785          944         1499          246          282          267 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        1091         2370          653          567          883          764 
TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
         686         1015          701         1479         1375           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
           2          993           24         1728          628         1189 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
        1126         1959           62         1305          864         1559 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
         866           31          573          427          385          174 
TCGA-67-6216 TCGA-67-6217 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
         141          422           61         1600          711          912 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
         800          467          131           40          164           38 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
         323         1940          310           79          417 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
             383                2 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
            1952             2370 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
             730              741 
[1] "383.0 - 1952.0 (730.0)" "2.0 - 2370.0 (741.0)"  
[1] "hr=" "2"  
D11V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  CDKN2A MUTATED          2        3         0         1          2          0
  CDKN2A WILD-TYPE       35       50        11        22         31          6
                  vv
clus               STAGE IV
  CDKN2A MUTATED          0
  CDKN2A WILD-TYPE        9
D11V3, multiclass
            clus
vv           CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE IA                2               35
  STAGE IB                3               50
  STAGE IIA               0               11
  STAGE IIB               1               22
  STAGE IIIA              2               31
  STAGE IIIB              0                6
  STAGE IV                0                9
[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     2   6   0   0
  CDKN2A WILD-TYPE  39 103  14   8
D11V4, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  T1              2               39
  T2              6              103
  T3              0               14
  T4              0                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               N0 N1 N2+N3
  CDKN2A MUTATED    4  1     2
  CDKN2A WILD-TYPE 91 36    33
D11V5, multiclass
       clus
vv      CDKN2A MUTATED CDKN2A WILD-TYPE
  N0                 4               91
  N1                 1               36
  N2+N3              2               33
[1] 3 2
[1] 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     7   0   0
  CDKN2A WILD-TYPE 136   9  18
D11V6, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  M0              7              136
  M1              0                9
  MX              0               18
[1] 3 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
  CDKN2A MUTATED    5  3
  CDKN2A WILD-TYPE 88 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      5    3
  CDKN2A WILD-TYPE   88   76
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              5               88
  MALE                3               76
[1] 2 2
[1] FALSE
D11V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CDKN2A MUTATED                            0                                 2
  CDKN2A WILD-TYPE                          2                                37
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CDKN2A MUTATED                                                    6
  CDKN2A WILD-TYPE                                                109
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CDKN2A MUTATED                                            0
  CDKN2A WILD-TYPE                                          1
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CDKN2A MUTATED                                               0
  CDKN2A WILD-TYPE                                             2
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  CDKN2A MUTATED                                0
  CDKN2A WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  CDKN2A MUTATED                                    0
  CDKN2A WILD-TYPE                                  2
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CDKN2A MUTATED                              0                             0
  CDKN2A WILD-TYPE                            2                             4
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CDKN2A MUTATED                                               0
  CDKN2A WILD-TYPE                                             1
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  CDKN2A MUTATED                              0
  CDKN2A WILD-TYPE                            2
D11V9, multiclass
                                                    clus
vv                                                   CDKN2A MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   CDKN2A WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              109
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     2
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                     4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      2
[1] 11  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
  CDKN2A MUTATED     0   8
  CDKN2A WILD-TYPE  15 149
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      0    8
  CDKN2A WILD-TYPE   15  149
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO               0               15
  YES              8              149
[1] 2 2
[1] FALSE
D11V11, continuous
                  vv
clus                R0  R1  R2  RX
  CDKN2A MUTATED     6   0   0   0
  CDKN2A WILD-TYPE 109   6   4   9
D11V12, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  R0              6              109
  R1              0                6
  R2              0                4
  RX              0                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               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDKN2A MUTATED                                  0     0
  CDKN2A WILD-TYPE                                1     3
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED                           2     4
  CDKN2A WILD-TYPE                         7   109
D11V13, multiclass
                                  clus
vv                                 CDKN2A MUTATED CDKN2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                3
  BLACK OR AFRICAN AMERICAN                     2                7
  WHITE                                         4              109
[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"

Clustering(12) Variable = MET MUTATION ANALYSIS
D12V1, survival
               sevent
clus2            0  1
  MET MUTATED    6  3
  MET WILD-TYPE 94 35
  MET MUTATED MET WILD-TYPE 
            9           129 
  MET MUTATED MET WILD-TYPE 
            3            35 
$`MET MUTATED`
TCGA-05-4396 TCGA-05-4403 TCGA-44-2657 TCGA-49-4507 TCGA-49-6745 TCGA-50-5933 
        1947          578          400          268          522         2370 
TCGA-50-6597 TCGA-55-6712 TCGA-64-5781 
        1015           24         1559 

$`MET WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 
        1523          607          426         1369         1126         1431 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
         610         1958         1997          455          912          365 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         913          669          791          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         730          457          151          882          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          62           14          225          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
        1962         1147         1492          864         1073          354 
TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 
        1357          448         1324         1429         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 
        1036          190          722         1013          383          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         328          302          845          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-49-4486 TCGA-49-4494 
        1938         1942         1864         1978         1932         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
        1421          428          999          896          157         1700 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         445          369          890         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
         785          944         1499          246          282          267 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        1091          653          567          883          764          686 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
         701         1178         1479         1375           87            2 
TCGA-55-6642 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 
         993         1728          628         1189         1126         1959 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
          62         1305          864          866           31          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         573          427          385          174          141          422 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
          61         1600          711          912          800          467 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-91-6828 TCGA-91-6829 
         131           40          164           38          323         1940 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
         310           79          417 

  MET MUTATED MET WILD-TYPE 
           24             2 
  MET MUTATED MET WILD-TYPE 
         2370          2174 
  MET MUTATED MET WILD-TYPE 
          578           741 
[1] "24.0 - 2370.0 (578.0)" "2.0 - 2174.0 (741.0)" 
[1] "hr=" "2.1"
D12V2, continuous
               vv
clus            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  MET MUTATED          0        6         1         0          2          2
  MET WILD-TYPE       37       47        10        23         31          4
               vv
clus            STAGE IV
  MET MUTATED          0
  MET WILD-TYPE        9
D12V3, multiclass
            clus
vv           MET MUTATED MET WILD-TYPE
  STAGE IA             0            37
  STAGE IB             6            47
  STAGE IIA            1            10
  STAGE IIB            0            23
  STAGE IIIA           2            31
  STAGE IIIB           2             4
  STAGE IV             0             9
[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
  MET MUTATED     0   8   1   2
  MET WILD-TYPE  41 101  13   6
D12V4, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  T1           0            41
  T2           8           101
  T3           1            13
  T4           2             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2+N3
  MET MUTATED    5  3     2
  MET WILD-TYPE 90 34    33
D12V5, multiclass
       clus
vv      MET MUTATED MET WILD-TYPE
  N0              5            90
  N1              3            34
  N2+N3           2            33
[1] 3 2
[1] 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
  MET MUTATED    10   0   1
  MET WILD-TYPE 133   9  17
D12V6, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  M0          10           133
  M1           0             9
  MX           1            17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
               cls
clus             0  1
  MET MUTATED    5  6
  MET WILD-TYPE 88 73
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      5    6
  MET WILD-TYPE   88   73
        clus
vv       MET MUTATED MET WILD-TYPE
  FEMALE           5            88
  MALE             6            73
[1] 2 2
[1] FALSE
D12V8, continuous
[1] "Remove cluster labels:" "MET MUTATED"           
clus
  MET MUTATED MET WILD-TYPE 
            1            11 
   TCGA-35-4122    TCGA-35-4123    TCGA-35-5375    TCGA-64-1677    TCGA-64-5778 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-71-6725    TCGA-73-4659    TCGA-73-4662    TCGA-73-4666    TCGA-73-4668 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-73-4676 
"MET WILD-TYPE" 
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MET MUTATED                            0                                 3
  MET WILD-TYPE                          2                                36
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MET MUTATED                                                    8
  MET WILD-TYPE                                                107
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MET MUTATED                                            0
  MET WILD-TYPE                                          1
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MET MUTATED                                               0
  MET WILD-TYPE                                             2
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  MET MUTATED                                0
  MET WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  MET MUTATED                                    0                            0
  MET WILD-TYPE                                  2                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  MET MUTATED                               0
  MET WILD-TYPE                             4
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MET MUTATED                                               0
  MET WILD-TYPE                                             1
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  MET MUTATED                              0
  MET WILD-TYPE                            2
D12V9, multiclass
                                                    clus
vv                                                   MET MUTATED MET WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0             2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            3            36
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           8           107
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                0             2
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             2
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0             4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             1
  MUCINOUS (COLLOID) CARCINOMA                                 0             2
[1] 11  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
  MET MUTATED     2   9
  MET WILD-TYPE  13 148
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      2    9
  MET WILD-TYPE   13  148
     clus
vv    MET MUTATED MET WILD-TYPE
  NO            2            13
  YES           9           148
[1] 2 2
[1] FALSE
D12V11, continuous
               vv
clus             R0  R1  R2  RX
  MET MUTATED     8   0   0   0
  MET WILD-TYPE 107   6   4   9
D12V12, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  R0           8           107
  R1           0             6
  R2           0             4
  RX           0             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            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MET MUTATED                                  0     0
  MET WILD-TYPE                                1     3
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MET MUTATED                           0     7
  MET WILD-TYPE                         9   106
D12V13, multiclass
                                  clus
vv                                 MET MUTATED MET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             3
  BLACK OR AFRICAN AMERICAN                  0             9
  WHITE                                      7           106
[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"

Clustering(13) Variable = ERBB2 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2              0  1
  ERBB2 MUTATED    5  1
  ERBB2 WILD-TYPE 95 37
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              6             132 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              1              37 
$`ERBB2 MUTATED`
TCGA-05-4384 TCGA-05-5715 TCGA-38-4629 TCGA-44-2656 TCGA-44-3919 TCGA-64-5815 
         426           62          864         1429          190          866 

$`ERBB2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
        1523          607         1369         1126         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         578          610         1958         1997          455          912 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         365          913          669          791          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
         761          730          457          151          882          670 
TCGA-05-5429 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          30           14          225          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
        1962         1147         1492         1073          354         1357 
TCGA-38-6178 TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
         448         1324          400         1367          741         1280 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
        1301           97          246         1130         1163         1036 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
         722         1013          383          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         845          704          658          705         1938         1942 
TCGA-44-6778 TCGA-44-6779 TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
        1864         1978         1932         1081         1421          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
         999          268          896          157         1700          445 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         369          890          522         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
         785          944         1499          246          282          267 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        1091         2370          653          567          883          764 
TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
         686         1015          701         1178         1479         1375 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-64-1676 TCGA-64-1677 
          87            2          993           24         1728          628 
TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1189         1126         1959           62         1305          864 
TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
        1559           31          610          573          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
         174          141          422           61         1600          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
         912          800          467          131           40          164 
TCGA-73-4677 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
          38          323         1940          310           79          417 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
             62               2 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
           1429            2370 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          645.0           735.5 
[1] "62.0 - 1429.0 (645.0)" "2.0 - 2370.0 (735.5)" 
[1] "hr=" "1.1"
D13V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  ERBB2 MUTATED          1        2         1         2          1          0
  ERBB2 WILD-TYPE       36       51        10        21         32          6
                 vv
clus              STAGE IV
  ERBB2 MUTATED          1
  ERBB2 WILD-TYPE        8
D13V3, multiclass
            clus
vv           ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE IA               1              36
  STAGE IB               2              51
  STAGE IIA              1              10
  STAGE IIB              2              21
  STAGE IIIA             1              32
  STAGE IIIB             0               6
  STAGE IV               1               8
[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
  ERBB2 MUTATED     1   5   1   1
  ERBB2 WILD-TYPE  40 104  13   7
D13V4, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  T1             1              40
  T2             5             104
  T3             1              13
  T4             1               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              N0 N1 N2+N3
  ERBB2 MUTATED    4  3     1
  ERBB2 WILD-TYPE 91 34    34
D13V5, multiclass
       clus
vv      ERBB2 MUTATED ERBB2 WILD-TYPE
  N0                4              91
  N1                3              34
  N2+N3             1              34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1  MX
  ERBB2 MUTATED     7   1   0
  ERBB2 WILD-TYPE 136   8  18
D13V6, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  M0             7             136
  M1             1               8
  MX             0              18
[1] 3 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
  ERBB2 MUTATED    3  5
  ERBB2 WILD-TYPE 90 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      3    5
  ERBB2 WILD-TYPE   90   74
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE             3              90
  MALE               5              74
[1] 2 2
[1] FALSE
D13V8, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ERBB2 MUTATED                            0                                 4
  ERBB2 WILD-TYPE                          2                                35
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ERBB2 MUTATED                                                    4
  ERBB2 WILD-TYPE                                                111
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ERBB2 MUTATED                                            0
  ERBB2 WILD-TYPE                                          1
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ERBB2 MUTATED                                               0
  ERBB2 WILD-TYPE                                             2
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ERBB2 MUTATED                                0
  ERBB2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ERBB2 MUTATED                                    0
  ERBB2 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ERBB2 MUTATED                              0                             0
  ERBB2 WILD-TYPE                            2                             4
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ERBB2 MUTATED                                               0
  ERBB2 WILD-TYPE                                             1
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ERBB2 MUTATED                              0
  ERBB2 WILD-TYPE                            2
D13V9, multiclass
                                                    clus
vv                                                   ERBB2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ERBB2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               35
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             111
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                    4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     2
[1] 11  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
  ERBB2 MUTATED     0   8
  ERBB2 WILD-TYPE  15 149
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      0    8
  ERBB2 WILD-TYPE   15  149
     clus
vv    ERBB2 MUTATED ERBB2 WILD-TYPE
  NO              0              15
  YES             8             149
[1] 2 2
[1] FALSE
D13V11, continuous
                 vv
clus               R0  R1  R2  RX
  ERBB2 MUTATED     5   0   1   1
  ERBB2 WILD-TYPE 110   6   3   8
D13V12, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  R0             5             110
  R1             0               6
  R2             1               3
  RX             1               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              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERBB2 MUTATED                                  0     0
  ERBB2 WILD-TYPE                                1     3
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ERBB2 MUTATED                           0     5
  ERBB2 WILD-TYPE                         9   108
D13V13, multiclass
                                  clus
vv                                 ERBB2 MUTATED ERBB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               3
  BLACK OR AFRICAN AMERICAN                    0               9
  WHITE                                        5             108
[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"

Clustering(14) Variable = CHRND MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2              0  1
  CHRND MUTATED    5  2
  CHRND WILD-TYPE 95 36
  CHRND MUTATED CHRND WILD-TYPE 
              7             131 
  CHRND MUTATED CHRND WILD-TYPE 
              2              36 
$`CHRND MUTATED`
TCGA-05-4396 TCGA-05-4420 TCGA-05-4432 TCGA-38-4632 TCGA-44-3918 TCGA-50-5049 
        1947          912          761         1357         1036         2146 
TCGA-64-5778 
        1305 

$`CHRND WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 
        1523          607          426         1369         1126         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 
         578          610         1958         1997          455          365 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 
         913          669          791          791          761          730 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         457          151          882          670           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
          14          225          182          264         1952         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
        1147         1492          864         1073          354          448 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
        1324         1429          400         1367          741         1280 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 
        1301           97          246         1130         1163          190 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
         722         1013          383          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         845          704          658          705         1938         1942 
TCGA-44-6778 TCGA-44-6779 TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
        1864         1978         1932         1081         1421          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
         999          268          896          157         1700          445 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
         369          890          522         2174          455          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         944         1499          246          282          267         1091 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        2370          653          567          883          764          686 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
        1015          701         1178         1479         1375           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
           2          993           24         1728          628         1189 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1126         1959           62          864         1559          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
          31          610          573          427          385          174 
TCGA-67-6216 TCGA-67-6217 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
         141          422           61         1600          711          912 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
         800          467          131           40          164           38 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
         323         1940          310           79          417 

  CHRND MUTATED CHRND WILD-TYPE 
            761               2 
  CHRND MUTATED CHRND WILD-TYPE 
           2146            2370 
  CHRND MUTATED CHRND WILD-TYPE 
           1305             711 
[1] "761.0 - 2146.0 (1305.0)" "2.0 - 2370.0 (711.0)"   
[1] "hr=" "1.9"
D14V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  CHRND MUTATED          2        3         0         1          1          1
  CHRND WILD-TYPE       35       50        11        22         32          5
                 vv
clus              STAGE IV
  CHRND MUTATED          1
  CHRND WILD-TYPE        8
D14V3, multiclass
            clus
vv           CHRND MUTATED CHRND WILD-TYPE
  STAGE IA               2              35
  STAGE IB               3              50
  STAGE IIA              0              11
  STAGE IIB              1              22
  STAGE IIIA             1              32
  STAGE IIIB             1               5
  STAGE IV               1               8
[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
  CHRND MUTATED     1   6   1   1
  CHRND WILD-TYPE  40 103  13   7
D14V4, multiclass
    clus
vv   CHRND MUTATED CHRND WILD-TYPE
  T1             1              40
  T2             6             103
  T3             1              13
  T4             1               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              N0 N1 N2+N3
  CHRND MUTATED    5  3     1
  CHRND WILD-TYPE 90 34    34
D14V5, multiclass
       clus
vv      CHRND MUTATED CHRND WILD-TYPE
  N0                5              90
  N1                3              34
  N2+N3             1              34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1  MX
  CHRND MUTATED     8   1   0
  CHRND WILD-TYPE 135   8  18
D14V6, multiclass
    clus
vv   CHRND MUTATED CHRND WILD-TYPE
  M0             8             135
  M1             1               8
  MX             0              18
[1] 3 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
  CHRND MUTATED    2  7
  CHRND WILD-TYPE 91 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRND MUTATED      2    7
  CHRND WILD-TYPE   91   72
        clus
vv       CHRND MUTATED CHRND WILD-TYPE
  FEMALE             2              91
  MALE               7              72
[1] 2 2
[1] FALSE
D14V8, continuous
[1] "Remove cluster labels:" "CHRND MUTATED"         
clus
  CHRND MUTATED CHRND WILD-TYPE 
              1              11 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-64-1677 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
     TCGA-71-6725      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4676      TCGA-75-5122 
"CHRND WILD-TYPE" "CHRND WILD-TYPE" "CHRND WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CHRND MUTATED                            0                                 4
  CHRND WILD-TYPE                          2                                35
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CHRND MUTATED                                                    4
  CHRND WILD-TYPE                                                111
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CHRND MUTATED                                            0
  CHRND WILD-TYPE                                          1
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CHRND MUTATED                                               1
  CHRND WILD-TYPE                                             1
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  CHRND MUTATED                                0
  CHRND WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  CHRND MUTATED                                    0
  CHRND WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CHRND MUTATED                              0                             0
  CHRND WILD-TYPE                            2                             4
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CHRND MUTATED                                               0
  CHRND WILD-TYPE                                             1
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  CHRND MUTATED                              0
  CHRND WILD-TYPE                            2
D14V9, multiclass
                                                    clus
vv                                                   CHRND MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   CHRND WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               35
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             111
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                    4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     2
[1] 11  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
  CHRND MUTATED     1   8
  CHRND WILD-TYPE  14 149
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRND MUTATED      1    8
  CHRND WILD-TYPE   14  149
     clus
vv    CHRND MUTATED CHRND WILD-TYPE
  NO              1              14
  YES             8             149
[1] 2 2
[1] FALSE
D14V11, continuous
                 vv
clus               R0  R1  R2  RX
  CHRND MUTATED     8   0   0   0
  CHRND WILD-TYPE 107   6   4   9
D14V12, multiclass
    clus
vv   CHRND MUTATED CHRND WILD-TYPE
  R0             8             107
  R1             0               6
  R2             0               4
  RX             0               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              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHRND MUTATED                                  0     0
  CHRND WILD-TYPE                                1     3
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CHRND MUTATED                           1     3
  CHRND WILD-TYPE                         8   110
D14V13, multiclass
                                  clus
vv                                 CHRND MUTATED CHRND WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               3
  BLACK OR AFRICAN AMERICAN                    1               8
  WHITE                                        3             110
[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"

Clustering(15) Variable = BRAF MUTATION ANALYSIS
D15V1, survival
                sevent
clus2             0  1
  BRAF MUTATED   10  2
  BRAF WILD-TYPE 90 36
  BRAF MUTATED BRAF WILD-TYPE 
            12            126 
  BRAF MUTATED BRAF WILD-TYPE 
             2             36 
$`BRAF MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4410 TCGA-05-5428 TCGA-44-2662 
        1523          607         1369         1958          670         1280 
TCGA-44-2666 TCGA-44-3918 TCGA-44-6774 TCGA-50-5933 TCGA-50-5941 TCGA-50-5942 
          97         1036          658         2370          567          883 

$`BRAF WILD-TYPE`
TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
         426         1126         1947         1431          578          610 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        1997          455          912          365          913          669 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
         791          791          761          761          730          457 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         151          882           30           62           14          225 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         182          264         1952         1962         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 
         864         1073          354         1357          448         1324 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-2668 
        1429          400         1367          741         1301          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
        1130         1163          190          722         1013          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 
         723          328          302          845          704          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-49-4486 TCGA-49-4494 
        1938         1942         1864         1978         1932         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
        1421          428          999          268          896          157 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 
        1700          445          369          890          522         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        2146          455          785          944         1499          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5944 TCGA-50-5946 
         282          267         1091          653          764          686 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
        1015          701         1178         1479         1375           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
           2          993           24         1728          628         1189 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
        1126         1959           62         1305          864         1559 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
         866           31          610          573          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
         174          141          422           61         1600          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
         912          800          467          131           40          164 
TCGA-73-4677 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
          38          323         1940          310           79          417 

  BRAF MUTATED BRAF WILD-TYPE 
            97              2 
  BRAF MUTATED BRAF WILD-TYPE 
          2370           2174 
  BRAF MUTATED BRAF WILD-TYPE 
         959.5          726.5 
[1] "97.0 - 2370.0 (959.5)" "2.0 - 2174.0 (726.5)" 
[1] "hr=" "5.8"
D15V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  BRAF MUTATED          3        6         1         0          3          2
  BRAF WILD-TYPE       34       47        10        23         30          4
                vv
clus             STAGE IV
  BRAF MUTATED          1
  BRAF WILD-TYPE        8
D15V3, multiclass
            clus
vv           BRAF MUTATED BRAF WILD-TYPE
  STAGE IA              3             34
  STAGE IB              6             47
  STAGE IIA             1             10
  STAGE IIB             0             23
  STAGE IIIA            3             30
  STAGE IIIB            2              4
  STAGE IV              1              8
[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
  BRAF MUTATED     5   8   1   2
  BRAF WILD-TYPE  36 101  13   6
D15V4, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T1            5             36
  T2            8            101
  T3            1             13
  T4            2              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2+N3
  BRAF MUTATED   10  2     4
  BRAF WILD-TYPE 85 35    31
D15V5, multiclass
       clus
vv      BRAF MUTATED BRAF WILD-TYPE
  N0              10             85
  N1               2             35
  N2+N3            4             31
[1] 3 2
[1] 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
  BRAF MUTATED    15   1   0
  BRAF WILD-TYPE 128   8  18
D15V6, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  M0           15            128
  M1            1              8
  MX            0             18
[1] 3 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
  BRAF MUTATED    7  9
  BRAF WILD-TYPE 86 70
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      7    9
  BRAF WILD-TYPE   86   70
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE            7             86
  MALE              9             70
[1] 2 2
[1] FALSE
D15V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  BRAF MUTATED                            0                                 4
  BRAF WILD-TYPE                          2                                35
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  BRAF MUTATED                                                   12
  BRAF WILD-TYPE                                                103
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  BRAF MUTATED                                            0
  BRAF WILD-TYPE                                          1
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  BRAF MUTATED                                               0
  BRAF WILD-TYPE                                             2
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  BRAF MUTATED                                0
  BRAF WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  BRAF MUTATED                                    0
  BRAF WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  BRAF MUTATED                              0                             0
  BRAF WILD-TYPE                            2                             4
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  BRAF MUTATED                                               0
  BRAF WILD-TYPE                                             1
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  BRAF MUTATED                              0
  BRAF WILD-TYPE                            2
D15V9, multiclass
                                                    clus
vv                                                   BRAF MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           12
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   BRAF WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              35
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            103
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   2
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                   4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    2
[1] 11  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
  BRAF MUTATED     3  13
  BRAF WILD-TYPE  12 144
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      3   13
  BRAF WILD-TYPE   12  144
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO             3             12
  YES           13            144
[1] 2 2
[1] FALSE
D15V11, continuous
                vv
clus              R0  R1  R2  RX
  BRAF MUTATED     9   0   0   1
  BRAF WILD-TYPE 106   6   4   8
D15V12, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0            9            106
  R1            0              6
  R2            0              4
  RX            1              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             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRAF MUTATED                                  0     0
  BRAF WILD-TYPE                                1     3
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED                           1     9
  BRAF WILD-TYPE                         8   104
D15V13, multiclass
                                  clus
vv                                 BRAF MUTATED BRAF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              3
  BLACK OR AFRICAN AMERICAN                   1              8
  WHITE                                       9            104
[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"

Clustering(16) Variable = GEN1 MUTATION ANALYSIS
D16V1, survival
                sevent
clus2             0  1
  GEN1 MUTATED    3  1
  GEN1 WILD-TYPE 97 37
  GEN1 MUTATED GEN1 WILD-TYPE 
             4            134 
  GEN1 MUTATED GEN1 WILD-TYPE 
             1             37 
$`GEN1 MUTATED`
TCGA-05-4396 TCGA-05-4427 TCGA-50-5941 TCGA-73-4668 
        1947          791          567          467 

$`GEN1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 
        1523          607          426         1369         1126         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         578          610         1958         1997          455          912 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
         365          913          669          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         730          457          151          882          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          62           14          225          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
        1962         1147         1492          864         1073          354 
TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
        1357          448         1324         1429          400         1367 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
         741         1280         1301           97          246         1130 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
        1163         1036          190          722         1013          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
         723          328          302          845          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-49-4486 
         705         1938         1942         1864         1978         1932 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
        1081         1421          428          999          268          896 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         157         1700          445          369          890          522 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
        2174         2146          455          785          944         1499 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
         246          282          267         1091         2370          653 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 
         883          764          686         1015          701         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        1479         1375           87            2          993           24 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 
        1728          628         1189         1126         1959           62 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        1305          864         1559          866           31          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         573          427          385          174          141          422 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
          61         1600          711          912          800          131 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 
          40          164           38          323         1940          310 
TCGA-91-6835 TCGA-91-6836 
          79          417 

  GEN1 MUTATED GEN1 WILD-TYPE 
           467              2 
  GEN1 MUTATED GEN1 WILD-TYPE 
          1947           2370 
  GEN1 MUTATED GEN1 WILD-TYPE 
         679.0          735.5 
[1] "467.0 - 1947.0 (679.0)" "2.0 - 2370.0 (735.5)"  
[1] "hr=" "1.3"
D16V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  GEN1 MUTATED          0        0         0         2          1          1
  GEN1 WILD-TYPE       37       53        11        21         32          5
                vv
clus             STAGE IV
  GEN1 MUTATED          0
  GEN1 WILD-TYPE        9
D16V3, multiclass
            clus
vv           GEN1 MUTATED GEN1 WILD-TYPE
  STAGE IA              0             37
  STAGE IB              0             53
  STAGE IIA             0             11
  STAGE IIB             2             21
  STAGE IIIA            1             32
  STAGE IIIB            1              5
  STAGE IV              0              9
[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
  GEN1 MUTATED     0   3   0   1
  GEN1 WILD-TYPE  41 106  14   7
D16V4, multiclass
    clus
vv   GEN1 MUTATED GEN1 WILD-TYPE
  T1            0             41
  T2            3            106
  T3            0             14
  T4            1              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             N0 N1 N2+N3
  GEN1 MUTATED    0  3     1
  GEN1 WILD-TYPE 95 34    34
D16V5, multiclass
       clus
vv      GEN1 MUTATED GEN1 WILD-TYPE
  N0               0             95
  N1               3             34
  N2+N3            1             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  GEN1 MUTATED     4   0   0
  GEN1 WILD-TYPE 139   9  18
D16V6, multiclass
    clus
vv   GEN1 MUTATED GEN1 WILD-TYPE
  M0            4            139
  M1            0              9
  MX            0             18
[1] 3 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
  GEN1 MUTATED    3  1
  GEN1 WILD-TYPE 90 78
[1] "tbl2"
                cls
clus             [,1] [,2]
  GEN1 MUTATED      3    1
  GEN1 WILD-TYPE   90   78
        clus
vv       GEN1 MUTATED GEN1 WILD-TYPE
  FEMALE            3             90
  MALE              1             78
[1] 2 2
[1] FALSE
D16V8, continuous
[1] "Remove cluster labels:" "GEN1 MUTATED"          
clus
  GEN1 MUTATED GEN1 WILD-TYPE 
             1             11 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-64-1677 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-64-5778     TCGA-71-6725     TCGA-73-4659     TCGA-73-4662 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-73-4666     TCGA-73-4676     TCGA-75-5122 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GEN1 MUTATED                            0                                 2
  GEN1 WILD-TYPE                          2                                37
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GEN1 MUTATED                                                    1
  GEN1 WILD-TYPE                                                114
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GEN1 MUTATED                                            0
  GEN1 WILD-TYPE                                          1
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GEN1 MUTATED                                               0
  GEN1 WILD-TYPE                                             2
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  GEN1 MUTATED                                0
  GEN1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  GEN1 MUTATED                                    1
  GEN1 WILD-TYPE                                  1
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GEN1 MUTATED                              0                             0
  GEN1 WILD-TYPE                            2                             4
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GEN1 MUTATED                                               0
  GEN1 WILD-TYPE                                             1
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  GEN1 MUTATED                              0
  GEN1 WILD-TYPE                            2
D16V9, multiclass
                                                    clus
vv                                                   GEN1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            1
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   GEN1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            114
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   2
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              1
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                   4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    2
[1] 11  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
  GEN1 MUTATED     0   4
  GEN1 WILD-TYPE  15 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  GEN1 MUTATED      0    4
  GEN1 WILD-TYPE   15  153
     clus
vv    GEN1 MUTATED GEN1 WILD-TYPE
  NO             0             15
  YES            4            153
[1] 2 2
[1] FALSE
D16V11, continuous
                vv
clus              R0  R1  R2  RX
  GEN1 MUTATED     3   0   0   0
  GEN1 WILD-TYPE 112   6   4   9
D16V12, multiclass
    clus
vv   GEN1 MUTATED GEN1 WILD-TYPE
  R0            3            112
  R1            0              6
  R2            0              4
  RX            0              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             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GEN1 MUTATED                                  1     0
  GEN1 WILD-TYPE                                0     3
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GEN1 MUTATED                           0     1
  GEN1 WILD-TYPE                         9   112
D16V13, multiclass
[1] "Remove cluster labels:" "GEN1 MUTATED"          
clus
  GEN1 MUTATED GEN1 WILD-TYPE 
             2            124 
    TCGA-35-3615     TCGA-35-4122     TCGA-35-4123     TCGA-35-5375 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-38-4625     TCGA-38-4626     TCGA-38-4627     TCGA-38-4628 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-38-4629     TCGA-38-4630     TCGA-38-4631     TCGA-38-4632 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-38-6178     TCGA-44-2655     TCGA-44-2656     TCGA-44-2657 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-44-2659     TCGA-44-2661     TCGA-44-2662     TCGA-44-2665 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-44-2666     TCGA-44-2668     TCGA-44-3396     TCGA-44-3398 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-44-3918     TCGA-44-3919     TCGA-44-4112     TCGA-44-5643 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-44-5645     TCGA-44-6144     TCGA-44-6145     TCGA-44-6146 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-44-6147     TCGA-44-6148     TCGA-44-6774     TCGA-44-6775 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-44-6776     TCGA-44-6777     TCGA-44-6778     TCGA-44-6779 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-49-4486     TCGA-49-4487     TCGA-49-4488     TCGA-49-4490 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-49-4494     TCGA-49-4501     TCGA-49-4505     TCGA-49-4506 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-49-4507     TCGA-49-4510     TCGA-49-4512     TCGA-49-4514 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-49-6742     TCGA-49-6743     TCGA-49-6744     TCGA-49-6745 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-49-6767     TCGA-50-5044     TCGA-50-5045     TCGA-50-5049 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-50-5051     TCGA-50-5055     TCGA-50-5066     TCGA-50-5068 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-50-5072     TCGA-50-5930     TCGA-50-5931     TCGA-50-5932 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-50-5933     TCGA-50-5935     TCGA-50-5936     TCGA-50-5939 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-50-5942     TCGA-50-5944     TCGA-50-5946     TCGA-50-6590 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-50-6591     TCGA-50-6592     TCGA-50-6593     TCGA-50-6594 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-50-6595     TCGA-50-6597     TCGA-55-1592     TCGA-55-1594 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-55-1595     TCGA-55-1596     TCGA-55-5899     TCGA-55-6543 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-55-6642     TCGA-55-6712     TCGA-64-1676     TCGA-64-1677 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-64-1678     TCGA-64-1680     TCGA-64-5774     TCGA-64-5775 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-64-5778     TCGA-64-5779     TCGA-64-5781     TCGA-64-5815 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-67-3770     TCGA-67-3771     TCGA-67-3772     TCGA-67-3773 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-67-3774     TCGA-67-4679     TCGA-67-6215     TCGA-67-6216 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-67-6217     TCGA-71-6725     TCGA-73-4658     TCGA-73-4659 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4670     TCGA-73-4675 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-73-4676     TCGA-73-4677     TCGA-86-6562     TCGA-91-6828 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 
    TCGA-91-6829     TCGA-91-6831     TCGA-91-6835     TCGA-91-6836 
"GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" "GEN1 WILD-TYPE" 

Clustering(17) Variable = STX2 MUTATION ANALYSIS
D17V1, survival
                sevent
clus2             0  1
  STX2 MUTATED    3  1
  STX2 WILD-TYPE 97 37
  STX2 MUTATED STX2 WILD-TYPE 
             4            134 
  STX2 MUTATED STX2 WILD-TYPE 
             1             37 
$`STX2 MUTATED`
TCGA-05-4396 TCGA-35-4123 TCGA-44-6774 TCGA-50-5066 
        1947          182          658          944 

$`STX2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 
        1523          607          426         1369         1126         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         578          610         1958         1997          455          912 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         365          913          669          791          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
         761          730          457          151          882          670 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 
          30           62           14          225          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
        1962         1147         1492          864         1073          354 
TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
        1357          448         1324         1429          400         1367 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
         741         1280         1301           97          246         1130 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
        1163         1036          190          722         1013          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 
         723          328          302          845          704          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-49-4486 TCGA-49-4494 
        1938         1942         1864         1978         1932         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
        1421          428          999          268          896          157 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 
        1700          445          369          890          522         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
        2146          455          785         1499          246          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         267         1091         2370          653          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
         764          686         1015          701         1178         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-64-1676 
        1375           87            2          993           24         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
         628         1189         1126         1959           62         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
         864         1559          866           31          610          573 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-71-6725 
         427          385          174          141          422           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        1600          711          912          800          467          131 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 
          40          164           38          323         1940          310 
TCGA-91-6835 TCGA-91-6836 
          79          417 

  STX2 MUTATED STX2 WILD-TYPE 
           182              2 
  STX2 MUTATED STX2 WILD-TYPE 
          1947           2370 
  STX2 MUTATED STX2 WILD-TYPE 
         801.0          735.5 
[1] "182.0 - 1947.0 (801.0)" "2.0 - 2370.0 (735.5)"  
[1] "hr=" "1.3"
D17V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  STX2 MUTATED          1        1         0         0          1          1
  STX2 WILD-TYPE       36       52        11        23         32          5
                vv
clus             STAGE IV
  STX2 MUTATED          0
  STX2 WILD-TYPE        9
D17V3, multiclass
            clus
vv           STX2 MUTATED STX2 WILD-TYPE
  STAGE IA              1             36
  STAGE IB              1             52
  STAGE IIA             0             11
  STAGE IIB             0             23
  STAGE IIIA            1             32
  STAGE IIIB            1              5
  STAGE IV              0              9
[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
  STX2 MUTATED     2   1   0   1
  STX2 WILD-TYPE  39 108  14   7
D17V4, multiclass
    clus
vv   STX2 MUTATED STX2 WILD-TYPE
  T1            2             39
  T2            1            108
  T3            0             14
  T4            1              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             N0 N1 N2+N3
  STX2 MUTATED    2  1     1
  STX2 WILD-TYPE 93 36    34
D17V5, multiclass
       clus
vv      STX2 MUTATED STX2 WILD-TYPE
  N0               2             93
  N1               1             36
  N2+N3            1             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  STX2 MUTATED     4   0   0
  STX2 WILD-TYPE 139   9  18
D17V6, multiclass
    clus
vv   STX2 MUTATED STX2 WILD-TYPE
  M0            4            139
  M1            0              9
  MX            0             18
[1] 3 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
  STX2 MUTATED    1  3
  STX2 WILD-TYPE 92 76
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX2 MUTATED      1    3
  STX2 WILD-TYPE   92   76
        clus
vv       STX2 MUTATED STX2 WILD-TYPE
  FEMALE            1             92
  MALE              3             76
[1] 2 2
[1] FALSE
D17V8, continuous
[1] "Remove cluster labels:" "STX2 MUTATED"          
clus
  STX2 MUTATED STX2 WILD-TYPE 
             1             11 
    TCGA-35-4122     TCGA-35-5375     TCGA-64-1677     TCGA-64-5778 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-71-6725     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4676     TCGA-75-5122 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  STX2 MUTATED                            0                                 2
  STX2 WILD-TYPE                          2                                37
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  STX2 MUTATED                                                    2
  STX2 WILD-TYPE                                                113
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  STX2 MUTATED                                            0
  STX2 WILD-TYPE                                          1
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  STX2 MUTATED                                               0
  STX2 WILD-TYPE                                             2
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  STX2 MUTATED                                0
  STX2 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  STX2 MUTATED                                    0
  STX2 WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  STX2 MUTATED                              0                             0
  STX2 WILD-TYPE                            2                             4
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  STX2 MUTATED                                               0
  STX2 WILD-TYPE                                             1
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  STX2 MUTATED                              0
  STX2 WILD-TYPE                            2
D17V9, multiclass
                                                    clus
vv                                                   STX2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   STX2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            113
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   2
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                   4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    2
[1] 11  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
  STX2 MUTATED     1   3
  STX2 WILD-TYPE  14 154
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX2 MUTATED      1    3
  STX2 WILD-TYPE   14  154
     clus
vv    STX2 MUTATED STX2 WILD-TYPE
  NO             1             14
  YES            3            154
[1] 2 2
[1] FALSE
D17V11, continuous
                vv
clus              R0  R1  R2  RX
  STX2 MUTATED     3   0   0   0
  STX2 WILD-TYPE 112   6   4   9
D17V12, multiclass
    clus
vv   STX2 MUTATED STX2 WILD-TYPE
  R0            3            112
  R1            0              6
  R2            0              4
  RX            0              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             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STX2 MUTATED                                  0     0
  STX2 WILD-TYPE                                1     3
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  STX2 MUTATED                           1     2
  STX2 WILD-TYPE                         8   111
D17V13, multiclass
                                  clus
vv                                 STX2 MUTATED STX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              3
  BLACK OR AFRICAN AMERICAN                   1              8
  WHITE                                       2            111
[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"

Clustering(18) Variable = MGA MUTATION ANALYSIS
D18V1, survival
               sevent
clus2            0  1
  MGA MUTATED    9  5
  MGA WILD-TYPE 91 33
  MGA MUTATED MGA WILD-TYPE 
           14           124 
  MGA MUTATED MGA WILD-TYPE 
            5            33 
$`MGA MUTATED`
TCGA-05-4396 TCGA-05-4405 TCGA-05-5428 TCGA-05-5715 TCGA-35-5375 TCGA-38-4628 
        1947          610          670           62          264         1492 
TCGA-49-4494 TCGA-49-6743 TCGA-49-6745 TCGA-50-5931 TCGA-55-6712 TCGA-64-5779 
        1081          369          522          267           24          864 
TCGA-73-4668 TCGA-91-6829 
         467         1940 

$`MGA WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 
        1523          607          426         1369         1126         1431 
TCGA-05-4403 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
         578         1958         1997          455          912          365 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         913          669          791          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-35-3615 
         730          457          151          882           30           14 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 
         225          182         1952         1962         1147          864 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 TCGA-44-2656 
        1073          354         1357          448         1324         1429 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
         400         1367          741         1280         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
        1013          383          723          328          302          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
         704          658          705         1938         1942         1864 
TCGA-44-6779 TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
        1978         1932         1421          428          999          268 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-50-5045 
         896          157         1700          445          890         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        2146          455          785          944         1499          246 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         282         1091         2370          653          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
         764          686         1015          701         1178         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-64-1676 TCGA-64-1677 
        1375           87            2          993         1728          628 
TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 
        1189         1126         1959           62         1305         1559 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
         866           31          610          573          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
         174          141          422           61         1600          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
         912          800          131           40          164           38 
TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
         323          310           79          417 

  MGA MUTATED MGA WILD-TYPE 
           24             2 
  MGA MUTATED MGA WILD-TYPE 
         1947          2370 
  MGA MUTATED MGA WILD-TYPE 
          566           761 
[1] "24.0 - 1947.0 (566.0)" "2.0 - 2370.0 (761.0)" 
[1] "hr=" "1.6"
D18V2, continuous
               vv
clus            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  MGA MUTATED          0        4         2         2          6          1
  MGA WILD-TYPE       37       49         9        21         27          5
               vv
clus            STAGE IV
  MGA MUTATED          0
  MGA WILD-TYPE        9
D18V3, multiclass
            clus
vv           MGA MUTATED MGA WILD-TYPE
  STAGE IA             0            37
  STAGE IB             4            49
  STAGE IIA            2             9
  STAGE IIB            2            21
  STAGE IIIA           6            27
  STAGE IIIB           1             5
  STAGE IV             0             9
[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
  MGA MUTATED    2 10  2  1
  MGA WILD-TYPE 39 99 12  7
D18V4, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  T1           2            39
  T2          10            99
  T3           2            12
  T4           1             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            N0 N1 N2+N3
  MGA MUTATED    4  5     6
  MGA WILD-TYPE 91 32    29
D18V5, multiclass
       clus
vv      MGA MUTATED MGA WILD-TYPE
  N0              4            91
  N1              5            32
  N2+N3           6            29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1  MX
  MGA MUTATED    12   0   3
  MGA WILD-TYPE 131   9  15
D18V6, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  M0          12           131
  M1           0             9
  MX           3            15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
               cls
clus             0  1
  MGA MUTATED    6  9
  MGA WILD-TYPE 87 70
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED      6    9
  MGA WILD-TYPE   87   70
        clus
vv       MGA MUTATED MGA WILD-TYPE
  FEMALE           6            87
  MALE             9            70
[1] 2 2
[1] FALSE
D18V8, continuous
[1] "Remove cluster labels:" "MGA MUTATED"           
clus
  MGA MUTATED MGA WILD-TYPE 
            2            10 
   TCGA-35-4122    TCGA-35-4123    TCGA-64-1677    TCGA-64-5778    TCGA-71-6725 
"MGA WILD-TYPE" "MGA WILD-TYPE" "MGA WILD-TYPE" "MGA WILD-TYPE" "MGA WILD-TYPE" 
   TCGA-73-4659    TCGA-73-4662    TCGA-73-4666    TCGA-73-4676    TCGA-75-5122 
"MGA WILD-TYPE" "MGA WILD-TYPE" "MGA WILD-TYPE" "MGA WILD-TYPE" "MGA WILD-TYPE" 
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MGA MUTATED                            1                                 5
  MGA WILD-TYPE                          1                                34
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MGA MUTATED                                                    6
  MGA WILD-TYPE                                                109
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MGA MUTATED                                            0
  MGA WILD-TYPE                                          1
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MGA MUTATED                                               1
  MGA WILD-TYPE                                             1
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  MGA MUTATED                                1
  MGA WILD-TYPE                              1
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  MGA MUTATED                                    1                            0
  MGA WILD-TYPE                                  1                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  MGA MUTATED                               0
  MGA WILD-TYPE                             4
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MGA MUTATED                                               0
  MGA WILD-TYPE                                             1
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  MGA MUTATED                              0
  MGA WILD-TYPE                            2
D18V9, multiclass
                                                    clus
vv                                                   MGA MUTATED MGA WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   1             1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            5            34
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           6           109
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                1             1
  LUNG CLEAR CELL ADENOCARCINOMA                               1             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                           1             1
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0             4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             1
  MUCINOUS (COLLOID) CARCINOMA                                 0             2
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, binary
               cls
clus              0   1
  MGA MUTATED     1  14
  MGA WILD-TYPE  14 143
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED      1   14
  MGA WILD-TYPE   14  143
     clus
vv    MGA MUTATED MGA WILD-TYPE
  NO            1            14
  YES          14           143
[1] 2 2
[1] FALSE
D18V11, continuous
               vv
clus             R0  R1  R2  RX
  MGA MUTATED    12   0   0   0
  MGA WILD-TYPE 103   6   4   9
D18V12, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  R0          12           103
  R1           0             6
  R2           0             4
  RX           0             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            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MGA MUTATED                                  1     0
  MGA WILD-TYPE                                0     3
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MGA MUTATED                           0     9
  MGA WILD-TYPE                         9   104
D18V13, multiclass
                                  clus
vv                                 MGA MUTATED MGA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      0             3
  BLACK OR AFRICAN AMERICAN                  0             9
  WHITE                                      9           104
[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"

Clustering(19) Variable = GALC MUTATION ANALYSIS
D19V1, survival
                sevent
clus2             0  1
  GALC MUTATED    4  0
  GALC WILD-TYPE 96 38
  GALC MUTATED GALC WILD-TYPE 
             4            134 
  GALC MUTATED GALC WILD-TYPE 
             0             38 
$`GALC MUTATED`
TCGA-05-4427 TCGA-44-2656 TCGA-55-5899 TCGA-55-6642 
         791         1429           87          993 

$`GALC WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1431          578          610         1958         1997          455 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
         912          365          913          669          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
         761          730          457          151          882          670 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
          30           62           14          225          182          264 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
        1952         1962         1147         1492          864         1073 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 
         354         1357          448         1324          400         1367 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
         741         1280         1301           97          246         1130 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
        1163         1036          190          722         1013          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
         723          328          302          845          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-49-4486 
         705         1938         1942         1864         1978         1932 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
        1081         1421          428          999          268          896 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         157         1700          445          369          890          522 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
        2174         2146          455          785          944         1499 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
         246          282          267         1091         2370          653 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 
         567          883          764          686         1015          701 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-64-1676 
        1178         1479         1375            2           24         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
         628         1189         1126         1959           62         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
         864         1559          866           31          610          573 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-71-6725 
         427          385          174          141          422           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        1600          711          912          800          467          131 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 
          40          164           38          323         1940          310 
TCGA-91-6835 TCGA-91-6836 
          79          417 

  GALC MUTATED GALC WILD-TYPE 
            87              2 
  GALC MUTATED GALC WILD-TYPE 
          1429           2370 
  GALC MUTATED GALC WILD-TYPE 
         892.0          726.5 
[1] "87.0 - 1429.0 (892.0)" "2.0 - 2370.0 (726.5)" 
[1] "hr="     "2.5e+07"
D19V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  GALC MUTATED          1        2         0         2          0          0
  GALC WILD-TYPE       36       51        11        21         33          6
                vv
clus             STAGE IV
  GALC MUTATED          0
  GALC WILD-TYPE        9
D19V3, multiclass
            clus
vv           GALC MUTATED GALC WILD-TYPE
  STAGE IA              1             36
  STAGE IB              2             51
  STAGE IIA             0             11
  STAGE IIB             2             21
  STAGE IIIA            0             33
  STAGE IIIB            0              6
  STAGE IV              0              9
[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
  GALC MUTATED     1   3   1   0
  GALC WILD-TYPE  40 106  13   8
D19V4, multiclass
    clus
vv   GALC MUTATED GALC WILD-TYPE
  T1            1             40
  T2            3            106
  T3            1             13
  T4            0              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             N0 N1 N2+N3
  GALC MUTATED    3  2     0
  GALC WILD-TYPE 92 35    35
D19V5, multiclass
       clus
vv      GALC MUTATED GALC WILD-TYPE
  N0               3             92
  N1               2             35
  N2+N3            0             35
[1] 3 2
[1] 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
  GALC MUTATED     3   0   2
  GALC WILD-TYPE 140   9  16
D19V6, multiclass
    clus
vv   GALC MUTATED GALC WILD-TYPE
  M0            3            140
  M1            0              9
  MX            2             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                cls
clus              0  1
  GALC MUTATED    2  3
  GALC WILD-TYPE 91 76
[1] "tbl2"
                cls
clus             [,1] [,2]
  GALC MUTATED      2    3
  GALC WILD-TYPE   91   76
        clus
vv       GALC MUTATED GALC WILD-TYPE
  FEMALE            2             91
  MALE              3             76
[1] 2 2
[1] FALSE
D19V8, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GALC MUTATED                            0                                 1
  GALC WILD-TYPE                          2                                38
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GALC MUTATED                                                    4
  GALC WILD-TYPE                                                111
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GALC MUTATED                                            0
  GALC WILD-TYPE                                          1
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GALC MUTATED                                               0
  GALC WILD-TYPE                                             2
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  GALC MUTATED                                0
  GALC WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  GALC MUTATED                                    0
  GALC WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GALC MUTATED                              0                             0
  GALC WILD-TYPE                            2                             4
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GALC MUTATED                                               0
  GALC WILD-TYPE                                             1
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  GALC MUTATED                              0
  GALC WILD-TYPE                            2
D19V9, multiclass
                                                    clus
vv                                                   GALC MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   GALC WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            111
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   2
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                   4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    2
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, binary
                cls
clus               0   1
  GALC MUTATED     0   5
  GALC WILD-TYPE  15 152
[1] "tbl2"
                cls
clus             [,1] [,2]
  GALC MUTATED      0    5
  GALC WILD-TYPE   15  152
     clus
vv    GALC MUTATED GALC WILD-TYPE
  NO             0             15
  YES            5            152
[1] 2 2
[1] FALSE
D19V11, continuous
                vv
clus              R0  R1  R2  RX
  GALC MUTATED     4   0   0   0
  GALC WILD-TYPE 111   6   4   9
D19V12, multiclass
    clus
vv   GALC MUTATED GALC WILD-TYPE
  R0            4            111
  R1            0              6
  R2            0              4
  RX            0              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             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GALC MUTATED                                  0     0
  GALC WILD-TYPE                                1     3
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GALC MUTATED                           0     4
  GALC WILD-TYPE                         9   109
D19V13, multiclass
                                  clus
vv                                 GALC MUTATED GALC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              3
  BLACK OR AFRICAN AMERICAN                   0              9
  WHITE                                       4            109
[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"

Clustering(20) Variable = CTNNB1 MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2               0  1
  CTNNB1 MUTATED    5  3
  CTNNB1 WILD-TYPE 95 35
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               8              130 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               3               35 
$`CTNNB1 MUTATED`
TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4422 TCGA-05-4425 TCGA-44-4112 
         426         1369         1947          365          669          722 
TCGA-44-6779 TCGA-67-3771 
        1978          610 

$`CTNNB1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4390 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        1523          607         1126         1431          578          610 
TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4426 
        1958         1997          455          912          913          791 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 
         791          761          761          730          457          151 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         882          670           30           62           14          225 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         182          264         1952         1962         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 
         864         1073          354         1357          448         1324 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        1429          400         1367          741         1280         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
          97          246         1130         1163         1036          190 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
        1013          383          723          328          302          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
         704          658          705         1938         1942         1864 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
        1932         1081         1421          428          999          268 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
         896          157         1700          445          369          890 
TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         522         2174         2146          455          785          944 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
        1499          246          282          267         1091         2370 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 
         653          567          883          764          686         1015 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
         701         1178         1479         1375           87            2 
TCGA-55-6642 TCGA-55-6712 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 
         993           24         1728          628         1189         1126 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1959           62         1305          864         1559          866 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
          31          573          427          385          174          141 
TCGA-67-6217 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         422           61         1600          711          912          800 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-91-6828 
         467          131           40          164           38          323 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
        1940          310           79          417 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
             365                2 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            1978             2370 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           695.5            751.0 
[1] "365.0 - 1978.0 (695.5)" "2.0 - 2370.0 (751.0)"  
[1] "hr=" "1"  
D20V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  CTNNB1 MUTATED          2        3         0         1          1          1
  CTNNB1 WILD-TYPE       35       50        11        22         32          5
                  vv
clus               STAGE IV
  CTNNB1 MUTATED          1
  CTNNB1 WILD-TYPE        8
D20V3, multiclass
            clus
vv           CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE IA                2               35
  STAGE IB                3               50
  STAGE IIA               0               11
  STAGE IIB               1               22
  STAGE IIIA              1               32
  STAGE IIIB              1                5
  STAGE IV                1                8
[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
  CTNNB1 MUTATED     2   5   1   1
  CTNNB1 WILD-TYPE  39 104  13   7
D20V4, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T1              2               39
  T2              5              104
  T3              1               13
  T4              1                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               N0 N1 N2+N3
  CTNNB1 MUTATED    6  2     1
  CTNNB1 WILD-TYPE 89 35    34
D20V5, multiclass
       clus
vv      CTNNB1 MUTATED CTNNB1 WILD-TYPE
  N0                 6               89
  N1                 2               35
  N2+N3              1               34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1  MX
  CTNNB1 MUTATED     7   1   1
  CTNNB1 WILD-TYPE 136   8  17
D20V6, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  M0              7              136
  M1              1                8
  MX              1               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    4  5
  CTNNB1 WILD-TYPE 89 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      4    5
  CTNNB1 WILD-TYPE   89   74
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE              4               89
  MALE                5               74
[1] 2 2
[1] FALSE
D20V8, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CTNNB1 MUTATED                            0                                 5
  CTNNB1 WILD-TYPE                          2                                34
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CTNNB1 MUTATED                                                    4
  CTNNB1 WILD-TYPE                                                111
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CTNNB1 MUTATED                                            0
  CTNNB1 WILD-TYPE                                          1
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CTNNB1 MUTATED                                               0
  CTNNB1 WILD-TYPE                                             2
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  CTNNB1 MUTATED                                0
  CTNNB1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  CTNNB1 MUTATED                                    0
  CTNNB1 WILD-TYPE                                  2
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CTNNB1 MUTATED                              0                             0
  CTNNB1 WILD-TYPE                            2                             4
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CTNNB1 MUTATED                                               0
  CTNNB1 WILD-TYPE                                             1
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  CTNNB1 MUTATED                              0
  CTNNB1 WILD-TYPE                            2
D20V9, multiclass
                                                    clus
vv                                                   CTNNB1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   CTNNB1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                34
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              111
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     2
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                     4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      2
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     0   9
  CTNNB1 WILD-TYPE  15 148
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      0    9
  CTNNB1 WILD-TYPE   15  148
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO               0               15
  YES              9              148
[1] 2 2
[1] FALSE
D20V11, continuous
                  vv
clus                R0  R1  R2  RX
  CTNNB1 MUTATED     6   1   0   1
  CTNNB1 WILD-TYPE 109   5   4   8
D20V12, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0              6              109
  R1              1                5
  R2              0                4
  RX              1                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               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTNNB1 MUTATED                                  0     0
  CTNNB1 WILD-TYPE                                1     3
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CTNNB1 MUTATED                           1     3
  CTNNB1 WILD-TYPE                         8   110
D20V13, multiclass
                                  clus
vv                                 CTNNB1 MUTATED CTNNB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                3
  BLACK OR AFRICAN AMERICAN                     1                8
  WHITE                                         3              110
[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"
