[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"        "-oTSTAD-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/STAD-TP/10006301/STAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STAD-TP/10687007/transformed.cor.cli.txt"

nPatients in clinical file=351, in cluster file=221, common to both=221
[1] "Reduce the number of clustering variables from 28 to 27."
[1]  27 221
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            99            122 
  TP53 MUTATED TP53 WILD-TYPE 
            99            122 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              48              173 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              48              173 
[1] "CBWD1 MUTATION ANALYSIS"
[1] 3
  CBWD1 MUTATED CBWD1 WILD-TYPE 
             28             193 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
             28             193 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            25            196 
  KRAS MUTATED KRAS WILD-TYPE 
            25            196 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              41              180 
  ARID1A MUTATED ARID1A WILD-TYPE 
              41              180 
[1] "PGM5 MUTATION ANALYSIS"
[1] 3
  PGM5 MUTATED PGM5 WILD-TYPE 
            22            199 
  PGM5 MUTATED PGM5 WILD-TYPE 
            22            199 
[1] "RHOA MUTATION ANALYSIS"
[1] 3
  RHOA MUTATED RHOA WILD-TYPE 
            13            208 
  RHOA MUTATED RHOA WILD-TYPE 
            13            208 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             19             202 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             19             202 
[1] "IRF2 MUTATION ANALYSIS"
[1] 3
  IRF2 MUTATED IRF2 WILD-TYPE 
            14            207 
  IRF2 MUTATED IRF2 WILD-TYPE 
            14            207 
[1] "LARP4B MUTATION ANALYSIS"
[1] 3
  LARP4B MUTATED LARP4B WILD-TYPE 
              12              209 
  LARP4B MUTATED LARP4B WILD-TYPE 
              12              209 
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
           33           188 
  APC MUTATED APC WILD-TYPE 
           33           188 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             19             202 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             19             202 
[1] "CDH1 MUTATION ANALYSIS"
[1] 3
  CDH1 MUTATED CDH1 WILD-TYPE 
            18            203 
  CDH1 MUTATED CDH1 WILD-TYPE 
            18            203 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
             12             209 
  HLA-B MUTATED HLA-B WILD-TYPE 
             12             209 
[1] "BCOR MUTATION ANALYSIS"
[1] 3
  BCOR MUTATED BCOR WILD-TYPE 
            16            205 
  BCOR MUTATED BCOR WILD-TYPE 
            16            205 
[1] "C13ORF33 MUTATION ANALYSIS"
[1] 3
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
                 6                215 
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
                 6                215 
[1] "CIC MUTATION ANALYSIS"
[1] 3
  CIC MUTATED CIC WILD-TYPE 
           14           207 
  CIC MUTATED CIC WILD-TYPE 
           14           207 
[1] "ACVR1B MUTATION ANALYSIS"
[1] 3
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              10              211 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              10              211 
[1] "ZBTB20 MUTATION ANALYSIS"
[1] 3
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              16              205 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              16              205 
[1] "MVK MUTATION ANALYSIS"
[1] 3
  MVK MUTATED MVK WILD-TYPE 
            8           213 
  MVK MUTATED MVK WILD-TYPE 
            8           213 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             11             210 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             11             210 
[1] "CR1 MUTATION ANALYSIS"
[1] 3
  CR1 MUTATED CR1 WILD-TYPE 
           20           201 
  CR1 MUTATED CR1 WILD-TYPE 
           20           201 
[1] "C1R MUTATION ANALYSIS"
[1] 3
  C1R MUTATED C1R WILD-TYPE 
            3           218 
  C1R MUTATED C1R WILD-TYPE 
            3           218 
[1] "CTNND1 MUTATION ANALYSIS"
[1] 3
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              13              208 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              13              208 
[1] "MLXIPL MUTATION ANALYSIS"
[1] 3
  MLXIPL MUTATED MLXIPL WILD-TYPE 
              13              208 
  MLXIPL MUTATED MLXIPL WILD-TYPE 
              13              208 
[1] "MLL4 MUTATION ANALYSIS"
[1] 3
  MLL4 MUTATED MLL4 WILD-TYPE 
            20            201 
  MLL4 MUTATED MLL4 WILD-TYPE 
            20            201 
[1] "NLK MUTATION ANALYSIS"
[1] 3
  NLK MUTATED NLK WILD-TYPE 
            5           216 
  NLK MUTATED NLK WILD-TYPE 
            5           216 
[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] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 221 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
         171          356           NA           NA           NA           NA 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-4292 TCGA-BR-4294 TCGA-BR-4357 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4361 TCGA-BR-4362 TCGA-BR-4363 TCGA-BR-4366 TCGA-BR-4368 TCGA-BR-4369 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4370 TCGA-BR-4371 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6454 TCGA-BR-6455 
          NA           NA         1055          485           NA          399 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
         308          416          213         1190           25           19 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
         997          421          402          491          273          642 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
         940          949         1002          390          280          753 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
         728          469          852           21            5          564 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 
         378           29           21           25           21           15 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 
         625           22           47           45          188          593 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
          90           29          418          131          101           11 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
         583          450            8          482          113           22 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
         280          615          389          481           65          409 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8679 TCGA-BR-8680 TCGA-BR-8682 
         229           15          351           NA          481          500 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
          18           19          325          411          392           24 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI 
          NA           16           20          589          411          415 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
         352           86           99          400          401            9 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
           2           NA           12            2            2            2 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 
           3            4            5            3            3           NA 
TCGA-CD-8535 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
           4            3            3           NA           92          822 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
         485           NA          243          245         1645           NA 
TCGA-CG-4441 TCGA-CG-4442 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
          NA           NA          912         1431          580          366 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4475 
          NA           NA          577           NA           NA          699 
TCGA-CG-4476 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
          NA          942           NA           31           31           NA 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
         183           30         3196           NA           NA         2405 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
        1980          122         1674           NA           NA          376 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
         385          363          582          625          573          564 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
         566          543          406          523          312          463 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
         486          389          321          344          375          752 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU 
         511          593          523          212          434          500 
TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
         180          449           19          200          440           NA 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
          12          594           92          678          519           NA 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7136 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
          NA           NA           NA           NA           NA          383 
TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP 
         368           23          739          692          912          273 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
          NA          190          589          538          374          294 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
         645           NA          572           NA           77 
Variable 1:'AGE':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=134,	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=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=7,	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=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=12,	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] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "RACE"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 221 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=49, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 7 66 90 49 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 7 66 90 49 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 7 66 90 49 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 7 66 90 49 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
70 63 35 41 
[1] "table(vv)"
vv
N0 N1 N2 N3 
70 63 35 41 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 N3 
70 63 35 41 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
70 63 35 41 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=8, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=26, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   61 28
  TP53 WILD-TYPE 69 37
  TP53 MUTATED TP53 WILD-TYPE 
            89            106 
  TP53 MUTATED TP53 WILD-TYPE 
            28             37 
$`TP53 MUTATED`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       11.70         6.61         6.97        10.13        13.68         7.00 
TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
        0.62        31.20        32.94         9.21        24.76        15.42 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8295 
       28.01        18.54         0.95         0.69         0.49         1.55 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8590 
        1.48         6.18        19.50         0.72        20.22         2.14 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A4IY TCGA-BR-A4J8 
       11.54        16.44         0.59        10.68        12.89        13.51 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.64         3.25        13.15         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CG-4300 
        0.07         0.10         0.16         0.10         0.13        20.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4466 
        7.99        54.08         4.01        47.05        19.07        18.97 
TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 
        7.07         6.97         1.02         6.02       105.07        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 
       79.07         4.01        55.04        12.66        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.54        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-A4YU 
       12.79        10.55        11.31        12.33         6.97        16.44 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-HJ-7597 
       14.47        72.23         0.39        19.53        17.06        26.47 
TCGA-HU-8243 TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
        5.92        22.75        29.98         8.98         0.10         6.25 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       19.36        17.69        21.21         3.45         2.53 

$`TP53 WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        5.62         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6563 
        9.57         6.61        34.68        15.95        13.12        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        0.82        32.78        13.84        13.22        16.14         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       21.11        30.90        12.82        23.93         0.69         0.16 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8365 
       12.43         0.69         0.82        20.55         0.72         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        13.74         4.31         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8588 
       14.79         0.26        15.85         3.72         9.21        12.79 
TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8687 
       15.81        13.45         7.53         0.49        15.81         0.62 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
       13.51         0.79         0.72         0.53         0.66        19.36 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8529 
       11.57         2.83        13.18         0.30         0.07         0.13 
TCGA-CD-8532 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10         0.10         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4465 
        1.02         8.05        14.01        29.98        12.03         9.01 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
       22.98        30.97         1.02         0.99         0.99        12.03 
TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6519 
       65.10        21.07         7.99        12.36        11.93        20.55 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       18.61        17.85        24.72        16.80        19.50        17.19 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6177 TCGA-FP-7916 
       14.27         5.92        14.76         0.62         6.58         3.02 
TCGA-FP-7998 TCGA-FP-8209 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 
       22.29        59.54        12.59        12.10         0.76        24.30 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-8462 TCGA-IN-8663 
       12.30         9.67        18.81         3.39 

  TP53 MUTATED TP53 WILD-TYPE 
          0.07           0.07 
  TP53 MUTATED TP53 WILD-TYPE 
        105.07          65.10 
  TP53 MUTATED TP53 WILD-TYPE 
         11.70          12.03 
[1] "0.1 - 105.1 (11.7)" "0.1 - 65.1 (12.0)" 
[1] "hr=" "1.2"
D1V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TP53 MUTATED         0        4       10       13         9        15
  TP53 WILD-TYPE       1        2       13       10        12        16
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TP53 MUTATED           1         17         10          7        8
  TP53 WILD-TYPE         2         16         14         10       16
D1V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I               0              1
  STAGE IA              4              2
  STAGE IB             10             13
  STAGE II             13             10
  STAGE IIA             9             12
  STAGE IIB            15             16
  STAGE III             1              2
  STAGE IIIA           17             16
  STAGE IIIB           10             14
  STAGE IIIC            7             10
  STAGE IV              8             16
[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"
                vv
clus             T1 T2 T3 T4
  TP53 MUTATED    4 32 43 18
  TP53 WILD-TYPE  3 34 47 31
D1V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1            4              3
  T2           32             34
  T3           43             47
  T4           18             31
[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   33 31 16 15
  TP53 WILD-TYPE 37 32 19 26
D1V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           33             37
  N1           31             32
  N2           16             19
  N3           15             26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  TP53 MUTATED    89   3   7
  TP53 WILD-TYPE 106  13   3
D1V6, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  M0           89            106
  M1            3             13
  MX            7              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                cls
clus              0  1
  TP53 MUTATED   38 61
  TP53 WILD-TYPE 50 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     38   61
  TP53 WILD-TYPE   50   72
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           38             50
  MALE             61             72
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  TP53 MUTATED                                      14
  TP53 WILD-TYPE                                    18
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TP53 MUTATED                                                       40
  TP53 WILD-TYPE                                                     68
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  TP53 MUTATED                                                                  18
  TP53 WILD-TYPE                                                                16
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  TP53 MUTATED                                                 16
  TP53 WILD-TYPE                                               10
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  TP53 MUTATED                                                           1
  TP53 WILD-TYPE                                                         0
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  TP53 MUTATED                                                          7
  TP53 WILD-TYPE                                                        7
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  TP53 MUTATED                                                           2
  TP53 WILD-TYPE                                                         2
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  TP53 MUTATED                                          1
  TP53 WILD-TYPE                                        0
D1V8, multiclass
                                                                   clus
vv                                                                  TP53 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      40
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            16
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     1
                                                                   clus
vv                                                                  TP53 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         18
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        68
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              10
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
                cls
clus               0   1
  TP53 MUTATED     4  95
  TP53 WILD-TYPE   2 120
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4   95
  TP53 WILD-TYPE    2  120
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO             4              2
  YES           95            120
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2 RX
  TP53 MUTATED   83  2  2  9
  TP53 WILD-TYPE 88  5  8 15
D1V10, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           83             88
  R1            2              5
  R2            2              8
  RX            9             15
[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"
D1V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED      22                         2    58
  TP53 WILD-TYPE    22                         1    75
D1V12, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                               22             22
  BLACK OR AFRICAN AMERICAN            2              1
  WHITE                               58             75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = PIK3CA MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    29  12
  PIK3CA WILD-TYPE 101  53
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              41              154 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              12               53 
$`PIK3CA MUTATED`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6706 TCGA-BR-6707 
        5.62        11.70        34.68        13.12        13.22        16.14 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7851 TCGA-BR-8081 TCGA-BR-8284 
       30.90        32.94        12.82        12.43        20.55         0.72 
TCGA-BR-8366 TCGA-BR-8381 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 
        0.95         0.26        12.79        15.81        13.45         7.53 
TCGA-BR-8680 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-5720 
       15.81        13.15        13.18         0.10        15.95         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 
        6.02         0.99        65.10        21.07        12.36        12.66 
TCGA-D7-6815 TCGA-D7-A4YV TCGA-F1-6177 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       15.98         5.92         6.58         0.39         3.02        22.29 
TCGA-HU-A4G2 TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 
       24.30         0.10         6.25        19.36        17.69 

$`PIK3CA WILD-TYPE`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57         6.61        15.95        10.13        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
        7.00        39.12         0.82         0.62        32.78        13.84 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
        8.98        21.11        31.20         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       15.42        28.01         0.69         0.16        18.54         0.95 
TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8295 TCGA-BR-8296 
        0.69         0.82         0.69         0.49         1.55         1.48 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
        6.18        19.50         2.96        13.74         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
        0.36        19.17        14.79        15.85         3.72         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.21        20.22         2.14         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        0.59         0.62        10.68        13.51        12.89         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI 
        0.72         0.53         0.66        19.36        13.51        13.64 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
       11.57         2.83         3.25         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        0.10         0.10         0.13         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 
       14.01        29.98        47.05        19.07        12.03         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97         1.02 
TCGA-CG-5719 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        1.02       105.07        12.03        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       55.04         7.99        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU 
       16.80        19.50        17.19         6.97        14.27        16.44 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8099 
       14.76         0.62        14.47        72.23        19.53        17.06 
TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 
       59.54        26.47         5.92        12.59        12.10         0.76 
TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 
       22.75        29.98         8.98        12.30         9.67        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.10             0.07 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           65.10           105.07 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          12.820           10.995 
[1] "0.1 - 65.1 (12.8)"  "0.1 - 105.1 (11.0)"
[1] "hr=" "1.2"
D2V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIK3CA MUTATED         1        0        5        3         5        10
  PIK3CA WILD-TYPE       0        6       18       20        16        21
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3CA MUTATED           0          9          3          6        5
  PIK3CA WILD-TYPE         3         24         21         11       19
D2V3, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                 1                0
  STAGE IA                0                6
  STAGE IB                5               18
  STAGE II                3               20
  STAGE IIA               5               16
  STAGE IIB              10               21
  STAGE III               0                3
  STAGE IIIA              9               24
  STAGE IIIB              3               21
  STAGE IIIC              6               11
  STAGE IV                5               19
[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"
                  vv
clus               T1 T2 T3 T4
  PIK3CA MUTATED    1 12 20 15
  PIK3CA WILD-TYPE  6 54 70 34
D2V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              1                6
  T2             12               54
  T3             20               70
  T4             15               34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PIK3CA MUTATED   16 14  9  8
  PIK3CA WILD-TYPE 54 49 26 33
D2V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             16               54
  N1             14               49
  N2              9               26
  N3              8               33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1  MX
  PIK3CA MUTATED    40   4   4
  PIK3CA WILD-TYPE 155  12   6
D2V6, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  M0             40              155
  M1              4               12
  MX              4                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    20  28
  PIK3CA WILD-TYPE  68 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     20   28
  PIK3CA WILD-TYPE   68  105
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             20               68
  MALE               28              105
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PIK3CA MUTATED                                       8
  PIK3CA WILD-TYPE                                    24
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIK3CA MUTATED                                                       23
  PIK3CA WILD-TYPE                                                     85
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PIK3CA MUTATED                                                                   8
  PIK3CA WILD-TYPE                                                                26
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PIK3CA MUTATED                                                  7
  PIK3CA WILD-TYPE                                               19
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  PIK3CA MUTATED                                                           0
  PIK3CA WILD-TYPE                                                         1
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PIK3CA MUTATED                                                          1
  PIK3CA WILD-TYPE                                                       13
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PIK3CA MUTATED                                                           1
  PIK3CA WILD-TYPE                                                         3
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PIK3CA MUTATED                                          0
  PIK3CA WILD-TYPE                                        1
D2V8, multiclass
                                                                   clus
vv                                                                  PIK3CA MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               7
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  PIK3CA WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           24
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          85
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               26
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                19
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     1  47
  PIK3CA WILD-TYPE   5 168
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1   47
  PIK3CA WILD-TYPE    5  168
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO               1                5
  YES             47              168
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED    41   0   2   3
  PIK3CA WILD-TYPE 130   7   8  21
D2V10, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             41              130
  R1              0                7
  R2              2                8
  RX              3               21
[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"
D2V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED      10                         2    27
  PIK3CA WILD-TYPE    34                         1   106
D2V12, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                 10               34
  BLACK OR AFRICAN AMERICAN              2                1
  WHITE                                 27              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = CBWD1 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  CBWD1 MUTATED    18   5
  CBWD1 WILD-TYPE 112  60
  CBWD1 MUTATED CBWD1 WILD-TYPE 
             23             172 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
              5              60 
$`CBWD1 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7851 
        5.62        34.68        32.78        32.94        23.93        12.43 
TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-A4QL 
       19.50         4.31        19.17        15.85        13.45        11.57 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5733 
        0.10         0.10        15.95         1.02         6.02        21.07 
TCGA-D7-A4YV TCGA-F1-6874 TCGA-HJ-7597 TCGA-HU-A4GQ TCGA-HU-A4H4 
        5.92        14.47        26.47         0.10        17.69 

$`CBWD1 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57         6.61        15.95        13.12 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       10.13        13.68         7.00        39.12         0.82         0.62 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.84        13.22        16.14         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 
       31.20        12.82         9.21        24.76        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 
        0.69         0.16        18.54         0.95         0.69         0.82 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 
        0.69         0.49        20.55         0.72         1.55         1.48 
TCGA-BR-8360 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 TCGA-BR-8371 
        6.18         2.96         0.95        13.74         3.32         0.36 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       14.79         0.26         3.72         0.72         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       12.79        15.81         2.14         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4IV 
       15.81        16.44         0.59         0.62        10.68        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
       12.89         0.79         0.72         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.51        13.64         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       20.02         3.02        27.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       28.96        79.07        65.10         4.01        55.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT 
       24.72        16.80        19.50        17.19         6.97        14.27 
TCGA-D7-A4YU TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6875 TCGA-FP-7735 
       16.44        14.76         0.62         6.58        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HU-8243 
       19.53         3.02        22.29        17.06        59.54         5.92 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GN 
       12.59        12.10         0.76        24.30        22.75        29.98 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 
        8.98         6.25        19.36        12.30         9.67        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  CBWD1 MUTATED CBWD1 WILD-TYPE 
           0.10            0.07 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
          34.68          105.07 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
          14.47           11.62 
[1] "0.1 - 34.7 (14.5)"  "0.1 - 105.1 (11.6)"
[1] "hr=" "1.8"
D3V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CBWD1 MUTATED         0        0        5        2         3         3
  CBWD1 WILD-TYPE       1        6       18       21        18        28
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CBWD1 MUTATED           0          2          2          5        3
  CBWD1 WILD-TYPE         3         31         22         12       21
D3V3, multiclass
            clus
vv           CBWD1 MUTATED CBWD1 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               6
  STAGE IB               5              18
  STAGE II               2              21
  STAGE IIA              3              18
  STAGE IIB              3              28
  STAGE III              0               3
  STAGE IIIA             2              31
  STAGE IIIB             2              22
  STAGE IIIC             5              12
  STAGE IV               3              21
[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"
                 vv
clus              T1 T2 T3 T4
  CBWD1 MUTATED    1  9  7  9
  CBWD1 WILD-TYPE  6 57 83 40
D3V4, multiclass
    clus
vv   CBWD1 MUTATED CBWD1 WILD-TYPE
  T1             1               6
  T2             9              57
  T3             7              83
  T4             9              40
[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
  CBWD1 MUTATED   10  6  6  4
  CBWD1 WILD-TYPE 60 57 29 37
D3V5, multiclass
    clus
vv   CBWD1 MUTATED CBWD1 WILD-TYPE
  N0            10              60
  N1             6              57
  N2             6              29
  N3             4              37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1  MX
  CBWD1 MUTATED    26   1   1
  CBWD1 WILD-TYPE 169  15   9
D3V6, multiclass
    clus
vv   CBWD1 MUTATED CBWD1 WILD-TYPE
  M0            26             169
  M1             1              15
  MX             1               9
[1] 3 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
  CBWD1 MUTATED    17  11
  CBWD1 WILD-TYPE  71 122
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD1 MUTATED     17   11
  CBWD1 WILD-TYPE   71  122
        clus
vv       CBWD1 MUTATED CBWD1 WILD-TYPE
  FEMALE            17              71
  MALE              11             122
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CBWD1 MUTATED                                       1
  CBWD1 WILD-TYPE                                    31
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CBWD1 MUTATED                                                       18
  CBWD1 WILD-TYPE                                                     90
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CBWD1 MUTATED                                                                   4
  CBWD1 WILD-TYPE                                                                30
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CBWD1 MUTATED                                                  3
  CBWD1 WILD-TYPE                                               23
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  CBWD1 MUTATED                                                           0
  CBWD1 WILD-TYPE                                                         1
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CBWD1 MUTATED                                                          1
  CBWD1 WILD-TYPE                                                       13
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CBWD1 MUTATED                                                           0
  CBWD1 WILD-TYPE                                                         4
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CBWD1 MUTATED                                          1
  CBWD1 WILD-TYPE                                        0
D3V8, multiclass
                                                                   clus
vv                                                                  CBWD1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
                                                                   clus
vv                                                                  CBWD1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          31
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         90
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               23
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
                 cls
clus                0   1
  CBWD1 MUTATED     1  27
  CBWD1 WILD-TYPE   5 188
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD1 MUTATED      1   27
  CBWD1 WILD-TYPE    5  188
     clus
vv    CBWD1 MUTATED CBWD1 WILD-TYPE
  NO              1               5
  YES            27             188
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CBWD1 MUTATED    21   0   1   4
  CBWD1 WILD-TYPE 150   7   9  20
D3V10, multiclass
    clus
vv   CBWD1 MUTATED CBWD1 WILD-TYPE
  R0            21             150
  R1             0               7
  R2             1               9
  RX             4              20
[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"
D3V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CBWD1 MUTATED       4                         0    19
  CBWD1 WILD-TYPE    40                         3   114
D3V12, multiclass
                           clus
vv                          CBWD1 MUTATED CBWD1 WILD-TYPE
  ASIAN                                 4              40
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                19             114
[1] 3 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    14   7
  KRAS WILD-TYPE 116  58
  KRAS MUTATED KRAS WILD-TYPE 
            21            174 
  KRAS MUTATED KRAS WILD-TYPE 
             7             58 
$`KRAS MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6705 TCGA-BR-6802 
        6.97        30.90         6.18         6.61        13.84        30.90 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8370 
       24.76        23.93         0.82         0.95         4.31         3.32 
TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-8535 TCGA-CD-A4MJ 
       15.81         0.62        11.57         2.83         0.13         0.10 
TCGA-CG-5719 TCGA-CG-5727 TCGA-HU-A4H3 
        1.02        79.07        19.36 

$`KRAS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57        34.68        15.95        13.12        10.13        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 
        7.00        39.12         0.82         0.62        32.78        13.22 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       16.14         8.98        21.11        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
        9.21        15.42        28.01         0.69         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       12.43         0.95         0.69         0.69         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8365 
        0.72         1.55         1.48         6.18        19.50         2.96 
TCGA-BR-8367 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       13.74         0.36        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        3.72         0.72         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        2.14        13.45         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.59        10.68        13.51        12.89         0.79         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5799 
        0.53         0.66        19.36        13.51        13.64         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
        7.07        22.98        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       19.50        17.19         6.97        14.27        16.44         5.92 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
       14.76         0.62         6.58        14.47        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 
       19.53         3.02        22.29        17.06        59.54        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD 
        5.92        12.59        12.10         0.76        24.30        22.75 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H5 
       29.98         8.98         0.10         6.25        17.69        12.30 
TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        9.67        21.21         3.45        18.81         3.39         2.53 

  KRAS MUTATED KRAS WILD-TYPE 
          0.10           0.07 
  KRAS MUTATED KRAS WILD-TYPE 
         79.07         105.07 
  KRAS MUTATED KRAS WILD-TYPE 
          6.61          12.20 
[1] "0.1 - 79.1 (6.6)"   "0.1 - 105.1 (12.2)"
[1] "hr=" "1"  
D4V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRAS MUTATED         0        1        5        2         1         0
  KRAS WILD-TYPE       1        5       18       21        20        31
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRAS MUTATED           2          4          3          2        3
  KRAS WILD-TYPE         1         29         21         15       21
D4V3, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              5
  STAGE IB              5             18
  STAGE II              2             21
  STAGE IIA             1             20
  STAGE IIB             0             31
  STAGE III             2              1
  STAGE IIIA            4             29
  STAGE IIIB            3             21
  STAGE IIIC            2             15
  STAGE IV              3             21
[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"
                vv
clus             T1 T2 T3 T4
  KRAS MUTATED    1  7  9  7
  KRAS WILD-TYPE  6 59 81 42
D4V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            1              6
  T2            7             59
  T3            9             81
  T4            7             42
[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   11  4  4  4
  KRAS WILD-TYPE 59 59 31 37
D4V5, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  N0           11             59
  N1            4             59
  N2            4             31
  N3            4             37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  KRAS MUTATED    22   2   1
  KRAS WILD-TYPE 173  14   9
D4V6, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  M0           22            173
  M1            2             14
  MX            1              9
[1] 3 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    15  10
  KRAS WILD-TYPE  73 123
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     15   10
  KRAS WILD-TYPE   73  123
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           15             73
  MALE             10            123
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  KRAS MUTATED                                       2
  KRAS WILD-TYPE                                    30
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KRAS MUTATED                                                       17
  KRAS WILD-TYPE                                                     91
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  KRAS MUTATED                                                                   3
  KRAS WILD-TYPE                                                                31
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  KRAS MUTATED                                                  1
  KRAS WILD-TYPE                                               25
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  KRAS MUTATED                                                           0
  KRAS WILD-TYPE                                                         1
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  KRAS MUTATED                                                          1
  KRAS WILD-TYPE                                                       13
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  KRAS MUTATED                                                           1
  KRAS WILD-TYPE                                                         3
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  KRAS MUTATED                                          0
  KRAS WILD-TYPE                                        1
D4V8, multiclass
                                                                   clus
vv                                                                  KRAS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  KRAS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         30
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        91
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              25
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
                cls
clus               0   1
  KRAS MUTATED     0  25
  KRAS WILD-TYPE   6 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0   25
  KRAS WILD-TYPE    6  190
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             0              6
  YES           25            190
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KRAS MUTATED    15   1   0   7
  KRAS WILD-TYPE 156   6  10  17
D4V10, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           15            156
  R1            1              6
  R2            0             10
  RX            7             17
[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"
D4V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       5                         0    18
  KRAS WILD-TYPE    39                         3   115
D4V12, multiclass
                           clus
vv                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                5             39
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                               18            115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = ARID1A MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    22  12
  ARID1A WILD-TYPE 108  53
  ARID1A MUTATED ARID1A WILD-TYPE 
              34              161 
  ARID1A MUTATED ARID1A WILD-TYPE 
              12               53 
$`ARID1A MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6455 TCGA-BR-6707 TCGA-BR-6802 
        5.62         6.97        30.90        13.12        16.14        30.90 
TCGA-BR-7196 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-8059 TCGA-BR-8284 TCGA-BR-8361 
       12.82         0.16        12.43         0.82         0.72        19.50 
TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8589 TCGA-BR-8677 
        4.31        19.17         0.26        15.85        15.81         0.49 
TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A4J1 TCGA-BR-A4QL TCGA-CD-5803 TCGA-CD-A4MJ 
       15.81         0.62         0.72        11.57         0.07         0.10 
TCGA-CG-4465 TCGA-CG-4469 TCGA-D7-5577 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-A4YU 
        9.01         7.07        12.36        18.54        17.85        16.44 
TCGA-F1-6177 TCGA-FP-7998 TCGA-FP-8099 TCGA-HU-A4GN 
        6.58        22.29        17.06        29.98 

$`ARID1A WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 
       11.70         6.61         4.64         7.43        18.35         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        10.13        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
        7.00        39.12         0.82         0.62        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 
       13.22         8.98        21.11        31.20        32.94         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 
       24.76        23.93        15.42        28.01         0.69        18.54 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8295 
        0.95         0.69         0.69         0.49        20.55         1.55 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 
        1.48         6.18         2.96         0.95        13.74         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.36        14.79         3.72         0.72         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8682 
       12.79         2.14        13.45         7.53        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J4 
        0.59        10.68        13.51        12.89         0.79         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 
        0.66        19.36        13.51        13.64         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18         0.30         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.13         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4475 
       29.98        47.05        19.07        12.03        18.97        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97         1.02         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 
        4.01        55.04        21.07         7.99        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 
       19.13        20.55        18.84        18.61        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       12.33        24.72        16.80        19.50        17.19         6.97 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 
       14.27         5.92        14.76         0.62        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8243 
        0.39        19.53         3.02        59.54        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GP 
       12.59        12.10         0.76        24.30        22.75         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.10         6.25        19.36        17.69        12.30         9.67 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.07             0.07 
  ARID1A MUTATED ARID1A WILD-TYPE 
           30.90           105.07 
  ARID1A MUTATED ARID1A WILD-TYPE 
          12.395           11.930 
[1] "0.1 - 30.9 (12.4)"  "0.1 - 105.1 (11.9)"
[1] "hr=" "1.2"
D5V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARID1A MUTATED         1        0        3        2         3         4
  ARID1A WILD-TYPE       0        6       20       21        18        27
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID1A MUTATED           1          8          4          6        4
  ARID1A WILD-TYPE         2         25         20         11       20
D5V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                 1                0
  STAGE IA                0                6
  STAGE IB                3               20
  STAGE II                2               21
  STAGE IIA               3               18
  STAGE IIB               4               27
  STAGE III               1                2
  STAGE IIIA              8               25
  STAGE IIIB              4               20
  STAGE IIIC              6               11
  STAGE IV                4               20
[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"
                  vv
clus               T1 T2 T3 T4
  ARID1A MUTATED    2  8 15 14
  ARID1A WILD-TYPE  5 58 75 35
D5V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              2                5
  T2              8               58
  T3             15               75
  T4             14               35
[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    9 12  5 11
  ARID1A WILD-TYPE 61 51 30 30
D5V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0              9               61
  N1             12               51
  N2              5               30
  N3             11               30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1  MX
  ARID1A MUTATED    33   3   5
  ARID1A WILD-TYPE 162  13   5
D5V6, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  M0             33              162
  M1              3               13
  MX              5                5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED    19  22
  ARID1A WILD-TYPE  69 111
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     19   22
  ARID1A WILD-TYPE   69  111
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE             19               69
  MALE               22              111
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ARID1A MUTATED                                       5
  ARID1A WILD-TYPE                                    27
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ARID1A MUTATED                                                       27
  ARID1A WILD-TYPE                                                     81
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ARID1A MUTATED                                                                   5
  ARID1A WILD-TYPE                                                                29
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ARID1A MUTATED                                                  4
  ARID1A WILD-TYPE                                               22
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  ARID1A MUTATED                                                           0
  ARID1A WILD-TYPE                                                         1
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ARID1A MUTATED                                                          0
  ARID1A WILD-TYPE                                                       14
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ARID1A MUTATED                                                           0
  ARID1A WILD-TYPE                                                         4
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ARID1A MUTATED                                          0
  ARID1A WILD-TYPE                                        1
D5V8, multiclass
                                                                   clus
vv                                                                  ARID1A MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        27
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               4
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ARID1A WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           27
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          81
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                22
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
                  cls
clus                 0   1
  ARID1A MUTATED     0  41
  ARID1A WILD-TYPE   6 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      0   41
  ARID1A WILD-TYPE    6  174
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO               0                6
  YES             41              174
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    27   3   1   8
  ARID1A WILD-TYPE 144   4   9  16
D5V10, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             27              144
  R1              3                4
  R2              1                9
  RX              8               16
[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"
D5V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       5                         1    32
  ARID1A WILD-TYPE    39                         2   101
D5V12, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  5               39
  BLACK OR AFRICAN AMERICAN              1                2
  WHITE                                 32              101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = PGM5 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  PGM5 MUTATED    12   5
  PGM5 WILD-TYPE 118  60
  PGM5 MUTATED PGM5 WILD-TYPE 
            17            178 
  PGM5 MUTATED PGM5 WILD-TYPE 
             5             60 
$`PGM5 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8368 
       30.90        34.68        23.93        20.55        19.50         4.31 
TCGA-BR-8382 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-5726 TCGA-CG-5728 
       15.85        15.81        11.57        15.95        28.96        65.10 
TCGA-D7-6521 TCGA-D7-A4YV TCGA-F1-6177 TCGA-HU-A4GQ TCGA-HU-A4H3 
       18.54         5.92         6.58         0.10        19.36 

$`PGM5 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57         6.61        15.95        13.12 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       10.13        13.68         7.00        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        13.84        13.22        16.14         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01         0.69         0.16        18.54        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 
        0.95         0.69         0.82         0.69         0.49         0.72 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        1.55         1.48         6.18         2.96         0.95        13.74 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32         0.36        19.17        14.79         0.26         3.72 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        0.72         9.21        20.22        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
       13.45         7.53         0.49        11.54        16.44         0.59 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.62        10.68        13.51        12.89         0.79         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5798 
        0.53         0.66        19.36        13.51        13.64         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.10         0.10         0.13         0.10         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       12.03        79.07         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU 
       16.80        19.50        17.19         6.97        14.27        16.44 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
       14.76         0.62        14.47        72.23         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8243 
        3.02        22.29        17.06        59.54        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GN 
       12.59        12.10         0.76        24.30        22.75        29.98 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 
        8.98         6.25        17.69        12.30         9.67        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  PGM5 MUTATED PGM5 WILD-TYPE 
          0.10           0.07 
  PGM5 MUTATED PGM5 WILD-TYPE 
         65.10         105.07 
  PGM5 MUTATED PGM5 WILD-TYPE 
        18.540         11.425 
[1] "0.1 - 65.1 (18.5)"  "0.1 - 105.1 (11.4)"
[1] "hr=" "1.6"
D6V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PGM5 MUTATED         1        1        3        2         1         2
  PGM5 WILD-TYPE       0        5       20       21        20        29
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PGM5 MUTATED           0          1          1          4        2
  PGM5 WILD-TYPE         3         32         23         13       22
D6V3, multiclass
            clus
vv           PGM5 MUTATED PGM5 WILD-TYPE
  STAGE I               1              0
  STAGE IA              1              5
  STAGE IB              3             20
  STAGE II              2             21
  STAGE IIA             1             20
  STAGE IIB             2             29
  STAGE III             0              3
  STAGE IIIA            1             32
  STAGE IIIB            1             23
  STAGE IIIC            4             13
  STAGE IV              2             22
[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"
                vv
clus             T1 T2 T3 T4
  PGM5 MUTATED    3  7  4  6
  PGM5 WILD-TYPE  4 59 86 43
D6V4, multiclass
    clus
vv   PGM5 MUTATED PGM5 WILD-TYPE
  T1            3              4
  T2            7             59
  T3            4             86
  T4            6             43
[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
  PGM5 MUTATED    6  5  4  4
  PGM5 WILD-TYPE 64 58 31 37
D6V5, multiclass
    clus
vv   PGM5 MUTATED PGM5 WILD-TYPE
  N0            6             64
  N1            5             58
  N2            4             31
  N3            4             37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  PGM5 MUTATED    19   2   1
  PGM5 WILD-TYPE 176  14   9
D6V6, multiclass
    clus
vv   PGM5 MUTATED PGM5 WILD-TYPE
  M0           19            176
  M1            2             14
  MX            1              9
[1] 3 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
  PGM5 MUTATED    15   7
  PGM5 WILD-TYPE  73 126
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM5 MUTATED     15    7
  PGM5 WILD-TYPE   73  126
        clus
vv       PGM5 MUTATED PGM5 WILD-TYPE
  FEMALE           15             73
  MALE              7            126
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  PGM5 MUTATED                                       3
  PGM5 WILD-TYPE                                    29
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PGM5 MUTATED                                                       13
  PGM5 WILD-TYPE                                                     95
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  PGM5 MUTATED                                                                   2
  PGM5 WILD-TYPE                                                                32
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  PGM5 MUTATED                                                  3
  PGM5 WILD-TYPE                                               23
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  PGM5 MUTATED                                                           0
  PGM5 WILD-TYPE                                                         1
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  PGM5 MUTATED                                                          1
  PGM5 WILD-TYPE                                                       13
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  PGM5 MUTATED                                                           0
  PGM5 WILD-TYPE                                                         4
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  PGM5 MUTATED                                          0
  PGM5 WILD-TYPE                                        1
D6V8, multiclass
                                                                   clus
vv                                                                  PGM5 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             3
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  PGM5 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         29
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        95
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              23
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
                cls
clus               0   1
  PGM5 MUTATED     1  21
  PGM5 WILD-TYPE   5 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM5 MUTATED      1   21
  PGM5 WILD-TYPE    5  194
     clus
vv    PGM5 MUTATED PGM5 WILD-TYPE
  NO             1              5
  YES           21            194
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PGM5 MUTATED    17   0   1   4
  PGM5 WILD-TYPE 154   7   9  20
D6V10, multiclass
    clus
vv   PGM5 MUTATED PGM5 WILD-TYPE
  R0           17            154
  R1            0              7
  R2            1              9
  RX            4             20
[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"
D6V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PGM5 MUTATED       3                         1    13
  PGM5 WILD-TYPE    41                         2   120
D6V12, multiclass
                           clus
vv                          PGM5 MUTATED PGM5 WILD-TYPE
  ASIAN                                3             41
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                               13            120
[1] 3 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 = RHOA MUTATION ANALYSIS
D7V1, survival
                sevent
clus2              0   1
  RHOA MUTATED     9   4
  RHOA WILD-TYPE 121  61
  RHOA MUTATED RHOA WILD-TYPE 
            13            182 
  RHOA MUTATED RHOA WILD-TYPE 
             4             61 
$`RHOA MUTATED`
TCGA-BR-4188 TCGA-BR-6563 TCGA-BR-6802 TCGA-BR-7722 TCGA-BR-8366 TCGA-BR-A4IV 
        7.43        39.12        30.90         0.16         0.95        13.51 
TCGA-CG-4465 TCGA-CG-5720 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-8574 
        9.01         0.99        18.84        18.54        18.61        17.19 
TCGA-D7-A4YU 
       16.44 

$`RHOA WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 
        5.62        11.70         6.61         6.97         4.64        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
       13.12        10.13        13.68         7.00         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        13.84        13.22        16.14         8.98        21.11 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       15.42        28.01         0.69        18.54        12.43         0.95 
TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        0.69         0.82         0.69         0.49        20.55         0.72 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8367 
        1.55         1.48         6.18        19.50         2.96        13.74 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31         3.32         0.36        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
       15.85         3.72         0.72         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         2.14        13.45         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4IY 
       15.81        16.44         0.59         0.62        10.68        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.79         0.72         0.53         0.66        19.36        13.51 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       13.64        11.57         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        0.30         0.07         0.39         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 
       29.98        47.05        19.07        12.03        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 
       22.98        30.97         6.97         1.02         1.02         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       11.93        19.13        20.55        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-A4YT 
       12.33        24.72        16.80        19.50         6.97        14.27 
TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        5.92        14.76         0.62         6.58        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39        19.53         3.02        22.29        17.06        59.54 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 
       26.47         5.92        12.59        12.10         0.76        24.30 
TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 
       22.75        29.98         8.98         0.10         6.25        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       17.69        12.30         9.67        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  RHOA MUTATED RHOA WILD-TYPE 
          0.16           0.07 
  RHOA MUTATED RHOA WILD-TYPE 
         39.12         105.07 
  RHOA MUTATED RHOA WILD-TYPE 
        16.440         11.815 
[1] "0.2 - 39.1 (16.4)"  "0.1 - 105.1 (11.8)"
[1] "hr=" "1.2"
D7V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RHOA MUTATED         0        0        2        0         1         2
  RHOA WILD-TYPE       1        6       21       23        20        29
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RHOA MUTATED           0          4          2          0        1
  RHOA WILD-TYPE         3         29         22         17       23
D7V3, multiclass
            clus
vv           RHOA MUTATED RHOA WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              6
  STAGE IB              2             21
  STAGE II              0             23
  STAGE IIA             1             20
  STAGE IIB             2             29
  STAGE III             0              3
  STAGE IIIA            4             29
  STAGE IIIB            2             22
  STAGE IIIC            0             17
  STAGE IV              1             23
[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"
                vv
clus             T1 T2 T3 T4
  RHOA MUTATED    0  5  5  2
  RHOA WILD-TYPE  7 61 85 47
D7V4, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  T1            0              7
  T2            5             61
  T3            5             85
  T4            2             47
[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
  RHOA MUTATED    3  3  4  3
  RHOA WILD-TYPE 67 60 31 38
D7V5, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  N0            3             67
  N1            3             60
  N2            4             31
  N3            3             38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  RHOA MUTATED    12   1   0
  RHOA WILD-TYPE 183  15  10
D7V6, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  M0           12            183
  M1            1             15
  MX            0             10
[1] 3 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
  RHOA MUTATED     4   9
  RHOA WILD-TYPE  84 124
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      4    9
  RHOA WILD-TYPE   84  124
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  FEMALE            4             84
  MALE              9            124
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  RHOA MUTATED                                       4
  RHOA WILD-TYPE                                    28
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RHOA MUTATED                                                        7
  RHOA WILD-TYPE                                                    101
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  RHOA MUTATED                                                                   0
  RHOA WILD-TYPE                                                                34
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  RHOA MUTATED                                                  2
  RHOA WILD-TYPE                                               24
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  RHOA MUTATED                                                           0
  RHOA WILD-TYPE                                                         1
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  RHOA MUTATED                                                          0
  RHOA WILD-TYPE                                                       14
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  RHOA MUTATED                                                           0
  RHOA WILD-TYPE                                                         4
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  RHOA MUTATED                                          0
  RHOA WILD-TYPE                                        1
D7V8, multiclass
                                                                   clus
vv                                                                  RHOA MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  RHOA WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         28
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       101
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              24
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
                cls
clus               0   1
  RHOA MUTATED     0  13
  RHOA WILD-TYPE   6 202
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      0   13
  RHOA WILD-TYPE    6  202
     clus
vv    RHOA MUTATED RHOA WILD-TYPE
  NO             0              6
  YES           13            202
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RHOA MUTATED    11   0   1   1
  RHOA WILD-TYPE 160   7   9  23
D7V10, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  R0           11            160
  R1            0              7
  R2            1              9
  RX            1             23
[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"
D7V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RHOA MUTATED       1                         0    10
  RHOA WILD-TYPE    43                         3   123
D7V12, multiclass
                           clus
vv                          RHOA MUTATED RHOA WILD-TYPE
  ASIAN                                1             43
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                               10            123
[1] 3 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 = SMAD4 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2               0   1
  SMAD4 MUTATED    12   6
  SMAD4 WILD-TYPE 118  59
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             18             177 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              6              59 
$`SMAD4 MUTATED`
TCGA-BR-4184 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-7722 TCGA-BR-8361 TCGA-BR-8366 
        6.97         6.18         9.57         0.16        19.50         0.95 
TCGA-BR-8372 TCGA-BR-A4J6 TCGA-CD-5799 TCGA-CD-8529 TCGA-CG-4469 TCGA-CG-5719 
       19.17         0.66         3.25         0.13         7.07         1.02 
TCGA-D7-6815 TCGA-FP-7829 TCGA-HU-8243 TCGA-HU-A4G2 TCGA-HU-A4H4 TCGA-IN-8462 
       15.98        19.53         5.92        24.30        17.69        18.81 

$`SMAD4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.61        34.68        15.95        13.12        10.13 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68         7.00        39.12         0.82         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.84        13.22        16.14         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       15.42        28.01         0.69        18.54        12.43         0.95 
TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        0.69         0.82         0.69         0.49        20.55         0.72 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 
        1.55         1.48         6.18         2.96        13.74         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32         0.36        14.79         0.26        15.85         3.72 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        0.72         9.21        20.22        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
       13.45         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        0.59         0.62        10.68        13.51        12.89         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-BR-A4QL 
        0.72         0.53        19.36        13.51        13.64        11.57 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        2.83        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.07         0.10         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        0.10         0.13         0.10         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97        22.98        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU 
       16.80        19.50        17.19         6.97        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        5.92        14.76         0.62         6.58        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 
        0.39         3.02        22.29        17.06        59.54        26.47 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP 
       12.59        12.10         0.76        22.75        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 
        0.10         6.25        19.36        12.30         9.67        21.21 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IP-7968 
        3.45         3.39         2.53 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           0.13            0.07 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          24.30          105.07 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
           7.02           12.10 
[1] "0.1 - 24.3 (7.0)"   "0.1 - 105.1 (12.1)"
[1] "hr=" "1.2"
D8V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMAD4 MUTATED         0        0        1        2         2         5
  SMAD4 WILD-TYPE       1        6       22       21        19        26
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMAD4 MUTATED           0          3          0          3        3
  SMAD4 WILD-TYPE         3         30         24         14       21
D8V3, multiclass
            clus
vv           SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               6
  STAGE IB               1              22
  STAGE II               2              21
  STAGE IIA              2              19
  STAGE IIB              5              26
  STAGE III              0               3
  STAGE IIIA             3              30
  STAGE IIIB             0              24
  STAGE IIIC             3              14
  STAGE IV               3              21
[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"
                 vv
clus              T1 T2 T3 T4
  SMAD4 MUTATED    0  6  8  5
  SMAD4 WILD-TYPE  7 60 82 44
D8V4, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  T1             0               7
  T2             6              60
  T3             8              82
  T4             5              44
[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
  SMAD4 MUTATED    5  8  3  3
  SMAD4 WILD-TYPE 65 55 32 38
D8V5, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  N0             5              65
  N1             8              55
  N2             3              32
  N3             3              38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1  MX
  SMAD4 MUTATED    16   2   1
  SMAD4 WILD-TYPE 179  14   9
D8V6, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  M0            16             179
  M1             2              14
  MX             1               9
[1] 3 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
  SMAD4 MUTATED     6  13
  SMAD4 WILD-TYPE  82 120
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      6   13
  SMAD4 WILD-TYPE   82  120
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE             6              82
  MALE              13             120
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  SMAD4 MUTATED                                       1
  SMAD4 WILD-TYPE                                    31
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SMAD4 MUTATED                                                       10
  SMAD4 WILD-TYPE                                                     98
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  SMAD4 MUTATED                                                                   3
  SMAD4 WILD-TYPE                                                                31
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  SMAD4 MUTATED                                                  3
  SMAD4 WILD-TYPE                                               23
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  SMAD4 MUTATED                                                           0
  SMAD4 WILD-TYPE                                                         1
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  SMAD4 MUTATED                                                          2
  SMAD4 WILD-TYPE                                                       12
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  SMAD4 MUTATED                                                           0
  SMAD4 WILD-TYPE                                                         4
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  SMAD4 MUTATED                                          0
  SMAD4 WILD-TYPE                                        1
D8V8, multiclass
                                                                   clus
vv                                                                  SMAD4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              3
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  SMAD4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          31
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         98
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               23
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
                 cls
clus                0   1
  SMAD4 MUTATED     0  19
  SMAD4 WILD-TYPE   6 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      0   19
  SMAD4 WILD-TYPE    6  196
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  NO              0               6
  YES            19             196
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  SMAD4 MUTATED    14   1   0   3
  SMAD4 WILD-TYPE 157   6  10  21
D8V10, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  R0            14             157
  R1             1               6
  R2             0              10
  RX             3              21
[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"
D8V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMAD4 MUTATED       6                         0    11
  SMAD4 WILD-TYPE    38                         3   122
D8V12, multiclass
                           clus
vv                          SMAD4 MUTATED SMAD4 WILD-TYPE
  ASIAN                                 6              38
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                11             122
[1] 3 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 = IRF2 MUTATION ANALYSIS
D9V1, survival
                sevent
clus2              0   1
  IRF2 MUTATED     8   2
  IRF2 WILD-TYPE 122  63
  IRF2 MUTATED IRF2 WILD-TYPE 
            10            185 
  IRF2 MUTATED IRF2 WILD-TYPE 
             2             63 
$`IRF2 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7715 TCGA-BR-7851 TCGA-BR-8360 
        5.62         6.97        34.68        15.42        12.43         6.18 
TCGA-BR-8680 TCGA-CG-5726 TCGA-D7-6524 TCGA-HU-8245 
       15.81        28.96        17.85        12.59 

$`IRF2 WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.12        10.13 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68         7.00        39.12         0.82         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.84        13.22        16.14         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       28.01         0.69         0.16        18.54         0.95         0.69 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 
        0.82         0.69         0.49        20.55         0.72         1.55 
TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        1.48        19.50         2.96         0.95        13.74         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32         0.36        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        3.72         0.72         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        2.14        13.45         7.53         0.49        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        0.59         0.62        10.68        13.51        12.89         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI 
        0.72         0.53         0.66        19.36        13.51        13.64 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       11.57         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
        0.07         0.39         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A4MI 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       47.05        19.07        12.03         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4Z0 
       17.19         6.97        14.27        16.44         5.92        14.76 
TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        0.62         6.58        14.47        72.23         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8243 
        3.02        22.29        17.06        59.54        26.47         5.92 
TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP 
       12.10         0.76        24.30        22.75        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.10         6.25        19.36        17.69        12.30         9.67 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  IRF2 MUTATED IRF2 WILD-TYPE 
          5.62           0.07 
  IRF2 MUTATED IRF2 WILD-TYPE 
         34.68         105.07 
  IRF2 MUTATED IRF2 WILD-TYPE 
        14.005         11.700 
[1] "5.6 - 34.7 (14.0)"  "0.1 - 105.1 (11.7)"
[1] "hr=" "2"  
D9V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IRF2 MUTATED         0        1        0        1         4         1
  IRF2 WILD-TYPE       1        5       23       22        17        30
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IRF2 MUTATED           0          2          0          0        2
  IRF2 WILD-TYPE         3         31         24         17       22
D9V3, multiclass
            clus
vv           IRF2 MUTATED IRF2 WILD-TYPE
  STAGE I               0              1
  STAGE IA              1              5
  STAGE IB              0             23
  STAGE II              1             22
  STAGE IIA             4             17
  STAGE IIB             1             30
  STAGE III             0              3
  STAGE IIIA            2             31
  STAGE IIIB            0             24
  STAGE IIIC            0             17
  STAGE IV              2             22
[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"
                vv
clus             T1 T2 T3 T4
  IRF2 MUTATED    1  1  5  4
  IRF2 WILD-TYPE  6 65 85 45
D9V4, multiclass
    clus
vv   IRF2 MUTATED IRF2 WILD-TYPE
  T1            1              6
  T2            1             65
  T3            5             85
  T4            4             45
[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
  IRF2 MUTATED    7  3  2  0
  IRF2 WILD-TYPE 63 60 33 41
D9V5, multiclass
    clus
vv   IRF2 MUTATED IRF2 WILD-TYPE
  N0            7             63
  N1            3             60
  N2            2             33
  N3            0             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  IRF2 MUTATED    12   1   1
  IRF2 WILD-TYPE 183  15   9
D9V6, multiclass
    clus
vv   IRF2 MUTATED IRF2 WILD-TYPE
  M0           12            183
  M1            1             15
  MX            1              9
[1] 3 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
  IRF2 MUTATED     6   8
  IRF2 WILD-TYPE  82 125
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED      6    8
  IRF2 WILD-TYPE   82  125
        clus
vv       IRF2 MUTATED IRF2 WILD-TYPE
  FEMALE            6             82
  MALE              8            125
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  IRF2 MUTATED                                       2
  IRF2 WILD-TYPE                                    30
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IRF2 MUTATED                                                        7
  IRF2 WILD-TYPE                                                    101
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  IRF2 MUTATED                                                                   3
  IRF2 WILD-TYPE                                                                31
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  IRF2 MUTATED                                                  1
  IRF2 WILD-TYPE                                               25
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  IRF2 MUTATED                                                           0
  IRF2 WILD-TYPE                                                         1
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  IRF2 MUTATED                                                          0
  IRF2 WILD-TYPE                                                       14
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  IRF2 MUTATED                                                           1
  IRF2 WILD-TYPE                                                         3
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  IRF2 MUTATED                                          0
  IRF2 WILD-TYPE                                        1
D9V8, multiclass
                                                                   clus
vv                                                                  IRF2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  IRF2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         30
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       101
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              25
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
                cls
clus               0   1
  IRF2 MUTATED     0  14
  IRF2 WILD-TYPE   6 201
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED      0   14
  IRF2 WILD-TYPE    6  201
     clus
vv    IRF2 MUTATED IRF2 WILD-TYPE
  NO             0              6
  YES           14            201
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IRF2 MUTATED     8   1   0   5
  IRF2 WILD-TYPE 163   6  10  19
D9V10, multiclass
    clus
vv   IRF2 MUTATED IRF2 WILD-TYPE
  R0            8            163
  R1            1              6
  R2            0             10
  RX            5             19
[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"
D9V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IRF2 MUTATED       2                         0    11
  IRF2 WILD-TYPE    42                         3   122
D9V12, multiclass
                           clus
vv                          IRF2 MUTATED IRF2 WILD-TYPE
  ASIAN                                2             42
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                               11            122
[1] 3 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 = LARP4B MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2                0   1
  LARP4B MUTATED     8   1
  LARP4B WILD-TYPE 122  64
  LARP4B MUTATED LARP4B WILD-TYPE 
               9              186 
  LARP4B MUTATED LARP4B WILD-TYPE 
               1               64 
$`LARP4B MUTATED`
TCGA-BR-7707 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8535 TCGA-CG-5721 
       23.93        13.45        15.81        11.57         0.13         6.02 
TCGA-CG-5733 TCGA-D7-5578 TCGA-F1-6874 
       21.07        12.66        14.47 

$`LARP4B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62        32.78        13.84        13.22        16.14 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 
       18.54        12.43         0.95         0.69         0.82         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
        0.49        20.55         0.72         1.55         1.48         6.18 
TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       19.50         2.96         0.95        13.74         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        0.36        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        0.72         9.21        20.22        12.79        15.81         2.14 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        7.53         0.49        11.54        16.44         0.59         0.62 
TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 
       10.68        13.51        12.89         0.79         0.72         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 
        0.66        19.36        13.51        13.64         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.10         0.10         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 
       14.01        29.98        47.05        19.07        12.03         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        55.04         7.99        12.36 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       19.50        17.19         6.97        14.27        16.44         5.92 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
       14.76         0.62         6.58        72.23         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8243 
        3.02        22.29        17.06        59.54        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GN 
       12.59        12.10         0.76        24.30        22.75        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        8.98         0.10         6.25        19.36        17.69        12.30 
TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        9.67        21.21         3.45        18.81         3.39         2.53 

  LARP4B MUTATED LARP4B WILD-TYPE 
            0.13             0.07 
  LARP4B MUTATED LARP4B WILD-TYPE 
           23.93           105.07 
  LARP4B MUTATED LARP4B WILD-TYPE 
          13.450           11.815 
[1] "0.1 - 23.9 (13.4)"  "0.1 - 105.1 (11.8)"
[1] "hr=" "3.3"
D10V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LARP4B MUTATED         0        0        2        0         0         1
  LARP4B WILD-TYPE       1        6       21       23        21        30
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LARP4B MUTATED           0          3          1          1        2
  LARP4B WILD-TYPE         3         30         23         16       22
D10V3, multiclass
            clus
vv           LARP4B MUTATED LARP4B WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                6
  STAGE IB                2               21
  STAGE II                0               23
  STAGE IIA               0               21
  STAGE IIB               1               30
  STAGE III               0                3
  STAGE IIIA              3               30
  STAGE IIIB              1               23
  STAGE IIIC              1               16
  STAGE IV                2               22
[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"
                  vv
clus               T1 T2 T3 T4
  LARP4B MUTATED    1  3  4  4
  LARP4B WILD-TYPE  6 63 86 45
D10V4, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  T1              1                6
  T2              3               63
  T3              4               86
  T4              4               45
[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
  LARP4B MUTATED    3  2  3  2
  LARP4B WILD-TYPE 67 61 32 39
D10V5, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  N0              3               67
  N1              2               61
  N2              3               32
  N3              2               39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1  MX
  LARP4B MUTATED    10   1   1
  LARP4B WILD-TYPE 185  15   9
D10V6, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  M0             10              185
  M1              1               15
  MX              1                9
[1] 3 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
  LARP4B MUTATED     6   6
  LARP4B WILD-TYPE  82 127
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED      6    6
  LARP4B WILD-TYPE   82  127
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  FEMALE              6               82
  MALE                6              127
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  LARP4B MUTATED                                       0
  LARP4B WILD-TYPE                                    32
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LARP4B MUTATED                                                        7
  LARP4B WILD-TYPE                                                    101
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  LARP4B MUTATED                                                                   3
  LARP4B WILD-TYPE                                                                31
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  LARP4B MUTATED                                                  2
  LARP4B WILD-TYPE                                               24
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  LARP4B MUTATED                                                           0
  LARP4B WILD-TYPE                                                         1
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  LARP4B MUTATED                                                          0
  LARP4B WILD-TYPE                                                       14
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  LARP4B MUTATED                                                           0
  LARP4B WILD-TYPE                                                         4
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  LARP4B MUTATED                                          0
  LARP4B WILD-TYPE                                        1
D10V8, multiclass
                                                                   clus
vv                                                                  LARP4B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  LARP4B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           32
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         101
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                24
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
                  cls
clus                 0   1
  LARP4B MUTATED     0  12
  LARP4B WILD-TYPE   6 203
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED      0   12
  LARP4B WILD-TYPE    6  203
     clus
vv    LARP4B MUTATED LARP4B WILD-TYPE
  NO               0                6
  YES             12              203
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  LARP4B MUTATED     9   0   0   3
  LARP4B WILD-TYPE 162   7  10  21
D10V10, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  R0              9              162
  R1              0                7
  R2              0               10
  RX              3               21
[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"
D10V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LARP4B MUTATED       2                         0     8
  LARP4B WILD-TYPE    42                         3   125
D10V12, multiclass
                           clus
vv                          LARP4B MUTATED LARP4B WILD-TYPE
  ASIAN                                  2               42
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  8              125
[1] 3 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 = APC MUTATION ANALYSIS
D11V1, survival
               sevent
clus2             0   1
  APC MUTATED    14  14
  APC WILD-TYPE 116  51
  APC MUTATED APC WILD-TYPE 
           28           167 
  APC MUTATED APC WILD-TYPE 
           14            51 
$`APC MUTATED`
TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6563 TCGA-BR-6565 
        6.97        18.35         6.18        34.68        39.12         0.62 
TCGA-BR-6566 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-8081 TCGA-BR-8680 TCGA-CD-8535 
       32.78         9.21        24.76        20.55        15.81         0.13 
TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5721 
        0.10         1.02         9.01         7.07         1.02         6.02 
TCGA-CG-5726 TCGA-CG-5733 TCGA-D7-6528 TCGA-D7-A4YV TCGA-F1-6875 TCGA-FP-7735 
       28.96        21.07        15.22         5.92        72.23         0.39 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GU TCGA-HU-A4H3 
        5.92        12.59         6.25        19.36 

$`APC WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        5.62        11.70         6.61         4.64         7.43        30.90 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.12        10.13        13.68 
TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        7.00         0.82        13.84        13.22        16.14         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7707 
       21.11        30.90        31.20        32.94        12.82        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01         0.69         0.16        18.54        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 
        0.95         0.69         0.82         0.69         0.49         0.72 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8366 
        1.55         1.48         6.18        19.50         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       13.74         4.31         3.32         0.36        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         3.72         0.72         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 
       12.79        15.81         2.14        13.45         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4IV 
       11.54        16.44         0.59         0.62        10.68        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
       12.89         0.79         0.72         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.51        13.64        11.57         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
        0.10        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       19.07        12.03        18.97        22.98        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        1.02         0.99         0.99       105.07        12.03        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        55.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4Z0 TCGA-EQ-5647 
       17.19         6.97        14.27        16.44        14.76         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
        6.58        14.47        19.53         3.02        22.29        17.06 
TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD 
       59.54        26.47        12.10         0.76        24.30        22.75 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
       29.98         8.98         0.10        17.69        12.30         9.67 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  APC MUTATED APC WILD-TYPE 
         0.10          0.07 
  APC MUTATED APC WILD-TYPE 
        72.23        105.07 
  APC MUTATED APC WILD-TYPE 
         9.11         12.03 
[1] "0.1 - 72.2 (9.1)"   "0.1 - 105.1 (12.0)"
[1] "hr=" "1.5"
D11V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  APC MUTATED         0        3        5        2         3         5
  APC WILD-TYPE       1        3       18       21        18        26
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  APC MUTATED           0          4          0          3        5
  APC WILD-TYPE         3         29         24         14       19
D11V3, multiclass
            clus
vv           APC MUTATED APC WILD-TYPE
  STAGE I              0             1
  STAGE IA             3             3
  STAGE IB             5            18
  STAGE II             2            21
  STAGE IIA            3            18
  STAGE IIB            5            26
  STAGE III            0             3
  STAGE IIIA           4            29
  STAGE IIIB           0            24
  STAGE IIIC           3            14
  STAGE IV             5            19
[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"
               vv
clus            T1 T2 T3 T4
  APC MUTATED    2  8 11  9
  APC WILD-TYPE  5 58 79 40
D11V4, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  T1           2             5
  T2           8            58
  T3          11            79
  T4           9            40
[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
  APC MUTATED   15  9  3  5
  APC WILD-TYPE 55 54 32 36
D11V5, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  N0          15            55
  N1           9            54
  N2           3            32
  N3           5            36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1  MX
  APC MUTATED    28   3   2
  APC WILD-TYPE 167  13   8
D11V6, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  M0          28           167
  M1           3            13
  MX           2             8
[1] 3 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
  APC MUTATED    12  21
  APC WILD-TYPE  76 112
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     12   21
  APC WILD-TYPE   76  112
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE          12            76
  MALE            21           112
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  APC MUTATED                                       4
  APC WILD-TYPE                                    28
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  APC MUTATED                                                       17
  APC WILD-TYPE                                                     91
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  APC MUTATED                                                                   6
  APC WILD-TYPE                                                                28
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  APC MUTATED                                                  4
  APC WILD-TYPE                                               22
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  APC MUTATED                                                           0
  APC WILD-TYPE                                                         1
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  APC MUTATED                                                          0
  APC WILD-TYPE                                                       14
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  APC MUTATED                                                           2
  APC WILD-TYPE                                                         2
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  APC MUTATED                                          0
  APC WILD-TYPE                                        1
D11V8, multiclass
                                                                   clus
vv                                                                  APC MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                     17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            4
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  APC WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        28
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       91
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            28
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             22
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
               cls
clus              0   1
  APC MUTATED     0  33
  APC WILD-TYPE   6 182
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      0   33
  APC WILD-TYPE    6  182
     clus
vv    APC MUTATED APC WILD-TYPE
  NO            0             6
  YES          33           182
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  APC MUTATED    23   1   2   6
  APC WILD-TYPE 148   6   8  18
D11V10, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0          23           148
  R1           1             6
  R2           2             8
  RX           6            18
[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"
D11V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  APC MUTATED       7                         2    15
  APC WILD-TYPE    37                         1   118
D11V12, multiclass
                           clus
vv                          APC MUTATED APC WILD-TYPE
  ASIAN                               7            37
  BLACK OR AFRICAN AMERICAN           2             1
  WHITE                              15           118
[1] 3 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 = FBXW7 MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    13   2
  FBXW7 WILD-TYPE 117  63
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             15             180 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              2              63 
$`FBXW7 MUTATED`
TCGA-BR-4201 TCGA-BR-6852 TCGA-BR-7851 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8372 
       30.90        32.94        12.43         6.18        19.50        19.17 
TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-CG-5721 
        9.21        11.54        15.81        11.57         0.10         6.02 
TCGA-CG-5723 TCGA-CG-5733 TCGA-HU-A4GN 
      105.07        21.07        29.98 

$`FBXW7 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        0.62        32.78        13.84        13.22        16.14         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        31.20        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01         0.69         0.16        18.54 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
        0.95         0.69         0.82         0.69         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        0.72         1.55         1.48         2.96         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        4.31         3.32         0.36        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72         0.72        20.22        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
       13.45         7.53         0.49        16.44         0.59         0.62 
TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 
       10.68        13.51        12.89         0.79         0.72         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 
        0.66        19.36        13.51        13.64         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.10         0.13         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 
       14.01        29.98        47.05        19.07        12.03         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        1.02         0.99         0.99        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        55.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       19.50        17.19         6.97        14.27        16.44         5.92 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
       14.76         0.62         6.58        14.47        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 
       19.53         3.02        22.29        17.06        59.54        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD 
        5.92        12.59        12.10         0.76        24.30        22.75 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        8.98         0.10         6.25        19.36        17.69        12.30 
TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        9.67        21.21         3.45        18.81         3.39         2.53 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           0.10            0.07 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         105.07           79.07 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         15.810          11.815 
[1] "0.1 - 105.1 (15.8)" "0.1 - 79.1 (11.8)" 
[1] "hr=" "3.9"
D12V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBXW7 MUTATED         0        0        2        2         3         1
  FBXW7 WILD-TYPE       1        6       21       21        18        30
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXW7 MUTATED           0          1          1          3        2
  FBXW7 WILD-TYPE         3         32         23         14       22
D12V3, multiclass
            clus
vv           FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               6
  STAGE IB               2              21
  STAGE II               2              21
  STAGE IIA              3              18
  STAGE IIB              1              30
  STAGE III              0               3
  STAGE IIIA             1              32
  STAGE IIIB             1              23
  STAGE IIIC             3              14
  STAGE IV               2              22
[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"
                 vv
clus              T1 T2 T3 T4
  FBXW7 MUTATED    0  8  3  6
  FBXW7 WILD-TYPE  7 58 87 43
D12V4, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  T1             0               7
  T2             8              58
  T3             3              87
  T4             6              43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FBXW7 MUTATED    5  6  3  3
  FBXW7 WILD-TYPE 65 57 32 38
D12V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0             5              65
  N1             6              57
  N2             3              32
  N3             3              38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1  MX
  FBXW7 MUTATED    18   1   0
  FBXW7 WILD-TYPE 177  15  10
D12V6, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  M0            18             177
  M1             1              15
  MX             0              10
[1] 3 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
  FBXW7 MUTATED     8  11
  FBXW7 WILD-TYPE  80 122
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      8   11
  FBXW7 WILD-TYPE   80  122
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE             8              80
  MALE              11             122
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  FBXW7 MUTATED                                       0
  FBXW7 WILD-TYPE                                    32
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FBXW7 MUTATED                                                       12
  FBXW7 WILD-TYPE                                                     96
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  FBXW7 MUTATED                                                                   4
  FBXW7 WILD-TYPE                                                                30
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  FBXW7 MUTATED                                                  2
  FBXW7 WILD-TYPE                                               24
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  FBXW7 MUTATED                                                           0
  FBXW7 WILD-TYPE                                                         1
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  FBXW7 MUTATED                                                          1
  FBXW7 WILD-TYPE                                                       13
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  FBXW7 MUTATED                                                           0
  FBXW7 WILD-TYPE                                                         4
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  FBXW7 MUTATED                                          0
  FBXW7 WILD-TYPE                                        1
D12V8, multiclass
                                                                   clus
vv                                                                  FBXW7 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              2
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  FBXW7 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          32
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         96
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               24
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, binary
                 cls
clus                0   1
  FBXW7 MUTATED     1  18
  FBXW7 WILD-TYPE   5 197
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      1   18
  FBXW7 WILD-TYPE    5  197
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO              1               5
  YES            18             197
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FBXW7 MUTATED    14   0   0   4
  FBXW7 WILD-TYPE 157   7  10  20
D12V10, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0            14             157
  R1             0               7
  R2             0              10
  RX             4              20
[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"
D12V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FBXW7 MUTATED       3                         0    12
  FBXW7 WILD-TYPE    41                         3   121
D12V12, multiclass
                           clus
vv                          FBXW7 MUTATED FBXW7 WILD-TYPE
  ASIAN                                 3              41
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                12             121
[1] 3 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 = CDH1 MUTATION ANALYSIS
D13V1, survival
                sevent
clus2              0   1
  CDH1 MUTATED    13   3
  CDH1 WILD-TYPE 117  62
  CDH1 MUTATED CDH1 WILD-TYPE 
            16            179 
  CDH1 MUTATED CDH1 WILD-TYPE 
             3             62 
$`CDH1 MUTATED`
TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6803 TCGA-BR-8370 
        7.43         9.57        34.68        32.78        31.20         3.32 
TCGA-BR-A4IV TCGA-CD-5799 TCGA-CD-5813 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-8572 
       13.51         3.25         0.39        19.13        18.61        16.80 
TCGA-D7-8574 TCGA-D7-A4YU TCGA-F1-6874 TCGA-IN-7808 
       17.19        16.44        14.47         3.45 

$`CDH1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 
        5.62        11.70         6.61         6.97         4.64        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         6.61        15.95        13.12        10.13 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68         7.00        39.12         0.82         0.62        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 
       13.22        16.14         8.98        21.11        30.90        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16        18.54        12.43         0.95         0.69 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 
        0.82         0.69         0.49        20.55         0.72         1.55 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        1.48         6.18        19.50         2.96         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        4.31         0.36        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        3.72         0.72         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        2.14        13.45         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4IY TCGA-BR-A4IZ 
       16.44         0.59         0.62        10.68        12.89         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI 
        0.72         0.53         0.66        19.36        13.51        13.64 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       11.57         2.83        13.15        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.10         0.10         0.13         0.10         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       12.03         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97         1.02         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.54        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YV 
       12.33        24.72        19.50         6.97        14.27         5.92 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
       14.76         0.62         6.58        72.23         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8243 
        3.02        22.29        17.06        59.54        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GN 
       12.59        12.10         0.76        24.30        22.75        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        8.98         0.10         6.25        19.36        17.69        12.30 
TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        9.67        21.21        18.81         3.39         2.53 

  CDH1 MUTATED CDH1 WILD-TYPE 
          0.39           0.07 
  CDH1 MUTATED CDH1 WILD-TYPE 
         34.68         105.07 
  CDH1 MUTATED CDH1 WILD-TYPE 
        15.455         11.700 
[1] "0.4 - 34.7 (15.5)"  "0.1 - 105.1 (11.7)"
[1] "hr=" "2.2"
D13V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDH1 MUTATED         0        0        2        3         3         1
  CDH1 WILD-TYPE       1        6       21       20        18        30
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDH1 MUTATED           1          1          3          0        2
  CDH1 WILD-TYPE         2         32         21         17       22
D13V3, multiclass
            clus
vv           CDH1 MUTATED CDH1 WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              6
  STAGE IB              2             21
  STAGE II              3             20
  STAGE IIA             3             18
  STAGE IIB             1             30
  STAGE III             1              2
  STAGE IIIA            1             32
  STAGE IIIB            3             21
  STAGE IIIC            0             17
  STAGE IV              2             22
[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"
                vv
clus             T1 T2 T3 T4
  CDH1 MUTATED    1  7  7  2
  CDH1 WILD-TYPE  6 59 83 47
D13V4, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  T1            1              6
  T2            7             59
  T3            7             83
  T4            2             47
[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
  CDH1 MUTATED    6  3  3  5
  CDH1 WILD-TYPE 64 60 32 36
D13V5, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  N0            6             64
  N1            3             60
  N2            3             32
  N3            5             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  CDH1 MUTATED    16   2   0
  CDH1 WILD-TYPE 179  14  10
D13V6, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  M0           16            179
  M1            2             14
  MX            0             10
[1] 3 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
  CDH1 MUTATED     6  12
  CDH1 WILD-TYPE  82 121
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED      6   12
  CDH1 WILD-TYPE   82  121
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  FEMALE            6             82
  MALE             12            121
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CDH1 MUTATED                                       7
  CDH1 WILD-TYPE                                    25
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDH1 MUTATED                                                        7
  CDH1 WILD-TYPE                                                    101
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CDH1 MUTATED                                                                   2
  CDH1 WILD-TYPE                                                                32
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CDH1 MUTATED                                                  1
  CDH1 WILD-TYPE                                               25
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  CDH1 MUTATED                                                           0
  CDH1 WILD-TYPE                                                         1
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CDH1 MUTATED                                                          1
  CDH1 WILD-TYPE                                                       13
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CDH1 MUTATED                                                           0
  CDH1 WILD-TYPE                                                         4
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CDH1 MUTATED                                          0
  CDH1 WILD-TYPE                                        1
D13V8, multiclass
                                                                   clus
vv                                                                  CDH1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             1
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  CDH1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         25
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       101
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              25
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, binary
                cls
clus               0   1
  CDH1 MUTATED     0  18
  CDH1 WILD-TYPE   6 197
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED      0   18
  CDH1 WILD-TYPE    6  197
     clus
vv    CDH1 MUTATED CDH1 WILD-TYPE
  NO             0              6
  YES           18            197
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CDH1 MUTATED    10   1   1   3
  CDH1 WILD-TYPE 161   6   9  21
D13V10, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  R0           10            161
  R1            1              6
  R2            1              9
  RX            3             21
[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"
D13V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDH1 MUTATED       3                         0    14
  CDH1 WILD-TYPE    41                         3   119
D13V12, multiclass
                           clus
vv                          CDH1 MUTATED CDH1 WILD-TYPE
  ASIAN                                3             41
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                               14            119
[1] 3 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 = HLA-B MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2               0   1
  HLA-B MUTATED     7   3
  HLA-B WILD-TYPE 123  62
  HLA-B MUTATED HLA-B WILD-TYPE 
             10             185 
  HLA-B MUTATED HLA-B WILD-TYPE 
              3              62 
$`HLA-B MUTATED`
TCGA-B7-5816 TCGA-BR-4280 TCGA-BR-6852 TCGA-BR-8589 TCGA-CD-8531 TCGA-CD-A4MJ 
        5.62         6.61        32.94        15.81         0.10         0.10 
TCGA-CG-5726 TCGA-CG-5728 TCGA-F1-6874 TCGA-HU-A4GQ 
       28.96        65.10        14.47         0.10 

$`HLA-B WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.70         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57        34.68        15.95        13.12 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       10.13        13.68         7.00        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        13.84        13.22        16.14         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01         0.69         0.16        18.54        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
        0.95         0.69         0.82         0.69         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8365 
        0.72         1.55         1.48         6.18        19.50         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        13.74         4.31         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26        15.85         3.72         0.72         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 
       20.22        12.79         2.14        13.45         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
       11.54        15.81        16.44         0.59         0.62        10.68 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.51        12.89         0.79         0.72         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 
       19.36        13.51        13.64        11.57         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8535 TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.13         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 
        0.99         6.02         0.99       105.07        12.03        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       19.50        17.19         6.97        14.27        16.44         5.92 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
       14.76         0.62         6.58        72.23         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8243 
        3.02        22.29        17.06        59.54        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GN 
       12.59        12.10         0.76        24.30        22.75        29.98 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        8.98         6.25        19.36        17.69        12.30         9.67 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  HLA-B MUTATED HLA-B WILD-TYPE 
           0.10            0.07 
  HLA-B MUTATED HLA-B WILD-TYPE 
          65.10          105.07 
  HLA-B MUTATED HLA-B WILD-TYPE 
          10.54           12.03 
[1] "0.1 - 65.1 (10.5)"  "0.1 - 105.1 (12.0)"
[1] "hr=" "1.2"
D14V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HLA-B MUTATED         0        1        3        0         1         0
  HLA-B WILD-TYPE       1        5       20       23        20        31
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HLA-B MUTATED           1          3          1          1        0
  HLA-B WILD-TYPE         2         30         23         16       24
D14V3, multiclass
            clus
vv           HLA-B MUTATED HLA-B WILD-TYPE
  STAGE I                0               1
  STAGE IA               1               5
  STAGE IB               3              20
  STAGE II               0              23
  STAGE IIA              1              20
  STAGE IIB              0              31
  STAGE III              1               2
  STAGE IIIA             3              30
  STAGE IIIB             1              23
  STAGE IIIC             1              16
  STAGE IV               0              24
[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"
                 vv
clus              T1 T2 T3 T4
  HLA-B MUTATED    1  4  3  4
  HLA-B WILD-TYPE  6 62 87 45
D14V4, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  T1             1               6
  T2             4              62
  T3             3              87
  T4             4              45
[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
  HLA-B MUTATED    7  3  1  0
  HLA-B WILD-TYPE 63 60 34 41
D14V5, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  N0             7              63
  N1             3              60
  N2             1              34
  N3             0              41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1  MX
  HLA-B MUTATED    11   0   1
  HLA-B WILD-TYPE 184  16   9
D14V6, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  M0            11             184
  M1             0              16
  MX             1               9
[1] 3 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
  HLA-B MUTATED     7   5
  HLA-B WILD-TYPE  81 128
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      7    5
  HLA-B WILD-TYPE   81  128
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  FEMALE             7              81
  MALE               5             128
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  HLA-B MUTATED                                       2
  HLA-B WILD-TYPE                                    30
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HLA-B MUTATED                                                        6
  HLA-B WILD-TYPE                                                    102
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  HLA-B MUTATED                                                                   3
  HLA-B WILD-TYPE                                                                31
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  HLA-B MUTATED                                                  1
  HLA-B WILD-TYPE                                               25
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  HLA-B MUTATED                                                           0
  HLA-B WILD-TYPE                                                         1
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  HLA-B MUTATED                                                          0
  HLA-B WILD-TYPE                                                       14
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  HLA-B MUTATED                                                           0
  HLA-B WILD-TYPE                                                         4
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  HLA-B MUTATED                                          0
  HLA-B WILD-TYPE                                        1
D14V8, multiclass
                                                                   clus
vv                                                                  HLA-B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              1
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  HLA-B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          30
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        102
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               25
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, binary
                 cls
clus                0   1
  HLA-B MUTATED     0  12
  HLA-B WILD-TYPE   6 203
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      0   12
  HLA-B WILD-TYPE    6  203
     clus
vv    HLA-B MUTATED HLA-B WILD-TYPE
  NO              0               6
  YES            12             203
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  HLA-B MUTATED     8   0   0   3
  HLA-B WILD-TYPE 163   7  10  21
D14V10, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  R0             8             163
  R1             0               7
  R2             0              10
  RX             3              21
[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"
D14V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HLA-B MUTATED       3                         0     7
  HLA-B WILD-TYPE    41                         3   126
D14V12, multiclass
                           clus
vv                          HLA-B MUTATED HLA-B WILD-TYPE
  ASIAN                                 3              41
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 7             126
[1] 3 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 = BCOR MUTATION ANALYSIS
D15V1, survival
                sevent
clus2              0   1
  BCOR MUTATED     7   7
  BCOR WILD-TYPE 123  58
  BCOR MUTATED BCOR WILD-TYPE 
            14            181 
  BCOR MUTATED BCOR WILD-TYPE 
             7             58 
$`BCOR MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6455 TCGA-BR-6707 TCGA-BR-7196 
        5.62         6.97         6.61        13.12        16.14        12.82 
TCGA-BR-7707 TCGA-BR-8366 TCGA-CG-4306 TCGA-CG-4455 TCGA-CG-5721 TCGA-CG-5724 
       23.93         0.95         1.02        12.03         6.02        12.03 
TCGA-HU-8604 TCGA-HU-A4GQ 
       12.10         0.10 

$`BCOR WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       11.70         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57        34.68        15.95        10.13        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
        7.00        39.12         0.82         0.62        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       13.22         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        15.42        28.01         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 
       18.54        12.43         0.95         0.69         0.82         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
        0.49        20.55         0.72         1.55         1.48         6.18 
TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       19.50         2.96        13.74         4.31         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       19.17        14.79         0.26        15.85         3.72         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         2.14        13.45 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         0.59 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.62        10.68        13.51        12.89         0.79         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-BR-A4QL 
        0.53         0.66        19.36        13.51        13.64        11.57 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 
        0.39         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.16         0.10         0.10         0.13         0.10         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 
        1.02         1.02         0.99         0.99       105.07        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT 
       24.72        16.80        19.50        17.19         6.97        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
       16.44         5.92        14.76         0.62         6.58        14.47 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         0.39        19.53         3.02        22.29        17.06 
TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8610 TCGA-HU-A4G2 
       59.54        26.47         5.92        12.59         0.76        24.30 
TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 
       22.75        29.98         8.98         6.25        19.36        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       12.30         9.67        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  BCOR MUTATED BCOR WILD-TYPE 
          0.10           0.07 
  BCOR MUTATED BCOR WILD-TYPE 
         23.93         105.07 
  BCOR MUTATED BCOR WILD-TYPE 
           9.5           12.3 
[1] "0.1 - 23.9 (9.5)"   "0.1 - 105.1 (12.3)"
[1] "hr=" "2"  
D15V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BCOR MUTATED         0        0        2        1         3         1
  BCOR WILD-TYPE       1        6       21       22        18        30
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCOR MUTATED           1          3          0          1        4
  BCOR WILD-TYPE         2         30         24         16       20
D15V3, multiclass
            clus
vv           BCOR MUTATED BCOR WILD-TYPE
  STAGE I               0              1
  STAGE IA              0              6
  STAGE IB              2             21
  STAGE II              1             22
  STAGE IIA             3             18
  STAGE IIB             1             30
  STAGE III             1              2
  STAGE IIIA            3             30
  STAGE IIIB            0             24
  STAGE IIIC            1             16
  STAGE IV              4             20
[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"
                vv
clus             T1 T2 T3 T4
  BCOR MUTATED    0  4  8  4
  BCOR WILD-TYPE  7 62 82 45
D15V4, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  T1            0              7
  T2            4             62
  T3            8             82
  T4            4             45
[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
  BCOR MUTATED    7  5  2  2
  BCOR WILD-TYPE 63 58 33 39
D15V5, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  N0            7             63
  N1            5             58
  N2            2             33
  N3            2             39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  BCOR MUTATED    12   3   1
  BCOR WILD-TYPE 183  13   9
D15V6, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  M0           12            183
  M1            3             13
  MX            1              9
[1] 3 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
  BCOR MUTATED     6  10
  BCOR WILD-TYPE  82 123
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED      6   10
  BCOR WILD-TYPE   82  123
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  FEMALE            6             82
  MALE             10            123
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  BCOR MUTATED                                       2
  BCOR WILD-TYPE                                    30
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BCOR MUTATED                                                        9
  BCOR WILD-TYPE                                                     99
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  BCOR MUTATED                                                                   2
  BCOR WILD-TYPE                                                                32
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  BCOR MUTATED                                                  2
  BCOR WILD-TYPE                                               24
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  BCOR MUTATED                                                           0
  BCOR WILD-TYPE                                                         1
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  BCOR MUTATED                                                          1
  BCOR WILD-TYPE                                                       13
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  BCOR MUTATED                                                           0
  BCOR WILD-TYPE                                                         4
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  BCOR MUTATED                                          0
  BCOR WILD-TYPE                                        1
D15V8, multiclass
                                                                   clus
vv                                                                  BCOR MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             2
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  BCOR WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         30
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        99
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              24
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, binary
                cls
clus               0   1
  BCOR MUTATED     0  16
  BCOR WILD-TYPE   6 199
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED      0   16
  BCOR WILD-TYPE    6  199
     clus
vv    BCOR MUTATED BCOR WILD-TYPE
  NO             0              6
  YES           16            199
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BCOR MUTATED    11   0   2   3
  BCOR WILD-TYPE 160   7   8  21
D15V10, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  R0           11            160
  R1            0              7
  R2            2              8
  RX            3             21
[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"
D15V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCOR MUTATED       2                         0     9
  BCOR WILD-TYPE    42                         3   124
D15V12, multiclass
                           clus
vv                          BCOR MUTATED BCOR WILD-TYPE
  ASIAN                                2             42
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                9            124
[1] 3 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 = C13ORF33 MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                  0   1
  C13ORF33 MUTATED     4   1
  C13ORF33 WILD-TYPE 126  64
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
                 5                190 
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
                 1                 64 
$`C13ORF33 MUTATED`
TCGA-BR-8361 TCGA-BR-8591 TCGA-BR-A4QL TCGA-HU-A4GQ TCGA-HU-A4H3 
       19.50        13.45        11.57         0.10        19.36 

$`C13ORF33 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62        32.78        13.84        13.22        16.14 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 
        0.16        18.54        12.43         0.95         0.69         0.82 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 
        0.69         0.49        20.55         0.72         1.55         1.48 
TCGA-BR-8360 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
        6.18         2.96         0.95        13.74         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        0.36        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        0.72         9.21        20.22        12.79        15.81         2.14 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         0.59 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.62        10.68        13.51        12.89         0.79         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5798 
        0.53         0.66        19.36        13.51        13.64         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.10         0.10         0.13         0.10         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       12.03         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97         1.02         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4Z0 
       17.19         6.97        14.27        16.44         5.92        14.76 
TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        0.62         6.58        14.47        72.23         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8243 
        3.02        22.29        17.06        59.54        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GN 
       12.59        12.10         0.76        24.30        22.75        29.98 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 
        8.98         6.25        17.69        12.30         9.67        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
              0.10               0.07 
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
             19.50             105.07 
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
             13.45              11.98 
[1] "0.1 - 19.5 (13.4)"  "0.1 - 105.1 (12.0)"
[1] "hr=" "1.7"
D16V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C13ORF33 MUTATED         0        0        0        1         0         0
  C13ORF33 WILD-TYPE       1        6       23       22        21        31
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C13ORF33 MUTATED           0          0          1          4        0
  C13ORF33 WILD-TYPE         3         33         23         13       24
D16V3, multiclass
            clus
vv           C13ORF33 MUTATED C13ORF33 WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  0                  6
  STAGE IB                  0                 23
  STAGE II                  1                 22
  STAGE IIA                 0                 21
  STAGE IIB                 0                 31
  STAGE III                 0                  3
  STAGE IIIA                0                 33
  STAGE IIIB                1                 23
  STAGE IIIC                4                 13
  STAGE IV                  0                 24
[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"
                    vv
clus                 T1 T2 T3 T4
  C13ORF33 MUTATED    0  1  1  4
  C13ORF33 WILD-TYPE  7 65 89 45
D16V4, multiclass
    clus
vv   C13ORF33 MUTATED C13ORF33 WILD-TYPE
  T1                0                  7
  T2                1                 65
  T3                1                 89
  T4                4                 45
[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
  C13ORF33 MUTATED    0  1  2  3
  C13ORF33 WILD-TYPE 70 62 33 38
D16V5, multiclass
    clus
vv   C13ORF33 MUTATED C13ORF33 WILD-TYPE
  N0                0                 70
  N1                1                 62
  N2                2                 33
  N3                3                 38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  C13ORF33 MUTATED     6   0   0
  C13ORF33 WILD-TYPE 189  16  10
D16V6, multiclass
    clus
vv   C13ORF33 MUTATED C13ORF33 WILD-TYPE
  M0                6                189
  M1                0                 16
  MX                0                 10
[1] 3 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
  C13ORF33 MUTATED     3   3
  C13ORF33 WILD-TYPE  85 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF33 MUTATED      3    3
  C13ORF33 WILD-TYPE   85  130
        clus
vv       C13ORF33 MUTATED C13ORF33 WILD-TYPE
  FEMALE                3                 85
  MALE                  3                130
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C13ORF33 MUTATED                                       1
  C13ORF33 WILD-TYPE                                    31
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C13ORF33 MUTATED                                                        3
  C13ORF33 WILD-TYPE                                                    105
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C13ORF33 MUTATED                                                                   0
  C13ORF33 WILD-TYPE                                                                34
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C13ORF33 MUTATED                                                  1
  C13ORF33 WILD-TYPE                                               25
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  C13ORF33 MUTATED                                                           0
  C13ORF33 WILD-TYPE                                                         1
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C13ORF33 MUTATED                                                          1
  C13ORF33 WILD-TYPE                                                       13
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C13ORF33 MUTATED                                                           0
  C13ORF33 WILD-TYPE                                                         4
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C13ORF33 MUTATED                                          0
  C13ORF33 WILD-TYPE                                        1
D16V8, multiclass
                                                                   clus
vv                                                                  C13ORF33 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 1
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  C13ORF33 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             31
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           105
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  25
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                          1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V9, binary
                    cls
clus                   0   1
  C13ORF33 MUTATED     1   5
  C13ORF33 WILD-TYPE   5 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF33 MUTATED      1    5
  C13ORF33 WILD-TYPE    5  210
     clus
vv    C13ORF33 MUTATED C13ORF33 WILD-TYPE
  NO                 1                  5
  YES                5                210
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  C13ORF33 MUTATED     6   0   0   0
  C13ORF33 WILD-TYPE 165   7  10  24
D16V10, multiclass
    clus
vv   C13ORF33 MUTATED C13ORF33 WILD-TYPE
  R0                6                165
  R1                0                  7
  R2                0                 10
  RX                0                 24
[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"
D16V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C13ORF33 MUTATED       2                         0     3
  C13ORF33 WILD-TYPE    42                         3   130
D16V12, multiclass
                           clus
vv                          C13ORF33 MUTATED C13ORF33 WILD-TYPE
  ASIAN                                    2                 42
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                    3                130
[1] 3 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(17) Variable = CIC MUTATION ANALYSIS
D17V1, survival
               sevent
clus2             0   1
  CIC MUTATED     6   6
  CIC WILD-TYPE 124  59
  CIC MUTATED CIC WILD-TYPE 
           12           183 
  CIC MUTATED CIC WILD-TYPE 
            6            59 
$`CIC MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8372 TCGA-BR-A4QL TCGA-CD-A4MI TCGA-CG-4465 
        6.97        30.90        19.17        11.57         0.10         9.01 
TCGA-CG-5733 TCGA-F1-6177 TCGA-F1-6874 TCGA-HJ-7597 TCGA-HU-A4GU TCGA-HU-A4H3 
       21.07         6.58        14.47        26.47         6.25        19.36 

$`CIC WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.12 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       10.13        13.68         7.00        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        13.84        13.22        16.14         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01         0.69         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 
       12.43         0.95         0.69         0.82         0.69         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 
       20.55         0.72         1.55         1.48         6.18        19.50 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
        2.96         0.95        13.74         4.31         3.32         0.36 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26        15.85         3.72         0.72         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 
       20.22        12.79        15.81         2.14        13.45         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        0.49        11.54        15.81        16.44         0.59         0.62 
TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 
       10.68        13.51        12.89         0.79         0.72         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 
        0.66        19.36        13.51        13.64         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.10         0.13         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 
       14.01        29.98        47.05        19.07        12.03        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        55.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU 
       16.80        19.50        17.19         6.97        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        5.92        14.76         0.62        72.23         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HU-8243 TCGA-HU-8245 
        3.02        22.29        17.06        59.54         5.92        12.59 
TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP 
       12.10         0.76        24.30        22.75        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-7808 
        0.10        17.69        12.30         9.67        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  CIC MUTATED CIC WILD-TYPE 
         0.10          0.07 
  CIC MUTATED CIC WILD-TYPE 
        30.90        105.07 
  CIC MUTATED CIC WILD-TYPE 
        13.02         12.03 
[1] "0.1 - 30.9 (13.0)"  "0.1 - 105.1 (12.0)"
[1] "hr=" "1.4"
D17V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CIC MUTATED         1        0        2        0         0         1
  CIC WILD-TYPE       0        6       21       23        21        30
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CIC MUTATED           0          2          2          2        2
  CIC WILD-TYPE         3         31         22         15       22
D17V3, multiclass
            clus
vv           CIC MUTATED CIC WILD-TYPE
  STAGE I              1             0
  STAGE IA             0             6
  STAGE IB             2            21
  STAGE II             0            23
  STAGE IIA            0            21
  STAGE IIB            1            30
  STAGE III            0             3
  STAGE IIIA           2            31
  STAGE IIIB           2            22
  STAGE IIIC           2            15
  STAGE IV             2            22
[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"
               vv
clus            T1 T2 T3 T4
  CIC MUTATED    1  4  5  4
  CIC WILD-TYPE  6 62 85 45
D17V4, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  T1           1             6
  T2           4            62
  T3           5            85
  T4           4            45
[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
  CIC MUTATED    2  4  2  4
  CIC WILD-TYPE 68 59 33 37
D17V5, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  N0           2            68
  N1           4            59
  N2           2            33
  N3           4            37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1  MX
  CIC MUTATED     9   1   4
  CIC WILD-TYPE 186  15   6
D17V6, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  M0           9           186
  M1           1            15
  MX           4             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
               cls
clus              0   1
  CIC MUTATED     8   6
  CIC WILD-TYPE  80 127
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED      8    6
  CIC WILD-TYPE   80  127
        clus
vv       CIC MUTATED CIC WILD-TYPE
  FEMALE           8            80
  MALE             6           127
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CIC MUTATED                                       3
  CIC WILD-TYPE                                    29
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CIC MUTATED                                                        8
  CIC WILD-TYPE                                                    100
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CIC MUTATED                                                                   2
  CIC WILD-TYPE                                                                32
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CIC MUTATED                                                  0
  CIC WILD-TYPE                                               26
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  CIC MUTATED                                                           0
  CIC WILD-TYPE                                                         1
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CIC MUTATED                                                          0
  CIC WILD-TYPE                                                       14
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CIC MUTATED                                                           0
  CIC WILD-TYPE                                                         4
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CIC MUTATED                                          1
  CIC WILD-TYPE                                        0
D17V8, multiclass
                                                                   clus
vv                                                                  CIC MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            0
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    1
                                                                   clus
vv                                                                  CIC WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        29
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      100
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             26
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V9, binary
               cls
clus              0   1
  CIC MUTATED     0  14
  CIC WILD-TYPE   6 201
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED      0   14
  CIC WILD-TYPE    6  201
     clus
vv    CIC MUTATED CIC WILD-TYPE
  NO            0             6
  YES          14           201
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CIC MUTATED     8   0   1   4
  CIC WILD-TYPE 163   7   9  20
D17V10, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  R0           8           163
  R1           0             7
  R2           1             9
  RX           4            20
[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"
D17V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CIC MUTATED       3                         1     8
  CIC WILD-TYPE    41                         2   125
D17V12, multiclass
                           clus
vv                          CIC MUTATED CIC WILD-TYPE
  ASIAN                               3            41
  BLACK OR AFRICAN AMERICAN           1             2
  WHITE                               8           125
[1] 3 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 = ACVR1B MUTATION ANALYSIS
D18V1, survival
                  sevent
clus2                0   1
  ACVR1B MUTATED     7   3
  ACVR1B WILD-TYPE 123  62
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              10              185 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
               3               62 
$`ACVR1B MUTATED`
TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-7703 TCGA-BR-8588 TCGA-BR-A4QL TCGA-CG-4305 
        6.97        32.78        24.76        12.79        11.57        15.95 
TCGA-CG-4477 TCGA-CG-5733 TCGA-F1-6177 TCGA-IN-7806 
       30.97        21.07         6.58        21.21 

$`ACVR1B WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        0.62        13.84        13.22        16.14         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 
       30.90        31.20        32.94        12.82         9.21        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01         0.69         0.16        18.54        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
        0.95         0.69         0.82         0.69         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8365 
        0.72         1.55         1.48         6.18        19.50         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        13.74         4.31         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26        15.85         3.72         0.72         9.21 
TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 
       20.22        15.81         2.14        13.45         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
       11.54        15.81        16.44         0.59         0.62        10.68 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.51        12.89         0.79         0.72         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       19.36        13.51        13.64         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.13         0.10         0.10        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        22.98         6.97         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        55.04         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       19.50        17.19         6.97        14.27        16.44         5.92 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
       14.76         0.62        14.47        72.23         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8243 
        3.02        22.29        17.06        59.54        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GN 
       12.59        12.10         0.76        24.30        22.75        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        8.98         0.10         6.25        19.36        17.69        12.30 
TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        9.67         3.45        18.81         3.39         2.53 

  ACVR1B MUTATED ACVR1B WILD-TYPE 
            6.58             0.07 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
           32.78           105.07 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
           18.51            11.70 
[1] "6.6 - 32.8 (18.5)"  "0.1 - 105.1 (11.7)"
[1] "hr=" "1.6"
D18V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ACVR1B MUTATED         1        1        1        1         1         2
  ACVR1B WILD-TYPE       0        5       22       22        20        29
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACVR1B MUTATED           0          2          1          0        0
  ACVR1B WILD-TYPE         3         31         23         17       24
D18V3, multiclass
            clus
vv           ACVR1B MUTATED ACVR1B WILD-TYPE
  STAGE I                 1                0
  STAGE IA                1                5
  STAGE IB                1               22
  STAGE II                1               22
  STAGE IIA               1               20
  STAGE IIB               2               29
  STAGE III               0                3
  STAGE IIIA              2               31
  STAGE IIIB              1               23
  STAGE IIIC              0               17
  STAGE IV                0               24
[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"
                  vv
clus               T1 T2 T3 T4
  ACVR1B MUTATED    2  3  4  1
  ACVR1B WILD-TYPE  5 63 86 48
D18V4, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  T1              2                5
  T2              3               63
  T3              4               86
  T4              1               48
[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
  ACVR1B MUTATED    4  4  1  1
  ACVR1B WILD-TYPE 66 59 34 40
D18V5, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  N0              4               66
  N1              4               59
  N2              1               34
  N3              1               40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1  MX
  ACVR1B MUTATED     8   0   2
  ACVR1B WILD-TYPE 187  16   8
D18V6, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  M0              8              187
  M1              0               16
  MX              2                8
[1] 3 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
  ACVR1B MUTATED     5   5
  ACVR1B WILD-TYPE  83 128
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED      5    5
  ACVR1B WILD-TYPE   83  128
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  FEMALE              5               83
  MALE                5              128
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ACVR1B MUTATED                                       1
  ACVR1B WILD-TYPE                                    31
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ACVR1B MUTATED                                                        6
  ACVR1B WILD-TYPE                                                    102
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ACVR1B MUTATED                                                                   2
  ACVR1B WILD-TYPE                                                                32
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ACVR1B MUTATED                                                  0
  ACVR1B WILD-TYPE                                               26
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  ACVR1B MUTATED                                                           0
  ACVR1B WILD-TYPE                                                         1
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ACVR1B MUTATED                                                          0
  ACVR1B WILD-TYPE                                                       14
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ACVR1B MUTATED                                                           1
  ACVR1B WILD-TYPE                                                         3
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ACVR1B MUTATED                                          0
  ACVR1B WILD-TYPE                                        1
D18V8, multiclass
                                                                   clus
vv                                                                  ACVR1B MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ACVR1B WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           31
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         102
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                26
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V9, binary
                  cls
clus                 0   1
  ACVR1B MUTATED     0  10
  ACVR1B WILD-TYPE   6 205
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED      0   10
  ACVR1B WILD-TYPE    6  205
     clus
vv    ACVR1B MUTATED ACVR1B WILD-TYPE
  NO               0                6
  YES             10              205
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ACVR1B MUTATED     9   0   0   1
  ACVR1B WILD-TYPE 162   7  10  23
D18V10, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  R0              9              162
  R1              0                7
  R2              0               10
  RX              1               23
[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"
D18V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACVR1B MUTATED       0                         1     6
  ACVR1B WILD-TYPE    44                         2   127
D18V12, multiclass
                           clus
vv                          ACVR1B MUTATED ACVR1B WILD-TYPE
  ASIAN                                  0               44
  BLACK OR AFRICAN AMERICAN              1                2
  WHITE                                  6              127
[1] 3 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 = ZBTB20 MUTATION ANALYSIS
D19V1, survival
                  sevent
clus2                0   1
  ZBTB20 MUTATED     8   6
  ZBTB20 WILD-TYPE 122  59
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              14              181 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
               6               59 
$`ZBTB20 MUTATED`
TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8382 TCGA-BR-8588 
       30.90         6.61        24.76        23.93        15.85        12.79 
TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5733 
       13.45        11.57         9.01         6.02        28.96        21.07 
TCGA-F1-6177 TCGA-HU-A4GU 
        6.58         6.25 

$`ZBTB20 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       18.35         6.18         9.57        34.68        15.95        13.12 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       10.13        13.68         7.00        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        13.84        13.22        16.14         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7715 
       30.90        31.20        32.94        12.82         9.21        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01         0.69         0.16        18.54        12.43         0.95 
TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        0.69         0.82         0.69         0.49        20.55         0.72 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8366 
        1.55         1.48         6.18        19.50         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       13.74         4.31         3.32         0.36        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 
        0.26         3.72         0.72         9.21        20.22        15.81 
TCGA-BR-8590 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        2.14         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        0.59         0.62        10.68        13.51        12.89         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI 
        0.72         0.53         0.66        19.36        13.51        13.64 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 
        0.39         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.16         0.10         0.10         0.13         0.10         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       19.07        12.03        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       12.03        79.07        65.10         4.01        55.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT 
       24.72        16.80        19.50        17.19         6.97        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 
       16.44         5.92        14.76         0.62        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39        19.53         3.02        22.29        17.06        59.54 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 
       26.47         5.92        12.59        12.10         0.76        24.30 
TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-HU-A4H4 
       22.75        29.98         8.98         0.10        19.36        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       12.30         9.67        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
            6.02             0.07 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
           30.90           105.07 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
           13.12            11.93 
[1] "6.0 - 30.9 (13.1)"  "0.1 - 105.1 (11.9)"
[1] "hr=" "1.1"
D19V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZBTB20 MUTATED         1        2        2        0         0         2
  ZBTB20 WILD-TYPE       0        4       21       23        21        29
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB20 MUTATED           1          1          1          2        3
  ZBTB20 WILD-TYPE         2         32         23         15       21
D19V3, multiclass
            clus
vv           ZBTB20 MUTATED ZBTB20 WILD-TYPE
  STAGE I                 1                0
  STAGE IA                2                4
  STAGE IB                2               21
  STAGE II                0               23
  STAGE IIA               0               21
  STAGE IIB               2               29
  STAGE III               1                2
  STAGE IIIA              1               32
  STAGE IIIB              1               23
  STAGE IIIC              2               15
  STAGE IV                3               21
[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"
                  vv
clus               T1 T2 T3 T4
  ZBTB20 MUTATED    3  5  2  6
  ZBTB20 WILD-TYPE  4 61 88 43
D19V4, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  T1              3                4
  T2              5               61
  T3              2               88
  T4              6               43
[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
  ZBTB20 MUTATED    5  4  2  4
  ZBTB20 WILD-TYPE 65 59 33 37
D19V5, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  N0              5               65
  N1              4               59
  N2              2               33
  N3              4               37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1  MX
  ZBTB20 MUTATED    14   1   1
  ZBTB20 WILD-TYPE 181  15   9
D19V6, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  M0             14              181
  M1              1               15
  MX              1                9
[1] 3 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
  ZBTB20 MUTATED     9   7
  ZBTB20 WILD-TYPE  79 126
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED      9    7
  ZBTB20 WILD-TYPE   79  126
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  FEMALE              9               79
  MALE                7              126
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ZBTB20 MUTATED                                       2
  ZBTB20 WILD-TYPE                                    30
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZBTB20 MUTATED                                                        9
  ZBTB20 WILD-TYPE                                                     99
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ZBTB20 MUTATED                                                                   4
  ZBTB20 WILD-TYPE                                                                30
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ZBTB20 MUTATED                                                  0
  ZBTB20 WILD-TYPE                                               26
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  ZBTB20 MUTATED                                                           0
  ZBTB20 WILD-TYPE                                                         1
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ZBTB20 MUTATED                                                          0
  ZBTB20 WILD-TYPE                                                       14
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ZBTB20 MUTATED                                                           1
  ZBTB20 WILD-TYPE                                                         3
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ZBTB20 MUTATED                                          0
  ZBTB20 WILD-TYPE                                        1
D19V8, multiclass
                                                                   clus
vv                                                                  ZBTB20 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               0
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  ZBTB20 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           30
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          99
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                26
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V9, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED     0  16
  ZBTB20 WILD-TYPE   6 199
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED      0   16
  ZBTB20 WILD-TYPE    6  199
     clus
vv    ZBTB20 MUTATED ZBTB20 WILD-TYPE
  NO               0                6
  YES             16              199
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZBTB20 MUTATED    12   0   1   3
  ZBTB20 WILD-TYPE 159   7   9  21
D19V10, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  R0             12              159
  R1              0                7
  R2              1                9
  RX              3               21
[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"
D19V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZBTB20 MUTATED       1                         1     9
  ZBTB20 WILD-TYPE    43                         2   124
D19V12, multiclass
                           clus
vv                          ZBTB20 MUTATED ZBTB20 WILD-TYPE
  ASIAN                                  1               43
  BLACK OR AFRICAN AMERICAN              1                2
  WHITE                                  9              124
[1] 3 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 = MVK MUTATION ANALYSIS
D20V1, survival
               sevent
clus2             0   1
  MVK MUTATED     3   3
  MVK WILD-TYPE 127  62
  MVK MUTATED MVK WILD-TYPE 
            6           189 
  MVK MUTATED MVK WILD-TYPE 
            3            62 
$`MVK MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-8361 TCGA-BR-8589 TCGA-CD-A4MI TCGA-CG-5733 
        6.97         6.61        19.50        15.81         0.10        21.07 

$`MVK WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         9.57        34.68        15.95        13.12 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       10.13        13.68         7.00        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        13.84        13.22        16.14         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01         0.69         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 
       12.43         0.95         0.69         0.82         0.69         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8365 
       20.55         0.72         1.55         1.48         6.18         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        13.74         4.31         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 
       14.79         0.26        15.85         3.72         0.72         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 
       20.22        12.79         2.14        13.45         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
       11.54        15.81        16.44         0.59         0.62        10.68 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.51        12.89         0.79         0.72         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 
       19.36        13.51        13.64        11.57         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.10         0.13         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 
       14.01        29.98        47.05        19.07        12.03         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       28.96        79.07        65.10         4.01        55.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT 
       24.72        16.80        19.50        17.19         6.97        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
       16.44         5.92        14.76         0.62         6.58        14.47 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         0.39        19.53         3.02        22.29        17.06 
TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 
       59.54        26.47         5.92        12.59        12.10         0.76 
TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       24.30        22.75        29.98         8.98         0.10         6.25 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-7808 
       19.36        17.69        12.30         9.67        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       18.81         3.39         2.53 

  MVK MUTATED MVK WILD-TYPE 
         0.10          0.07 
  MVK MUTATED MVK WILD-TYPE 
        21.07        105.07 
  MVK MUTATED MVK WILD-TYPE 
        11.39         12.03 
[1] "0.1 - 21.1 (11.4)"  "0.1 - 105.1 (12.0)"
[1] "hr=" "1.6"
D20V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MVK MUTATED         0        0        1        0         0         0
  MVK WILD-TYPE       1        6       22       23        21        31
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MVK MUTATED           1          2          2          1        0
  MVK WILD-TYPE         2         31         22         16       24
D20V3, multiclass
            clus
vv           MVK MUTATED MVK WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             6
  STAGE IB             1            22
  STAGE II             0            23
  STAGE IIA            0            21
  STAGE IIB            0            31
  STAGE III            1             2
  STAGE IIIA           2            31
  STAGE IIIB           2            22
  STAGE IIIC           1            16
  STAGE IV             0            24
[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"
               vv
clus            T1 T2 T3 T4
  MVK MUTATED    1  3  2  2
  MVK WILD-TYPE  6 63 88 47
D20V4, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  T1           1             6
  T2           3            63
  T3           2            88
  T4           2            47
[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
  MVK MUTATED    1  4  2  0
  MVK WILD-TYPE 69 59 33 41
D20V5, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  N0           1            69
  N1           4            59
  N2           2            33
  N3           0            41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1  MX
  MVK MUTATED     7   0   1
  MVK WILD-TYPE 188  16   9
D20V6, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  M0           7           188
  M1           0            16
  MX           1             9
[1] 3 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
  MVK MUTATED     4   4
  MVK WILD-TYPE  84 129
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED      4    4
  MVK WILD-TYPE   84  129
        clus
vv       MVK MUTATED MVK WILD-TYPE
  FEMALE           4            84
  MALE             4           129
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MVK MUTATED                                       0
  MVK WILD-TYPE                                    32
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MVK MUTATED                                                        6
  MVK WILD-TYPE                                                    102
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MVK MUTATED                                                                   2
  MVK WILD-TYPE                                                                32
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MVK MUTATED                                                  0
  MVK WILD-TYPE                                               26
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  MVK MUTATED                                                           0
  MVK WILD-TYPE                                                         1
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MVK MUTATED                                                          0
  MVK WILD-TYPE                                                       14
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MVK MUTATED                                                           0
  MVK WILD-TYPE                                                         4
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MVK MUTATED                                          0
  MVK WILD-TYPE                                        1
D20V8, multiclass
                                                                   clus
vv                                                                  MVK MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            0
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  MVK WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        32
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      102
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             26
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, binary
               cls
clus              0   1
  MVK MUTATED     0   8
  MVK WILD-TYPE   6 207
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED      0    8
  MVK WILD-TYPE    6  207
     clus
vv    MVK MUTATED MVK WILD-TYPE
  NO            0             6
  YES           8           207
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  MVK MUTATED     4   0   0   3
  MVK WILD-TYPE 167   7  10  21
D20V10, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  R0           4           167
  R1           0             7
  R2           0            10
  RX           3            21
[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"
D20V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MVK MUTATED       1                         0     5
  MVK WILD-TYPE    43                         3   128
D20V12, multiclass
                           clus
vv                          MVK MUTATED MVK WILD-TYPE
  ASIAN                               1            43
  BLACK OR AFRICAN AMERICAN           0             3
  WHITE                               5           128
[1] 3 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(21) Variable = ERBB2 MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  ERBB2 MUTATED     6   3
  ERBB2 WILD-TYPE 124  62
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              9             186 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              3              62 
$`ERBB2 MUTATED`
TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7957 TCGA-BR-8588 TCGA-CG-4466 
       32.78        30.90        32.94         0.69        12.79        18.97 
TCGA-CG-4469 TCGA-CG-5730 TCGA-IN-8663 
        7.07         4.01         3.39 

$`ERBB2 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        0.82         0.62        13.84        13.22        16.14         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       21.11        31.20        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01         0.69         0.16        18.54        12.43 
TCGA-BR-7901 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        0.95         0.82         0.69         0.49        20.55         0.72 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8366 
        1.55         1.48         6.18        19.50         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       13.74         4.31         3.32         0.36        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         3.72         0.72         9.21        20.22 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       15.81         2.14        13.45         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4IV 
       15.81        16.44         0.59         0.62        10.68        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
       12.89         0.79         0.72         0.53         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.51        13.64        11.57         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.13         0.10         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 
       14.01        29.98        47.05        19.07        12.03         9.01 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       19.50        17.19         6.97        14.27        16.44         5.92 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
       14.76         0.62         6.58        14.47        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 
       19.53         3.02        22.29        17.06        59.54        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD 
        5.92        12.59        12.10         0.76        24.30        22.75 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 
       29.98         8.98         0.10         6.25        19.36        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IP-7968 
       12.30         9.67        21.21         3.45        18.81         2.53 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
           0.69            0.07 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          32.94          105.07 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          12.79           11.98 
[1] "0.7 - 32.9 (12.8)"  "0.1 - 105.1 (12.0)"
[1] "hr=" "1.2"
D21V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERBB2 MUTATED         0        0        1        1         2         2
  ERBB2 WILD-TYPE       1        6       22       22        19        29
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERBB2 MUTATED           0          1          0          0        3
  ERBB2 WILD-TYPE         3         32         24         17       21
D21V3, multiclass
            clus
vv           ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I                0               1
  STAGE IA               0               6
  STAGE IB               1              22
  STAGE II               1              22
  STAGE IIA              2              19
  STAGE IIB              2              29
  STAGE III              0               3
  STAGE IIIA             1              32
  STAGE IIIB             0              24
  STAGE IIIC             0              17
  STAGE IV               3              21
[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"
                 vv
clus              T1 T2 T3 T4
  ERBB2 MUTATED    0  4  5  1
  ERBB2 WILD-TYPE  7 62 85 48
D21V4, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  T1             0               7
  T2             4              62
  T3             5              85
  T4             1              48
[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  2  2  2
  ERBB2 WILD-TYPE 66 61 33 39
D21V5, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  N0             4              66
  N1             2              61
  N2             2              33
  N3             2              39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1  MX
  ERBB2 MUTATED     9   2   0
  ERBB2 WILD-TYPE 186  14  10
D21V6, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  M0             9             186
  M1             2              14
  MX             0              10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                 cls
clus                0   1
  ERBB2 MUTATED     7   4
  ERBB2 WILD-TYPE  81 129
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      7    4
  ERBB2 WILD-TYPE   81  129
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE             7              81
  MALE               4             129
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  ERBB2 MUTATED                                       0
  ERBB2 WILD-TYPE                                    32
                 vv
clus              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ERBB2 MUTATED                                                        6
  ERBB2 WILD-TYPE                                                    102
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  ERBB2 MUTATED                                                                   4
  ERBB2 WILD-TYPE                                                                30
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  ERBB2 MUTATED                                                  0
  ERBB2 WILD-TYPE                                               26
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  ERBB2 MUTATED                                                           0
  ERBB2 WILD-TYPE                                                         1
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  ERBB2 MUTATED                                                          1
  ERBB2 WILD-TYPE                                                       13
                 vv
clus              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  ERBB2 MUTATED                                                           0
  ERBB2 WILD-TYPE                                                         4
                 vv
clus              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  ERBB2 MUTATED                                          0
  ERBB2 WILD-TYPE                                        1
D21V8, multiclass
                                                                   clus
vv                                                                  ERBB2 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              0
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      0
                                                                   clus
vv                                                                  ERBB2 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          32
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        102
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               26
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V9, binary
                 cls
clus                0   1
  ERBB2 MUTATED     1  10
  ERBB2 WILD-TYPE   5 205
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      1   10
  ERBB2 WILD-TYPE    5  205
     clus
vv    ERBB2 MUTATED ERBB2 WILD-TYPE
  NO              1               5
  YES            10             205
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ERBB2 MUTATED     8   1   1   1
  ERBB2 WILD-TYPE 163   6   9  23
D21V10, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  R0             8             163
  R1             1               6
  R2             1               9
  RX             1              23
[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"
D21V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERBB2 MUTATED       0                         0     7
  ERBB2 WILD-TYPE    44                         3   126
D21V12, multiclass
                           clus
vv                          ERBB2 MUTATED ERBB2 WILD-TYPE
  ASIAN                                 0              44
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 7             126
[1] 3 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(22) Variable = CR1 MUTATION ANALYSIS
D22V1, survival
               sevent
clus2             0   1
  CR1 MUTATED    13   3
  CR1 WILD-TYPE 117  62
  CR1 MUTATED CR1 WILD-TYPE 
           16           179 
  CR1 MUTATED CR1 WILD-TYPE 
            3            62 
$`CR1 MUTATED`
TCGA-BR-4183 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-7851 
        6.61         6.61        34.68        30.90        23.93        12.43 
TCGA-BR-8081 TCGA-BR-8382 TCGA-BR-8589 TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4436 
       20.55        15.85        15.81         0.10        15.95         7.99 
TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-6527 TCGA-D7-A4YU 
        6.02        65.10        10.26        16.44 

$`CR1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         6.18         9.57        15.95        13.12        10.13 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68         7.00        39.12         0.82         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       13.84        13.22        16.14         8.98        21.11        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 
       32.94        12.82         9.21        24.76        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 
        0.69         0.16        18.54         0.95         0.69         0.82 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
        0.69         0.49         0.72         1.55         1.48         6.18 
TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       19.50         2.96         0.95        13.74         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8484 
        0.36        19.17        14.79         0.26         3.72         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 
        9.21        20.22        12.79         2.14        13.45         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        0.49        11.54        15.81        16.44         0.59         0.62 
TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 
       10.68        13.51        12.89         0.79         0.72         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 
        0.66        19.36        13.51        13.64        11.57         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
        0.10         0.10         0.13         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        0.99         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-EQ-5647 
       17.19         6.97        14.27         5.92        14.76         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        6.58        14.47        72.23         0.39        19.53         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       22.29        17.06        59.54        26.47         5.92        12.59 
TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP 
       12.10         0.76        24.30        22.75        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.10         6.25        19.36        17.69        12.30         9.67 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  CR1 MUTATED CR1 WILD-TYPE 
         0.10          0.07 
  CR1 MUTATED CR1 WILD-TYPE 
        65.10        105.07 
  CR1 MUTATED CR1 WILD-TYPE 
        15.83         11.70 
[1] "0.1 - 65.1 (15.8)"  "0.1 - 105.1 (11.7)"
[1] "hr=" "2.4"
D22V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CR1 MUTATED         0        0        5        3         1         2
  CR1 WILD-TYPE       1        6       18       20        20        29
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CR1 MUTATED           1          3          2          1        1
  CR1 WILD-TYPE         2         30         22         16       23
D22V3, multiclass
            clus
vv           CR1 MUTATED CR1 WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             6
  STAGE IB             5            18
  STAGE II             3            20
  STAGE IIA            1            20
  STAGE IIB            2            29
  STAGE III            1             2
  STAGE IIIA           3            30
  STAGE IIIB           2            22
  STAGE IIIC           1            16
  STAGE IV             1            23
[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"
               vv
clus            T1 T2 T3 T4
  CR1 MUTATED    0  9  4  6
  CR1 WILD-TYPE  7 57 86 43
D22V4, multiclass
    clus
vv   CR1 MUTATED CR1 WILD-TYPE
  T1           0             7
  T2           9            57
  T3           4            86
  T4           6            43
[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
  CR1 MUTATED    9  7  1  2
  CR1 WILD-TYPE 61 56 34 39
D22V5, multiclass
    clus
vv   CR1 MUTATED CR1 WILD-TYPE
  N0           9            61
  N1           7            56
  N2           1            34
  N3           2            39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1  MX
  CR1 MUTATED    20   0   0
  CR1 WILD-TYPE 175  16  10
D22V6, multiclass
    clus
vv   CR1 MUTATED CR1 WILD-TYPE
  M0          20           175
  M1           0            16
  MX           0            10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
               cls
clus              0   1
  CR1 MUTATED     9  11
  CR1 WILD-TYPE  79 122
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR1 MUTATED      9   11
  CR1 WILD-TYPE   79  122
        clus
vv       CR1 MUTATED CR1 WILD-TYPE
  FEMALE           9            79
  MALE            11           122
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CR1 MUTATED                                       0
  CR1 WILD-TYPE                                    32
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CR1 MUTATED                                                       12
  CR1 WILD-TYPE                                                     96
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CR1 MUTATED                                                                   5
  CR1 WILD-TYPE                                                                29
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CR1 MUTATED                                                  1
  CR1 WILD-TYPE                                               25
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  CR1 MUTATED                                                           1
  CR1 WILD-TYPE                                                         0
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CR1 MUTATED                                                          1
  CR1 WILD-TYPE                                                       13
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CR1 MUTATED                                                           0
  CR1 WILD-TYPE                                                         4
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CR1 MUTATED                                          0
  CR1 WILD-TYPE                                        1
D22V8, multiclass
                                                                   clus
vv                                                                  CR1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                     12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            1
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                   1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  CR1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        32
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                       96
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             25
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V9, binary
               cls
clus              0   1
  CR1 MUTATED     2  18
  CR1 WILD-TYPE   4 197
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR1 MUTATED      2   18
  CR1 WILD-TYPE    4  197
     clus
vv    CR1 MUTATED CR1 WILD-TYPE
  NO            2             4
  YES          18           197
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  CR1 MUTATED    15   0   0   4
  CR1 WILD-TYPE 156   7  10  20
D22V10, multiclass
    clus
vv   CR1 MUTATED CR1 WILD-TYPE
  R0          15           156
  R1           0             7
  R2           0            10
  RX           4            20
[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"
D22V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CR1 MUTATED       1                         0    13
  CR1 WILD-TYPE    43                         3   120
D22V12, multiclass
                           clus
vv                          CR1 MUTATED CR1 WILD-TYPE
  ASIAN                               1            43
  BLACK OR AFRICAN AMERICAN           0             3
  WHITE                              13           120
[1] 3 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(23) Variable = C1R MUTATION ANALYSIS
D23V1, survival
               sevent
clus2             0   1
  C1R MUTATED     2   0
  C1R WILD-TYPE 128  65
  C1R MUTATED C1R WILD-TYPE 
            2           193 
  C1R MUTATED C1R WILD-TYPE 
            0            65 
$`C1R MUTATED`
TCGA-BR-A4QL TCGA-CG-5723 
       11.57       105.07 

$`C1R WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62        32.78        13.84        13.22        16.14 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 
        0.16        18.54        12.43         0.95         0.69         0.82 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 
        0.69         0.49        20.55         0.72         1.55         1.48 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        6.18        19.50         2.96         0.95        13.74         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32         0.36        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        3.72         0.72         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        2.14        13.45         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY 
       16.44         0.59         0.62        10.68        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.79         0.72         0.53         0.66        19.36        13.51 
TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       13.64         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
        0.07         0.39         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A4MI 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       47.05        19.07        12.03         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       19.50        17.19         6.97        14.27        16.44         5.92 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
       14.76         0.62         6.58        14.47        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 
       19.53         3.02        22.29        17.06        59.54        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD 
        5.92        12.59        12.10         0.76        24.30        22.75 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 
       29.98         8.98         0.10         6.25        19.36        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       12.30         9.67        21.21         3.45        18.81         3.39 
TCGA-IP-7968 
        2.53 

  C1R MUTATED C1R WILD-TYPE 
        11.57          0.07 
  C1R MUTATED C1R WILD-TYPE 
       105.07         79.07 
  C1R MUTATED C1R WILD-TYPE 
        58.32         12.03 
[1] "11.6 - 105.1 (58.3)" "0.1 - 79.1 (12.0)"  
[1] "Remove cluster labels:" "C1R MUTATED"           
D23V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C1R MUTATED         0        0        1        1         0         0
  C1R WILD-TYPE       1        6       22       22        21        31
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1R MUTATED           0          0          1          0        0
  C1R WILD-TYPE         3         33         23         17       24
D23V3, multiclass
            clus
vv           C1R MUTATED C1R WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             6
  STAGE IB             1            22
  STAGE II             1            22
  STAGE IIA            0            21
  STAGE IIB            0            31
  STAGE III            0             3
  STAGE IIIA           0            33
  STAGE IIIB           1            23
  STAGE IIIC           0            17
  STAGE IV             0            24
[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"
               vv
clus            T1 T2 T3 T4
  C1R MUTATED    0  2  1  0
  C1R WILD-TYPE  7 64 89 49
D23V4, multiclass
    clus
vv   C1R MUTATED C1R WILD-TYPE
  T1           0             7
  T2           2            64
  T3           1            89
  T4           0            49
[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
  C1R MUTATED    1  1  0  1
  C1R WILD-TYPE 69 62 35 40
D23V5, multiclass
    clus
vv   C1R MUTATED C1R WILD-TYPE
  N0           1            69
  N1           1            62
  N2           0            35
  N3           1            40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1  MX
  C1R MUTATED     3   0   0
  C1R WILD-TYPE 192  16  10
D23V6, multiclass
    clus
vv   C1R MUTATED C1R WILD-TYPE
  M0           3           192
  M1           0            16
  MX           0            10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
               cls
clus              0   1
  C1R MUTATED     1   2
  C1R WILD-TYPE  87 131
[1] "tbl2"
               cls
clus            [,1] [,2]
  C1R MUTATED      1    2
  C1R WILD-TYPE   87  131
        clus
vv       C1R MUTATED C1R WILD-TYPE
  FEMALE           1            87
  MALE             2           131
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  C1R MUTATED                                       0
  C1R WILD-TYPE                                    32
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C1R MUTATED                                                        2
  C1R WILD-TYPE                                                    106
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  C1R MUTATED                                                                   1
  C1R WILD-TYPE                                                                33
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  C1R MUTATED                                                  0
  C1R WILD-TYPE                                               26
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  C1R MUTATED                                                           0
  C1R WILD-TYPE                                                         1
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  C1R MUTATED                                                          0
  C1R WILD-TYPE                                                       14
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  C1R MUTATED                                                           0
  C1R WILD-TYPE                                                         4
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  C1R MUTATED                                          0
  C1R WILD-TYPE                                        1
D23V8, multiclass
                                                                   clus
vv                                                                  C1R MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            0
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  C1R WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        32
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      106
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             26
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V9, binary
               cls
clus              0   1
  C1R MUTATED     0   3
  C1R WILD-TYPE   6 212
[1] "tbl2"
               cls
clus            [,1] [,2]
  C1R MUTATED      0    3
  C1R WILD-TYPE    6  212
     clus
vv    C1R MUTATED C1R WILD-TYPE
  NO            0             6
  YES           3           212
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  C1R MUTATED     3   0   0   0
  C1R WILD-TYPE 168   7  10  24
D23V10, multiclass
    clus
vv   C1R MUTATED C1R WILD-TYPE
  R0           3           168
  R1           0             7
  R2           0            10
  RX           0            24
[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"
D23V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C1R MUTATED       0                         0     1
  C1R WILD-TYPE    44                         3   132
D23V12, multiclass
[1] "Remove cluster labels:" "C1R MUTATED"           
clus
  C1R MUTATED C1R WILD-TYPE 
            1           179 
   TCGA-B7-5816    TCGA-B7-5818    TCGA-BR-4183    TCGA-BR-4184    TCGA-BR-4187 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-4188    TCGA-BR-4191    TCGA-BR-4201    TCGA-BR-4253    TCGA-BR-4255 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-4256    TCGA-BR-4257    TCGA-BR-4267    TCGA-BR-4279    TCGA-BR-4280 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-4292    TCGA-BR-4294    TCGA-BR-4357    TCGA-BR-4361    TCGA-BR-4362 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-4363    TCGA-BR-4366    TCGA-BR-4368    TCGA-BR-4369    TCGA-BR-4370 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-4371    TCGA-BR-6452    TCGA-BR-6453    TCGA-BR-6454    TCGA-BR-6455 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-6456    TCGA-BR-6457    TCGA-BR-6458    TCGA-BR-6563    TCGA-BR-6564 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-6565    TCGA-BR-6566    TCGA-BR-6705    TCGA-BR-6706    TCGA-BR-6707 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-6710    TCGA-BR-6801    TCGA-BR-6802    TCGA-BR-6803    TCGA-BR-6852 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-7196    TCGA-BR-7197    TCGA-BR-7703    TCGA-BR-7707    TCGA-BR-7715 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-7716    TCGA-BR-7717    TCGA-BR-7722    TCGA-BR-7723    TCGA-BR-7851 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-7901    TCGA-BR-7957    TCGA-BR-8059    TCGA-BR-8077    TCGA-BR-8080 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-8081    TCGA-BR-8284    TCGA-BR-8295    TCGA-BR-8296    TCGA-BR-8360 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-8361    TCGA-BR-8365    TCGA-BR-8366    TCGA-BR-8367    TCGA-BR-8368 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-8370    TCGA-BR-8371    TCGA-BR-8372    TCGA-BR-8373    TCGA-BR-8381 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-8382    TCGA-BR-8384    TCGA-BR-8484    TCGA-BR-8485    TCGA-BR-8486 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-8588    TCGA-BR-8589    TCGA-BR-8590    TCGA-BR-8591    TCGA-BR-8676 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-8677    TCGA-BR-8678    TCGA-BR-8679    TCGA-BR-8680    TCGA-BR-8682 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-8683    TCGA-BR-8687    TCGA-BR-8690    TCGA-BR-A4IV    TCGA-BR-A4IY 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-A4IZ    TCGA-BR-A4J1    TCGA-BR-A4J4    TCGA-BR-A4J6    TCGA-BR-A4J7 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-BR-A4J8    TCGA-BR-A4QI    TCGA-CD-5798    TCGA-CD-5799    TCGA-CD-5800 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-CD-5801    TCGA-CD-5802    TCGA-CD-5803    TCGA-CD-5804    TCGA-CD-5813 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-CD-8524    TCGA-CD-8525    TCGA-CD-8526    TCGA-CD-8528    TCGA-CD-8529 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-CD-8530    TCGA-CD-8531    TCGA-CD-8532    TCGA-CD-8534    TCGA-CD-8535 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-CD-A4MI    TCGA-CD-A4MJ    TCGA-D7-5577    TCGA-D7-5578    TCGA-D7-5579 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-D7-6518    TCGA-D7-6519    TCGA-D7-6520    TCGA-D7-6521    TCGA-D7-6522 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-D7-6524    TCGA-D7-6525    TCGA-D7-6526    TCGA-D7-6527    TCGA-D7-6528 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-D7-6815    TCGA-D7-6817    TCGA-D7-6818    TCGA-D7-6820    TCGA-D7-6822 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-D7-8570    TCGA-D7-8572    TCGA-D7-8573    TCGA-D7-8574    TCGA-D7-8576 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-D7-A4YT    TCGA-D7-A4YU    TCGA-D7-A4YV    TCGA-D7-A4Z0    TCGA-EQ-5647 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-F1-6177    TCGA-F1-6874    TCGA-F1-6875    TCGA-FP-7735    TCGA-FP-7829 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-FP-7916    TCGA-FP-7998    TCGA-FP-8099    TCGA-FP-8209    TCGA-HJ-7597 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-HU-8243    TCGA-HU-8245    TCGA-HU-8604    TCGA-HU-8610    TCGA-HU-A4G2 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-HU-A4GD    TCGA-HU-A4GN    TCGA-HU-A4GP    TCGA-HU-A4GQ    TCGA-HU-A4GU 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-HU-A4H3    TCGA-HU-A4H4    TCGA-HU-A4H5    TCGA-HU-A4H6    TCGA-IN-7806 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 
   TCGA-IN-7808    TCGA-IN-8462    TCGA-IN-8663    TCGA-IP-7968 
"C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" "C1R WILD-TYPE" 

Clustering(24) Variable = CTNND1 MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2                0   1
  CTNND1 MUTATED    11   2
  CTNND1 WILD-TYPE 119  63
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              13              182 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
               2               63 
$`CTNND1 MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-8372 TCGA-BR-8382 
       34.68        32.78        12.82        24.76        19.17        15.85 
TCGA-BR-8678 TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5733 
       11.54        15.81        15.95         9.01         6.02        21.07 
TCGA-D7-A4Z0 
       14.76 

$`CTNND1 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
        0.62        13.84        13.22        16.14         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 
       30.90        31.20        32.94         9.21        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01         0.69         0.16        18.54        12.43         0.95 
TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        0.69         0.82         0.69         0.49        20.55         0.72 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8366 
        1.55         1.48         6.18        19.50         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
       13.74         4.31         3.32         0.36        14.79         0.26 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        3.72         0.72         9.21        20.22        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 
        2.14        13.45         7.53         0.49        16.44         0.59 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.62        10.68        13.51        12.89         0.79         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-BR-A4QL 
        0.53         0.66        19.36        13.51        13.64        11.57 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 
        0.39         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.16         0.10         0.10         0.13         0.10         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       12.03        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       28.96        79.07        65.10         4.01        55.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT 
       24.72        16.80        19.50        17.19         6.97        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
       16.44         5.92         0.62         6.58        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39        19.53         3.02        22.29        17.06        59.54 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 
       26.47         5.92        12.59        12.10         0.76        24.30 
TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 
       22.75        29.98         8.98         0.10         6.25        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       17.69        12.30         9.67        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

  CTNND1 MUTATED CTNND1 WILD-TYPE 
            6.02             0.07 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
           34.68           105.07 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
           15.85            11.44 
[1] "6.0 - 34.7 (15.8)"  "0.1 - 105.1 (11.4)"
[1] "hr=" "3.1"
D24V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTNND1 MUTATED         0        1        1        1         2         1
  CTNND1 WILD-TYPE       1        5       22       22        19        30
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNND1 MUTATED           0          1          0          2        4
  CTNND1 WILD-TYPE         3         32         24         15       20
D24V3, multiclass
            clus
vv           CTNND1 MUTATED CTNND1 WILD-TYPE
  STAGE I                 0                1
  STAGE IA                1                5
  STAGE IB                1               22
  STAGE II                1               22
  STAGE IIA               2               19
  STAGE IIB               1               30
  STAGE III               0                3
  STAGE IIIA              1               32
  STAGE IIIB              0               24
  STAGE IIIC              2               15
  STAGE IV                4               20
[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"
                  vv
clus               T1 T2 T3 T4
  CTNND1 MUTATED    1  4  3  5
  CTNND1 WILD-TYPE  6 62 87 44
D24V4, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  T1              1                6
  T2              4               62
  T3              3               87
  T4              5               44
[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
  CTNND1 MUTATED    4  2  3  4
  CTNND1 WILD-TYPE 66 61 32 37
D24V5, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  N0              4               66
  N1              2               61
  N2              3               32
  N3              4               37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1  MX
  CTNND1 MUTATED    10   3   0
  CTNND1 WILD-TYPE 185  13  10
D24V6, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  M0             10              185
  M1              3               13
  MX              0               10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                  cls
clus                 0   1
  CTNND1 MUTATED     6   7
  CTNND1 WILD-TYPE  82 126
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED      6    7
  CTNND1 WILD-TYPE   82  126
        clus
vv       CTNND1 MUTATED CTNND1 WILD-TYPE
  FEMALE              6               82
  MALE                7              126
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  CTNND1 MUTATED                                       1
  CTNND1 WILD-TYPE                                    31
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CTNND1 MUTATED                                                        7
  CTNND1 WILD-TYPE                                                    101
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  CTNND1 MUTATED                                                                   2
  CTNND1 WILD-TYPE                                                                32
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  CTNND1 MUTATED                                                  1
  CTNND1 WILD-TYPE                                               25
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  CTNND1 MUTATED                                                           0
  CTNND1 WILD-TYPE                                                         1
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  CTNND1 MUTATED                                                          1
  CTNND1 WILD-TYPE                                                       13
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  CTNND1 MUTATED                                                           1
  CTNND1 WILD-TYPE                                                         3
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  CTNND1 MUTATED                                          0
  CTNND1 WILD-TYPE                                        1
D24V8, multiclass
                                                                   clus
vv                                                                  CTNND1 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               1
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  CTNND1 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           31
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         101
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                25
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V9, binary
                  cls
clus                 0   1
  CTNND1 MUTATED     0  13
  CTNND1 WILD-TYPE   6 202
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED      0   13
  CTNND1 WILD-TYPE    6  202
     clus
vv    CTNND1 MUTATED CTNND1 WILD-TYPE
  NO               0                6
  YES             13              202
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CTNND1 MUTATED    12   0   1   0
  CTNND1 WILD-TYPE 159   7   9  24
D24V10, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  R0             12              159
  R1              0                7
  R2              1                9
  RX              0               24
[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"
D24V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CTNND1 MUTATED       1                         0     8
  CTNND1 WILD-TYPE    43                         3   125
D24V12, multiclass
                           clus
vv                          CTNND1 MUTATED CTNND1 WILD-TYPE
  ASIAN                                  1               43
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  8              125
[1] 3 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(25) Variable = MLXIPL MUTATION ANALYSIS
D25V1, survival
                  sevent
clus2                0   1
  MLXIPL MUTATED     8   2
  MLXIPL WILD-TYPE 122  63
  MLXIPL MUTATED MLXIPL WILD-TYPE 
              10              185 
  MLXIPL MUTATED MLXIPL WILD-TYPE 
               2               63 
$`MLXIPL MUTATED`
TCGA-BR-6452 TCGA-BR-8382 TCGA-BR-8680 TCGA-CD-8535 TCGA-CG-4305 TCGA-CG-4306 
       34.68        15.85        15.81         0.13        15.95         1.02 
TCGA-CG-5721 TCGA-CG-5723 TCGA-HU-A4GQ TCGA-HU-A4GU 
        6.02       105.07         0.10         6.25 

$`MLXIPL WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        0.62        32.78        13.84        13.22        16.14         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 
       18.54        12.43         0.95         0.69         0.82         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
        0.49        20.55         0.72         1.55         1.48         6.18 
TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       19.50         2.96         0.95        13.74         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8484 
        0.36        19.17        14.79         0.26         3.72         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        15.81         2.14        13.45 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        7.53         0.49        11.54        16.44         0.59         0.62 
TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 
       10.68        13.51        12.89         0.79         0.72         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 
        0.66        19.36        13.51        13.64        11.57         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18         0.30         0.07         0.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        0.10         0.10         0.10         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       19.50        17.19         6.97        14.27        16.44         5.92 
TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
       14.76         0.62         6.58        14.47        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 
       19.53         3.02        22.29        17.06        59.54        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD 
        5.92        12.59        12.10         0.76        24.30        22.75 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
       29.98         8.98        19.36        17.69        12.30         9.67 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  MLXIPL MUTATED MLXIPL WILD-TYPE 
            0.10             0.07 
  MLXIPL MUTATED MLXIPL WILD-TYPE 
          105.07            79.07 
  MLXIPL MUTATED MLXIPL WILD-TYPE 
           11.03            12.03 
[1] "0.1 - 105.1 (11.0)" "0.1 - 79.1 (12.0)" 
[1] "hr=" "2"  
D25V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLXIPL MUTATED         0        0        1        2         1         1
  MLXIPL WILD-TYPE       1        6       22       21        20        30
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MLXIPL MUTATED           0          1          0          2        4
  MLXIPL WILD-TYPE         3         32         24         15       20
D25V3, multiclass
            clus
vv           MLXIPL MUTATED MLXIPL WILD-TYPE
  STAGE I                 0                1
  STAGE IA                0                6
  STAGE IB                1               22
  STAGE II                2               21
  STAGE IIA               1               20
  STAGE IIB               1               30
  STAGE III               0                3
  STAGE IIIA              1               32
  STAGE IIIB              0               24
  STAGE IIIC              2               15
  STAGE IV                4               20
[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"
                  vv
clus               T1 T2 T3 T4
  MLXIPL MUTATED    1  3  4  5
  MLXIPL WILD-TYPE  6 63 86 44
D25V4, multiclass
    clus
vv   MLXIPL MUTATED MLXIPL WILD-TYPE
  T1              1                6
  T2              3               63
  T3              4               86
  T4              5               44
[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
  MLXIPL MUTATED    2  5  4  1
  MLXIPL WILD-TYPE 68 58 31 40
D25V5, multiclass
    clus
vv   MLXIPL MUTATED MLXIPL WILD-TYPE
  N0              2               68
  N1              5               58
  N2              4               31
  N3              1               40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1  MX
  MLXIPL MUTATED    11   2   0
  MLXIPL WILD-TYPE 184  14  10
D25V6, multiclass
    clus
vv   MLXIPL MUTATED MLXIPL WILD-TYPE
  M0             11              184
  M1              2               14
  MX              0               10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                  cls
clus                 0   1
  MLXIPL MUTATED     4   9
  MLXIPL WILD-TYPE  84 124
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLXIPL MUTATED      4    9
  MLXIPL WILD-TYPE   84  124
        clus
vv       MLXIPL MUTATED MLXIPL WILD-TYPE
  FEMALE              4               84
  MALE                9              124
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MLXIPL MUTATED                                       1
  MLXIPL WILD-TYPE                                    31
                  vv
clus               STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MLXIPL MUTATED                                                        8
  MLXIPL WILD-TYPE                                                    100
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MLXIPL MUTATED                                                                   2
  MLXIPL WILD-TYPE                                                                32
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MLXIPL MUTATED                                                  2
  MLXIPL WILD-TYPE                                               24
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  MLXIPL MUTATED                                                           0
  MLXIPL WILD-TYPE                                                         1
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MLXIPL MUTATED                                                          0
  MLXIPL WILD-TYPE                                                       14
                  vv
clus               STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MLXIPL MUTATED                                                           0
  MLXIPL WILD-TYPE                                                         4
                  vv
clus               STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MLXIPL MUTATED                                          0
  MLXIPL WILD-TYPE                                        1
D25V8, multiclass
                                                                   clus
vv                                                                  MLXIPL MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               2
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                      0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       0
                                                                   clus
vv                                                                  MLXIPL WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           31
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         100
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                24
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, binary
                  cls
clus                 0   1
  MLXIPL MUTATED     0  13
  MLXIPL WILD-TYPE   6 202
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLXIPL MUTATED      0   13
  MLXIPL WILD-TYPE    6  202
     clus
vv    MLXIPL MUTATED MLXIPL WILD-TYPE
  NO               0                6
  YES             13              202
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MLXIPL MUTATED    10   0   1   2
  MLXIPL WILD-TYPE 161   7   9  22
D25V10, multiclass
    clus
vv   MLXIPL MUTATED MLXIPL WILD-TYPE
  R0             10              161
  R1              0                7
  R2              1                9
  RX              2               22
[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"
D25V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLXIPL MUTATED       4                         0     4
  MLXIPL WILD-TYPE    40                         3   129
D25V12, multiclass
                           clus
vv                          MLXIPL MUTATED MLXIPL WILD-TYPE
  ASIAN                                  4               40
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  4              129
[1] 3 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(26) Variable = MLL4 MUTATION ANALYSIS
D26V1, survival
                sevent
clus2              0   1
  MLL4 MUTATED     8   9
  MLL4 WILD-TYPE 122  56
  MLL4 MUTATED MLL4 WILD-TYPE 
            17            178 
  MLL4 MUTATED MLL4 WILD-TYPE 
             9             56 
$`MLL4 MUTATED`
TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6456 TCGA-BR-6458 
        6.97         7.43         6.61        34.68        10.13         7.00 
TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8381 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MJ 
       32.94        20.55         0.26        13.45        11.57         0.10 
TCGA-CG-4306 TCGA-CG-5720 TCGA-CG-5726 TCGA-F1-6177 TCGA-HU-A4H3 
        1.02         0.99        28.96         6.58        19.36 

$`MLL4 WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 
        5.62        11.70         6.61         4.64        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.18         9.57        15.95        13.12        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62        32.78        13.84        13.22        16.14 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        31.20        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 
       18.54        12.43         0.95         0.69         0.82         0.69 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 
        0.49         0.72         1.55         1.48         6.18        19.50 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
        2.96         0.95        13.74         4.31         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 
       19.17        14.79        15.85         3.72         0.72         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8676 TCGA-BR-8677 
       20.22        12.79        15.81         2.14         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
       11.54        15.81        16.44         0.59         0.62        10.68 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.51        12.89         0.79         0.72         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       19.36        13.51        13.64         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18         0.30         0.07         0.39         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.13         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       47.05        19.07        12.03         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 
       22.98        30.97         6.97         1.02         1.02         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4Z0 
       17.19         6.97        14.27        16.44         5.92        14.76 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        0.62        14.47        72.23         0.39        19.53         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       22.29        17.06        59.54        26.47         5.92        12.59 
TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP 
       12.10         0.76        24.30        22.75        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 
        0.10         6.25        17.69        12.30         9.67        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
        3.45        18.81         3.39         2.53 

  MLL4 MUTATED MLL4 WILD-TYPE 
          0.10           0.07 
  MLL4 MUTATED MLL4 WILD-TYPE 
         34.68         105.07 
  MLL4 MUTATED MLL4 WILD-TYPE 
          7.43          12.20 
[1] "0.1 - 34.7 (7.4)"   "0.1 - 105.1 (12.2)"
[1] "hr=" "1.7"
D26V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLL4 MUTATED         1        1        3        0         2         4
  MLL4 WILD-TYPE       0        5       20       23        19        27
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MLL4 MUTATED           1          2          1          2        2
  MLL4 WILD-TYPE         2         31         23         15       22
D26V3, multiclass
            clus
vv           MLL4 MUTATED MLL4 WILD-TYPE
  STAGE I               1              0
  STAGE IA              1              5
  STAGE IB              3             20
  STAGE II              0             23
  STAGE IIA             2             19
  STAGE IIB             4             27
  STAGE III             1              2
  STAGE IIIA            2             31
  STAGE IIIB            1             23
  STAGE IIIC            2             15
  STAGE IV              2             22
[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"
                vv
clus             T1 T2 T3 T4
  MLL4 MUTATED    2  4  8  5
  MLL4 WILD-TYPE  5 62 82 44
D26V4, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  T1            2              5
  T2            4             62
  T3            8             82
  T4            5             44
[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
  MLL4 MUTATED    8  7  2  3
  MLL4 WILD-TYPE 62 56 33 38
D26V5, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  N0            8             62
  N1            7             56
  N2            2             33
  N3            3             38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1  MX
  MLL4 MUTATED    17   1   2
  MLL4 WILD-TYPE 178  15   8
D26V6, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  M0           17            178
  M1            1             15
  MX            2              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                cls
clus               0   1
  MLL4 MUTATED    11   9
  MLL4 WILD-TYPE  77 124
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     11    9
  MLL4 WILD-TYPE   77  124
        clus
vv       MLL4 MUTATED MLL4 WILD-TYPE
  FEMALE           11             77
  MALE              9            124
[1] 2 2
[1] FALSE
                vv
clus             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  MLL4 MUTATED                                       1
  MLL4 WILD-TYPE                                    31
                vv
clus             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MLL4 MUTATED                                                       17
  MLL4 WILD-TYPE                                                     91
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  MLL4 MUTATED                                                                   2
  MLL4 WILD-TYPE                                                                32
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  MLL4 MUTATED                                                  0
  MLL4 WILD-TYPE                                               26
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  MLL4 MUTATED                                                           0
  MLL4 WILD-TYPE                                                         1
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  MLL4 MUTATED                                                          0
  MLL4 WILD-TYPE                                                       14
                vv
clus             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  MLL4 MUTATED                                                           0
  MLL4 WILD-TYPE                                                         4
                vv
clus             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  MLL4 MUTATED                                          0
  MLL4 WILD-TYPE                                        1
D26V8, multiclass
                                                                   clus
vv                                                                  MLL4 MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             0
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                     0
                                                                   clus
vv                                                                  MLL4 WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                         31
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        91
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)             32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                              26
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                       1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V9, binary
                cls
clus               0   1
  MLL4 MUTATED     0  20
  MLL4 WILD-TYPE   6 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      0   20
  MLL4 WILD-TYPE    6  195
     clus
vv    MLL4 MUTATED MLL4 WILD-TYPE
  NO             0              6
  YES           20            195
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLL4 MUTATED    13   0   1   5
  MLL4 WILD-TYPE 158   7   9  19
D26V10, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  R0           13            158
  R1            0              7
  R2            1              9
  RX            5             19
[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"
D26V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL4 MUTATED       2                         1    13
  MLL4 WILD-TYPE    42                         2   120
D26V12, multiclass
                           clus
vv                          MLL4 MUTATED MLL4 WILD-TYPE
  ASIAN                                2             42
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                               13            120
[1] 3 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(27) Variable = NLK MUTATION ANALYSIS
D27V1, survival
               sevent
clus2             0   1
  NLK MUTATED     4   0
  NLK WILD-TYPE 126  65
  NLK MUTATED NLK WILD-TYPE 
            4           191 
  NLK MUTATED NLK WILD-TYPE 
            0            65 
$`NLK MUTATED`
TCGA-BR-6452 TCGA-BR-7715 TCGA-BR-8368 TCGA-BR-8372 
       34.68        15.42         4.31        19.17 

$`NLK WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       18.35        30.90         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        0.62        32.78        13.84        13.22        16.14         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        23.93        28.01         0.69         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 
       12.43         0.95         0.69         0.82         0.69         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 
       20.55         0.72         1.55         1.48         6.18        19.50 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
        2.96         0.95        13.74         3.32         0.36        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         3.72         0.72         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 
       12.79        15.81         2.14        13.45         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
       11.54        15.81        16.44         0.59         0.62        10.68 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.51        12.89         0.79         0.72         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 
       19.36        13.51        13.64        11.57         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18         0.30         0.07         0.39         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        0.10         0.13         0.10         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-EQ-5647 
        6.97        14.27        16.44         5.92        14.76         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        6.58        14.47        72.23         0.39        19.53         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
       22.29        17.06        59.54        26.47         5.92        12.59 
TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP 
       12.10         0.76        24.30        22.75        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.10         6.25        19.36        17.69        12.30         9.67 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       21.21         3.45        18.81         3.39         2.53 

  NLK MUTATED NLK WILD-TYPE 
         4.31          0.07 
  NLK MUTATED NLK WILD-TYPE 
        34.68        105.07 
  NLK MUTATED NLK WILD-TYPE 
       17.295        11.930 
[1] "4.3 - 34.7 (17.3)"  "0.1 - 105.1 (11.9)"
[1] "hr="     "2.5e+07"
D27V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NLK MUTATED         0        0        1        0         2         0
  NLK WILD-TYPE       1        6       22       23        19        31
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NLK MUTATED           0          0          0          1        0
  NLK WILD-TYPE         3         33         24         16       24
D27V3, multiclass
            clus
vv           NLK MUTATED NLK WILD-TYPE
  STAGE I              0             1
  STAGE IA             0             6
  STAGE IB             1            22
  STAGE II             0            23
  STAGE IIA            2            19
  STAGE IIB            0            31
  STAGE III            0             3
  STAGE IIIA           0            33
  STAGE IIIB           0            24
  STAGE IIIC           1            16
  STAGE IV             0            24
[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"
               vv
clus            T1 T2 T3 T4
  NLK MUTATED    0  1  3  1
  NLK WILD-TYPE  7 65 87 48
D27V4, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  T1           0             7
  T2           1            65
  T3           3            87
  T4           1            48
[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
  NLK MUTATED    3  0  0  1
  NLK WILD-TYPE 67 63 35 40
D27V5, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  N0           3            67
  N1           0            63
  N2           0            35
  N3           1            40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1  MX
  NLK MUTATED     4   0   1
  NLK WILD-TYPE 191  16   9
D27V6, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  M0           4           191
  M1           0            16
  MX           1             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
               cls
clus              0   1
  NLK MUTATED     3   2
  NLK WILD-TYPE  85 131
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED      3    2
  NLK WILD-TYPE   85  131
        clus
vv       NLK MUTATED NLK WILD-TYPE
  FEMALE           3            85
  MALE             2           131
[1] 2 2
[1] FALSE
               vv
clus            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  NLK MUTATED                                       0
  NLK WILD-TYPE                                    32
               vv
clus            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NLK MUTATED                                                        5
  NLK WILD-TYPE                                                    103
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  NLK MUTATED                                                                   0
  NLK WILD-TYPE                                                                34
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  NLK MUTATED                                                  0
  NLK WILD-TYPE                                               26
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE
  NLK MUTATED                                                           0
  NLK WILD-TYPE                                                         1
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  NLK MUTATED                                                          0
  NLK WILD-TYPE                                                       14
               vv
clus            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  NLK MUTATED                                                           0
  NLK WILD-TYPE                                                         4
               vv
clus            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  NLK MUTATED                                          0
  NLK WILD-TYPE                                        1
D27V8, multiclass
                                                                   clus
vv                                                                  NLK MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                       0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      5
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                            0
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                   0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                    0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                    0
                                                                   clus
vv                                                                  NLK WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                        32
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                      103
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)            34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                             26
  STOMACH  INTESTINAL ADENOCARCINOMA <U+00A0>PAPILLARY TYPE                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                      1
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V9, binary
               cls
clus              0   1
  NLK MUTATED     0   5
  NLK WILD-TYPE   6 210
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED      0    5
  NLK WILD-TYPE    6  210
     clus
vv    NLK MUTATED NLK WILD-TYPE
  NO            0             6
  YES           5           210
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  NLK MUTATED     4   0   0   1
  NLK WILD-TYPE 167   7  10  23
D27V10, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  R0           4           167
  R1           0             7
  R2           0            10
  RX           1            23
[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"
D27V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NLK MUTATED       0                         0     5
  NLK WILD-TYPE    44                         3   128
D27V12, multiclass
                           clus
vv                          NLK MUTATED NLK WILD-TYPE
  ASIAN                               0            44
  BLACK OR AFRICAN AMERICAN           0             3
  WHITE                               5           128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
