[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"        "-oTKIRP-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/KIRP-TP/11541540/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/11561829/transformed.cor.cli.txt"

nPatients in clinical file=223, in cluster file=161, common to both=161
[1]  19 161
[1] "HNRNPM MUTATION ANALYSIS"
[1] 3
  HNRNPM MUTATED HNRNPM WILD-TYPE 
              10              151 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
              10              151 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
            10            151 
  NEFH MUTATED NEFH WILD-TYPE 
            10            151 
[1] "ZNF598 MUTATION ANALYSIS"
[1] 3
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              10              151 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              10              151 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
           10           151 
  NF2 MUTATED NF2 WILD-TYPE 
           10           151 
[1] "TDG MUTATION ANALYSIS"
[1] 3
  TDG MUTATED TDG WILD-TYPE 
            5           156 
  TDG MUTATED TDG WILD-TYPE 
            5           156 
[1] "SKI MUTATION ANALYSIS"
[1] 3
  SKI MUTATED SKI WILD-TYPE 
            6           155 
  SKI MUTATED SKI WILD-TYPE 
            6           155 
[1] "MUC5B MUTATION ANALYSIS"
[1] 3
  MUC5B MUTATED MUC5B WILD-TYPE 
             14             147 
  MUC5B MUTATED MUC5B WILD-TYPE 
             14             147 
[1] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               8              153 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               8              153 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
           15           146 
  MET MUTATED MET WILD-TYPE 
           15           146 
[1] "SMARCB1 MUTATION ANALYSIS"
[1] 3
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                4               157 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                4               157 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
              7             154 
  KDM6A MUTATED KDM6A WILD-TYPE 
              7             154 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             10             151 
  SETD2 MUTATED SETD2 WILD-TYPE 
             10             151 
[1] "AHNAK2 MUTATION ANALYSIS"
[1] 3
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               7              154 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               7              154 
[1] "AHCY MUTATION ANALYSIS"
[1] 3
  AHCY MUTATED AHCY WILD-TYPE 
             4            157 
  AHCY MUTATED AHCY WILD-TYPE 
             4            157 
[1] "IDUA MUTATION ANALYSIS"
[1] 3
  IDUA MUTATED IDUA WILD-TYPE 
             5            156 
  IDUA MUTATED IDUA WILD-TYPE 
             5            156 
[1] "OR2L8 MUTATION ANALYSIS"
[1] 3
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              4             157 
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              4             157 
[1] "HOXD8 MUTATION ANALYSIS"
[1] 3
  HOXD8 MUTATED HOXD8 WILD-TYPE 
              4             157 
  HOXD8 MUTATED HOXD8 WILD-TYPE 
              4             157 
[1] "PAM MUTATION ANALYSIS"
[1] 3
  PAM MUTATED PAM WILD-TYPE 
            3           158 
  PAM MUTATED PAM WILD-TYPE 
            3           158 
[1] "CSGALNACT2 MUTATION ANALYSIS"
[1] 3
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   5                  156 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   5                  156 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 161 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
         554           21          493            3           NA           NA 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
         582           27           NA            7           49            2 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
         140          780          729           NA          709          597 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
         600          436          379          516           NA           NA 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
           2          118           87            4           NA         1778 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         923          763         1357           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         747          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
         307          930         1049          379         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
         803          627           14         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
         585          207            5          452         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
         270         1938           NA           NA         1454           NA 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1242          792          921          792          771          403 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
          NA          233           29          364           NA           84 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        3760           NA         2948         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799           NA          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
         116          353          414         3950         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        2460           NA         1856         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
         757           97          208         1575         1479           NA 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1194         1059          765          446          786          194 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          378 
TCGA-GL-A59T TCGA-HE-7128 TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NF TCGA-HE-A5NH 
         546           NA           NA           NA         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         360         1726         2228          167          511          608 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
          62          677          649          146          376           NA 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
           4          364          885         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
         841          616         3035         2653           NA           NA 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2584         2816          391          540          428 
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=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=133,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=18,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
 [3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
 [5] "PATHOLOGY.M.STAGE"           "GENDER"                     
 [7] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
 [9] "RACE"                        "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 161 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=49, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
103  16  41   1 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  103    16    42 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
103  16  41   1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  103    16    42 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
28 17  4 
[1] "table(vv)"
vv
N0 N1 N2 
28 17  4 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
28 17  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
28 17  4 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=13, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = HNRNPM MUTATION ANALYSIS
D1V1, survival
                  sevent
clus2                0   1
  HNRNPM MUTATED    10   0
  HNRNPM WILD-TYPE 125   5
  HNRNPM MUTATED HNRNPM WILD-TYPE 
              10              130 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
               0                5 
$`HNRNPM MUTATED`
TCGA-BQ-5887 TCGA-BQ-7055 TCGA-BQ-7062 TCGA-DW-7841 TCGA-DZ-6132 TCGA-EV-5902 
         771          799          116          445         2460          578 
TCGA-G7-7502 TCGA-GL-6846 TCGA-IA-A40X TCGA-PJ-A5Z8 
         786         5925          608          391 

$`HNRNPM WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
         709          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
        1968            2          118           87            4         1778 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         923          763         1357           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         747          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
         307          930         1049          379         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
         803          627           14         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
         585          207            5          452         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
         792          403          233           29          364           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         232          214          218          353          414         3950 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-DW-7963 
        1142          744          419          114           92         1240 
TCGA-DZ-6131 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ 
        2429         1856         1670         1040          757           97 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
         208         1575         1479         1194         1059          765 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
         446          194          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         378          546         2072          408          360         1726 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        2228          167          511           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
         146          376            4          364          885         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
         845          924          841          616         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2584         2816          540          428 

  HNRNPM MUTATED HNRNPM WILD-TYPE 
             116                2 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
            5925             3950 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
           689.5            590.5 
[1] "116.0 - 5925.0 (689.5)" "2.0 - 3950.0 (590.5)"  
[1] "hr="     "7.6e+07"
D1V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  HNRNPM MUTATED         8        0         1        1
  HNRNPM WILD-TYPE      87        9        35        9
D1V3, multiclass
           clus
vv          HNRNPM MUTATED HNRNPM WILD-TYPE
  STAGE I                8               87
  STAGE II               0                9
  STAGE III              1               35
  STAGE IV               1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  HNRNPM MUTATED    8  0     2
  HNRNPM WILD-TYPE 95 16    40
D1V4, multiclass
       clus
vv      HNRNPM MUTATED HNRNPM WILD-TYPE
  T1                 8               95
  T2                 0               16
  T3+T4              2               40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2
  HNRNPM MUTATED    1  1  0
  HNRNPM WILD-TYPE 27 16  4
D1V5, multiclass
[1] "Remove cluster labels:" "HNRNPM MUTATED"        
clus
  HNRNPM MUTATED HNRNPM WILD-TYPE 
               2               47 
      TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-A4-A5Y1       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-5398       TCGA-B1-A655       TCGA-B1-A656 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-B1-A657       TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-BQ-5879       TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-BQ-5888       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-BQ-5892       TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-BQ-7048       TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7058 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-DW-7963       TCGA-DZ-6131       TCGA-G7-6789       TCGA-G7-6793 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-7966       TCGA-GL-A59R 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A40Y       TCGA-J7-6720       TCGA-J7-8537 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
                  vv
clus               M0 M1 MX
  HNRNPM MUTATED    5  0  5
  HNRNPM WILD-TYPE 58  6 75
D1V6, multiclass
    clus
vv   HNRNPM MUTATED HNRNPM WILD-TYPE
  M0              5               58
  M1              0                6
  MX              5               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"
D1V7, binary
                  cls
clus                 0   1
  HNRNPM MUTATED     2   8
  HNRNPM WILD-TYPE  45 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPM MUTATED      2    8
  HNRNPM WILD-TYPE   45  106
        clus
vv       HNRNPM MUTATED HNRNPM WILD-TYPE
  FEMALE              2               45
  MALE                8              106
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNRNPM MUTATED                                  0     0
  HNRNPM WILD-TYPE                                2     2
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HNRNPM MUTATED                           3     6
  HNRNPM WILD-TYPE                        39    96
D1V10, multiclass
                                  clus
vv                                 HNRNPM MUTATED HNRNPM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0                2
  BLACK OR AFRICAN AMERICAN                     3               39
  WHITE                                         6               96
[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, binary
                  cls
clus                 0   1
  HNRNPM MUTATED     0   6
  HNRNPM WILD-TYPE   6 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPM MUTATED      0    6
  HNRNPM WILD-TYPE    6  114
                        clus
vv                       HNRNPM MUTATED HNRNPM WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              6              114
[1] 2 2
[1] FALSE

Clustering(2) Variable = NEFH MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  NEFH MUTATED     9   0
  NEFH WILD-TYPE 126   5
  NEFH MUTATED NEFH WILD-TYPE 
             9            131 
  NEFH MUTATED NEFH WILD-TYPE 
             0              5 
$`NEFH MUTATED`
TCGA-B9-4117 TCGA-B9-A5W8 TCGA-GL-A59T TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X 
          14          207          546         2228          167          608 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-P4-A5EB 
         845          924         2584 

$`NEFH WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
         709          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
        1968            2          118           87            4         1778 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         923          763         1357           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         747          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
         307          930         1049          379         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
         803          627         1338          671           64          585 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
           5          452         2639          586          270         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1454         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         403          233           29          364           84         3760 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2948         2839         1864         1533         1516          799 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        3950         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
          92         1240         2429         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
        1040          578          757           97          208         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
        1479         1194         1059          765          446          786 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
         194         5925          393          112          841           32 
TCGA-GL-A59R TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-IA-A40U 
         378         2072          408          360         1726          511 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
          62          677          649          146          376            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
         364          885         1043          841          616         3035 
TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2816          391          540          428 

  NEFH MUTATED NEFH WILD-TYPE 
            14              2 
  NEFH MUTATED NEFH WILD-TYPE 
          2584           5925 
  NEFH MUTATED NEFH WILD-TYPE 
           608            595 
[1] "14.0 - 2584.0 (608.0)" "2.0 - 5925.0 (595.0)" 
[1] "hr="     "7.4e+07"
D2V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NEFH MUTATED         7        1         0        0
  NEFH WILD-TYPE      88        8        36       10
D2V3, multiclass
           clus
vv          NEFH MUTATED NEFH WILD-TYPE
  STAGE I              7             88
  STAGE II             1              8
  STAGE III            0             36
  STAGE IV             0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  NEFH MUTATED    8  2     0
  NEFH WILD-TYPE 95 14    42
D2V4, multiclass
       clus
vv      NEFH MUTATED NEFH WILD-TYPE
  T1               8             95
  T2               2             14
  T3+T4            0             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2
  NEFH MUTATED    0  0  0
  NEFH WILD-TYPE 28 17  4
D2V5, multiclass
                vv
clus             M0 M1 MX
  NEFH MUTATED    2  0  7
  NEFH WILD-TYPE 61  6 73
D2V6, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  M0            2             61
  M1            0              6
  MX            7             73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                cls
clus               0   1
  NEFH MUTATED     3   7
  NEFH WILD-TYPE  44 107
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      3    7
  NEFH WILD-TYPE   44  107
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  FEMALE            3             44
  MALE              7            107
[1] 2 2
[1] FALSE
D2V8, continuous
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             2             36 
    TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8310     TCGA-A4-8311 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A4-8312     TCGA-A4-8518     TCGA-A4-8630     TCGA-A4-A4ZT 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5XZ     TCGA-A4-A6HP     TCGA-AL-3466 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DW-7842     TCGA-DW-7963     TCGA-EV-5901     TCGA-EV-5902 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-EV-5903     TCGA-G7-6790     TCGA-G7-6793     TCGA-G7-6796 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A40Y     TCGA-J7-8537     TCGA-Q2-A5QZ 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
D2V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEFH MUTATED                                  0     0
  NEFH WILD-TYPE                                2     2
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NEFH MUTATED                           4     4
  NEFH WILD-TYPE                        38    98
D2V10, multiclass
                                  clus
vv                                 NEFH MUTATED NEFH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0              2
  BLACK OR AFRICAN AMERICAN                   4             38
  WHITE                                       4             98
[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, binary
                cls
clus               0   1
  NEFH MUTATED     0   8
  NEFH WILD-TYPE   6 112
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      0    8
  NEFH WILD-TYPE    6  112
                        clus
vv                       NEFH MUTATED NEFH WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            8            112
[1] 2 2
[1] FALSE

Clustering(3) Variable = ZNF598 MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2                0   1
  ZNF598 MUTATED     8   1
  ZNF598 WILD-TYPE 127   4
  ZNF598 MUTATED ZNF598 WILD-TYPE 
               9              131 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
               1                4 
$`ZNF598 MUTATED`
TCGA-AL-3473 TCGA-AT-A5NU TCGA-B3-8121 TCGA-BQ-5877 TCGA-DW-7834 TCGA-DW-7838 
         763           67          379          270         3950          744 
TCGA-EV-5903 TCGA-G7-7501 TCGA-G7-7502 
         757          446          786 

$`ZNF598 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
         709          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
        1968            2          118           87            4         1778 
TCGA-AL-3472 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
         923         1357          595          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         510           14          200         1029          307          930 
TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
        1049         1536          857          803          627           14 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1338          671           64          585          207            5 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
         452         2639          586         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 
         792          921          792          771          403          233 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
          29          364           84         3760         2948         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 
        1864         1533         1516          799          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 
         218          116          353          414         1142          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-G7-6789 
        1856         1670         1040          578           97          208 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-A4TM 
        1575         1479         1194         1059          765          194 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          378 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         546         2072          408          360         1726         2228 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         167          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
         146          376            4          364          885         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
         845          924          841          616         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2584         2816          391          540          428 

  ZNF598 MUTATED ZNF598 WILD-TYPE 
              67                2 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
            3950             5925 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
             744              595 
[1] "67.0 - 3950.0 (744.0)" "2.0 - 5925.0 (595.0)" 
[1] "hr=" "3.6"
D3V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF598 MUTATED         6        1         1        2
  ZNF598 WILD-TYPE      89        8        35        8
D3V3, multiclass
           clus
vv          ZNF598 MUTATED ZNF598 WILD-TYPE
  STAGE I                6               89
  STAGE II               1                8
  STAGE III              1               35
  STAGE IV               2                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF598 MUTATED    6  1     3
  ZNF598 WILD-TYPE 97 15    39
D3V4, multiclass
       clus
vv      ZNF598 MUTATED ZNF598 WILD-TYPE
  T1                 6               97
  T2                 1               15
  T3+T4              3               39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2
  ZNF598 MUTATED    1  3  0
  ZNF598 WILD-TYPE 27 14  4
D3V5, multiclass
    clus
vv   ZNF598 MUTATED ZNF598 WILD-TYPE
  N0              1               27
  N1              3               14
  N2              0                4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               M0 M1 MX
  ZNF598 MUTATED    2  2  6
  ZNF598 WILD-TYPE 61  4 74
D3V6, multiclass
    clus
vv   ZNF598 MUTATED ZNF598 WILD-TYPE
  M0              2               61
  M1              2                4
  MX              6               74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                  cls
clus                 0   1
  ZNF598 MUTATED     2   8
  ZNF598 WILD-TYPE  45 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      2    8
  ZNF598 WILD-TYPE   45  106
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  FEMALE              2               45
  MALE                8              106
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF598 MUTATED                                  0     0
  ZNF598 WILD-TYPE                                2     2
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF598 MUTATED                           3     7
  ZNF598 WILD-TYPE                        39    95
D3V10, multiclass
                                  clus
vv                                 ZNF598 MUTATED ZNF598 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0                2
  BLACK OR AFRICAN AMERICAN                     3               39
  WHITE                                         7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
                  cls
clus                 0   1
  ZNF598 MUTATED     1   8
  ZNF598 WILD-TYPE   5 112
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      1    8
  ZNF598 WILD-TYPE    5  112
                        clus
vv                       ZNF598 MUTATED ZNF598 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO              8              112
[1] 2 2
[1] FALSE

Clustering(4) Variable = NF2 MUTATION ANALYSIS
D4V1, survival
               sevent
clus2             0   1
  NF2 MUTATED     8   1
  NF2 WILD-TYPE 127   4
  NF2 MUTATED NF2 WILD-TYPE 
            9           131 
  NF2 MUTATED NF2 WILD-TYPE 
            1             4 
$`NF2 MUTATED`
TCGA-A4-8098 TCGA-B1-A47M TCGA-B9-4117 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5894 
         140          659           14         2639          270           84 
TCGA-EV-5902 TCGA-G7-6797 TCGA-GL-7966 
         578          765          112 

$`NF2 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
           7           49            2          780          729          709 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
         597          600          436          379          516         1968 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 
           2          118           87            4         1778          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 
         763         1357           67          595          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         510           14          200         1029          307          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
        1049          379         1536          857          803          627 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1338          671           64          585          207            5 
TCGA-B9-A69E TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
         452          586         1938         1454         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
         921          792          771          403          233           29 
TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
         364         3760         2948         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
        1516          799          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         353          414         3950         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
        1856         1670         1040          757           97          208 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 
        1575         1479         1194         1059          446          786 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
         194         5925          393          841           32          378 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         546         2072          408          360         1726         2228 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         167          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
         146          376            4          364          885         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
         845          924          841          616         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2584         2816          391          540          428 

  NF2 MUTATED NF2 WILD-TYPE 
           14             2 
  NF2 MUTATED NF2 WILD-TYPE 
         2639          5925 
  NF2 MUTATED NF2 WILD-TYPE 
          270           600 
[1] "14.0 - 2639.0 (270.0)" "2.0 - 5925.0 (600.0)" 
[1] "hr=" "4.7"
D4V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NF2 MUTATED         2        0         5        2
  NF2 WILD-TYPE      93        9        31        8
D4V3, multiclass
           clus
vv          NF2 MUTATED NF2 WILD-TYPE
  STAGE I             2            93
  STAGE II            0             9
  STAGE III           5            31
  STAGE IV            2             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2 T3+T4
  NF2 MUTATED     3   1     6
  NF2 WILD-TYPE 100  15    36
D4V4, multiclass
       clus
vv      NF2 MUTATED NF2 WILD-TYPE
  T1              3           100
  T2              1            15
  T3+T4           6            36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2
  NF2 MUTATED    0  4  0
  NF2 WILD-TYPE 28 13  4
D4V5, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  N0           0            28
  N1           4            13
  N2           0             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            M0 M1 MX
  NF2 MUTATED    2  2  5
  NF2 WILD-TYPE 61  4 75
D4V6, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  M0           2            61
  M1           2             4
  MX           5            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"
D4V7, binary
               cls
clus              0   1
  NF2 MUTATED     4   6
  NF2 WILD-TYPE  43 108
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      4    6
  NF2 WILD-TYPE   43  108
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  FEMALE           4            43
  MALE             6           108
[1] 2 2
[1] FALSE
D4V8, continuous
[1] "Remove cluster labels:" "NF2 MUTATED"           
clus
  NF2 MUTATED NF2 WILD-TYPE 
            2            36 
   TCGA-A4-7286    TCGA-A4-7828    TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8312 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A4ZT    TCGA-A4-A57E    TCGA-A4-A5DU 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-A4-A5XZ    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-DW-5560    TCGA-DW-5561 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839    TCGA-DW-7840 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7841    TCGA-DW-7842    TCGA-DW-7963    TCGA-EV-5901    TCGA-EV-5903 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-6790    TCGA-G7-6793    TCGA-G7-6796    TCGA-G7-7501    TCGA-G7-7502 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-A4TM    TCGA-IA-A40U    TCGA-IA-A40X    TCGA-IA-A40Y    TCGA-J7-8537 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-Q2-A5QZ 
"NF2 WILD-TYPE" 
D4V9, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF2 MUTATED                                  0     0
  NF2 WILD-TYPE                                2     2
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF2 MUTATED                           4     5
  NF2 WILD-TYPE                        38    97
D4V10, multiclass
                                  clus
vv                                 NF2 MUTATED NF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0             2
  BLACK OR AFRICAN AMERICAN                  4            38
  WHITE                                      5            97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
               cls
clus              0   1
  NF2 MUTATED     1   6
  NF2 WILD-TYPE   5 114
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      1    6
  NF2 WILD-TYPE    5  114
                        clus
vv                       NF2 MUTATED NF2 WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO           6           114
[1] 2 2
[1] FALSE

Clustering(5) Variable = TDG MUTATION ANALYSIS
D5V1, survival
               sevent
clus2             0   1
  TDG MUTATED     5   0
  TDG WILD-TYPE 130   5
  TDG MUTATED TDG WILD-TYPE 
            5           135 
  TDG MUTATED TDG WILD-TYPE 
            0             5 
$`TDG MUTATED`
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-DW-7840 TCGA-GL-6846 
          29          364         2948          114         5925 

$`TDG WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
         709          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
        1968            2          118           87            4         1778 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         923          763         1357           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         747          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
         307          930         1049          379         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
         803          627           14         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
         585          207            5          452         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7044 
         792          771          403          233           84         3760 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 
        2839         1864         1533         1516          799          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
        1142          744          419          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        2429         2460         1856         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
         757           97          208         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-7773 
        1059          765          446          786          194          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
         112          841           32          378          546         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
         408          360         1726         2228          167          511 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         608           62          677          649          146          376 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
           4          364          885         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         841          616         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         391          540          428 

  TDG MUTATED TDG WILD-TYPE 
           29             2 
  TDG MUTATED TDG WILD-TYPE 
         5925          3950 
  TDG MUTATED TDG WILD-TYPE 
          364           597 
[1] "29.0 - 5925.0 (364.0)" "2.0 - 3950.0 (597.0)" 
[1] "hr="     "2.6e+07"
D5V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  TDG MUTATED         3        0         1        1
  TDG WILD-TYPE      92        9        35        9
D5V3, multiclass
           clus
vv          TDG MUTATED TDG WILD-TYPE
  STAGE I             3            92
  STAGE II            0             9
  STAGE III           1            35
  STAGE IV            1             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2 T3+T4
  TDG MUTATED     3   0     2
  TDG WILD-TYPE 100  16    40
D5V4, multiclass
       clus
vv      TDG MUTATED TDG WILD-TYPE
  T1              3           100
  T2              0            16
  T3+T4           2            40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2
  TDG MUTATED    2  1  0
  TDG WILD-TYPE 26 16  4
D5V5, multiclass
    clus
vv   TDG MUTATED TDG WILD-TYPE
  N0           2            26
  N1           1            16
  N2           0             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            M0 M1 MX
  TDG MUTATED    3  0  2
  TDG WILD-TYPE 60  6 78
D5V6, multiclass
    clus
vv   TDG MUTATED TDG WILD-TYPE
  M0           3            60
  M1           0             6
  MX           2            78
[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
  TDG MUTATED     1   4
  TDG WILD-TYPE  46 110
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      1    4
  TDG WILD-TYPE   46  110
        clus
vv       TDG MUTATED TDG WILD-TYPE
  FEMALE           1            46
  MALE             4           110
[1] 2 2
[1] FALSE
D5V8, continuous
[1] "Remove cluster labels:" "TDG MUTATED"           
clus
  TDG MUTATED TDG WILD-TYPE 
            1            37 
   TCGA-A4-7286    TCGA-A4-7828    TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8312 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A4ZT    TCGA-A4-A57E    TCGA-A4-A5DU 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-A4-A5XZ    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-DW-5560    TCGA-DW-5561 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839    TCGA-DW-7841 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-DW-7842    TCGA-DW-7963    TCGA-EV-5901    TCGA-EV-5902    TCGA-EV-5903 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-G7-6790    TCGA-G7-6793    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7501 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-G7-7502    TCGA-G7-A4TM    TCGA-IA-A40U    TCGA-IA-A40X    TCGA-IA-A40Y 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-J7-8537    TCGA-Q2-A5QZ 
"TDG WILD-TYPE" "TDG WILD-TYPE" 
D5V9, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TDG MUTATED                                  0     0
  TDG WILD-TYPE                                2     2
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  TDG MUTATED                           1     4
  TDG WILD-TYPE                        41    98
D5V10, multiclass
                                  clus
vv                                 TDG MUTATED TDG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0             2
  BLACK OR AFRICAN AMERICAN                  1            41
  WHITE                                      4            98
[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, binary
               cls
clus              0   1
  TDG MUTATED     0   4
  TDG WILD-TYPE   6 116
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      0    4
  TDG WILD-TYPE    6  116
                        clus
vv                       TDG MUTATED TDG WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           4           116
[1] 2 2
[1] FALSE

Clustering(6) Variable = SKI MUTATION ANALYSIS
D6V1, survival
               sevent
clus2             0   1
  SKI MUTATED     5   0
  SKI WILD-TYPE 130   5
  SKI MUTATED SKI WILD-TYPE 
            5           135 
  SKI MUTATED SKI WILD-TYPE 
            0             5 
$`SKI MUTATED`
TCGA-B9-7268 TCGA-BQ-5884 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
         671          792         2460         1856         1670 

$`SKI WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
         709          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
        1968            2          118           87            4         1778 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         923          763         1357           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         747          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
         307          930         1049          379         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W7 
         803          627           14         1338           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         207            5          452         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1938         1454         1242          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         403          233           29          364           84         3760 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2948         2839         1864         1533         1516          799 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        3950         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
          92         1240         2429         1040          578          757 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          97          208         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
         765          446          786          194         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
         112          841           32          378          546         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
         408          360         1726         2228          167          511 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         608           62          677          649          146          376 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
           4          364          885         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         841          616         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         391          540          428 

  SKI MUTATED SKI WILD-TYPE 
          671             2 
  SKI MUTATED SKI WILD-TYPE 
         2460          5925 
  SKI MUTATED SKI WILD-TYPE 
         1670           585 
[1] "671.0 - 2460.0 (1670.0)" "2.0 - 5925.0 (585.0)"   
[1] "hr="     "2.8e+07"
D6V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  SKI MUTATED         4        1         1        0
  SKI WILD-TYPE      91        8        35       10
D6V3, multiclass
           clus
vv          SKI MUTATED SKI WILD-TYPE
  STAGE I             4            91
  STAGE II            1             8
  STAGE III           1            35
  STAGE IV            0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  SKI MUTATED    4  1     1
  SKI WILD-TYPE 99 15    41
D6V4, multiclass
       clus
vv      SKI MUTATED SKI WILD-TYPE
  T1              4            99
  T2              1            15
  T3+T4           1            41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2
  SKI MUTATED    2  0  0
  SKI WILD-TYPE 26 17  4
D6V5, multiclass
[1] "Remove cluster labels:" "SKI MUTATED"           
clus
  SKI MUTATED SKI WILD-TYPE 
            2            47 
   TCGA-A4-7583    TCGA-A4-7915    TCGA-A4-A57E    TCGA-A4-A5Y1    TCGA-AL-3466 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173    TCGA-B1-5398    TCGA-B1-A655 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-B1-A656    TCGA-B1-A657    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-BQ-5880    TCGA-BQ-5882    TCGA-BQ-5885    TCGA-BQ-5887    TCGA-BQ-5888 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-BQ-5889    TCGA-BQ-5890    TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-BQ-5894    TCGA-BQ-7045    TCGA-BQ-7048    TCGA-BQ-7050    TCGA-BQ-7051 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-BQ-7058    TCGA-DW-7963    TCGA-DZ-6131    TCGA-G7-6789    TCGA-G7-6793 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-G7-6795    TCGA-G7-7501    TCGA-GL-6846    TCGA-GL-7966    TCGA-GL-A59R 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-IA-A40U    TCGA-IA-A40Y    TCGA-J7-6720    TCGA-J7-8537    TCGA-P4-A5E6 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-P4-A5E8    TCGA-P4-A5EA 
"SKI WILD-TYPE" "SKI WILD-TYPE" 
               vv
clus            M0 M1 MX
  SKI MUTATED    3  0  3
  SKI WILD-TYPE 60  6 77
D6V6, multiclass
    clus
vv   SKI MUTATED SKI WILD-TYPE
  M0           3            60
  M1           0             6
  MX           3            77
[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
  SKI MUTATED     1   5
  SKI WILD-TYPE  46 109
[1] "tbl2"
               cls
clus            [,1] [,2]
  SKI MUTATED      1    5
  SKI WILD-TYPE   46  109
        clus
vv       SKI MUTATED SKI WILD-TYPE
  FEMALE           1            46
  MALE             5           109
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SKI MUTATED                                  0     0
  SKI WILD-TYPE                                2     2
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SKI MUTATED                           1     3
  SKI WILD-TYPE                        41    99
D6V10, multiclass
                                  clus
vv                                 SKI MUTATED SKI WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0             2
  BLACK OR AFRICAN AMERICAN                  1            41
  WHITE                                      3            99
[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, binary
               cls
clus              0   1
  SKI MUTATED     0   2
  SKI WILD-TYPE   6 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  SKI MUTATED      0    2
  SKI WILD-TYPE    6  118
                        clus
vv                       SKI MUTATED SKI WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           2           118
[1] 2 2
[1] FALSE

Clustering(7) Variable = MUC5B MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2               0   1
  MUC5B MUTATED    11   1
  MUC5B WILD-TYPE 124   4
  MUC5B MUTATED MUC5B WILD-TYPE 
             12             128 
  MUC5B MUTATED MUC5B WILD-TYPE 
              1               4 
$`MUC5B MUTATED`
TCGA-A4-7288 TCGA-A4-8311 TCGA-A4-8518 TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         493          729          600         1968          118           87 
TCGA-B1-A47N TCGA-BQ-5888 TCGA-BQ-7044 TCGA-BQ-7062 TCGA-DW-7963 TCGA-P4-A5E7 
         747          403         3760          116         1240         2653 

$`MUC5B WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554           21            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-8517 
          49            2          140          780          709          597 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3467 
         436          379          516            2            4         1778 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         923          763         1357           67          595          659 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
         930         1049          379         1536          857          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
         627           14         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         207            5          452         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 
         771          233           29          364           84         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 
        2839         1864         1533         1516          799          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
         214          218          353          414         3950         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 
         744          419          114          445           92         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          97          208         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
         765          446          786          194         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
         112          841           32          378          546         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
         408          360         1726         2228          167          511 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         608           62          677          649          146          376 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
           4          364          885         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         841          616         3035         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         540          428 

  MUC5B MUTATED MUC5B WILD-TYPE 
             87               2 
  MUC5B MUTATED MUC5B WILD-TYPE 
           3760            5925 
  MUC5B MUTATED MUC5B WILD-TYPE 
          664.5           590.5 
[1] "87.0 - 3760.0 (664.5)" "2.0 - 5925.0 (590.5)" 
[1] "hr=" "2.3"
D7V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MUC5B MUTATED         8        1         2        2
  MUC5B WILD-TYPE      87        8        34        8
D7V3, multiclass
           clus
vv          MUC5B MUTATED MUC5B WILD-TYPE
  STAGE I               8              87
  STAGE II              1               8
  STAGE III             2              34
  STAGE IV              2               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  MUC5B MUTATED   11  1     2
  MUC5B WILD-TYPE 92 15    40
D7V4, multiclass
       clus
vv      MUC5B MUTATED MUC5B WILD-TYPE
  T1               11              92
  T2                1              15
  T3+T4             2              40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2
  MUC5B MUTATED    3  2  0
  MUC5B WILD-TYPE 25 15  4
D7V5, multiclass
    clus
vv   MUC5B MUTATED MUC5B WILD-TYPE
  N0             3              25
  N1             2              15
  N2             0               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              M0 M1 MX
  MUC5B MUTATED    4  2  8
  MUC5B WILD-TYPE 59  4 72
D7V6, multiclass
    clus
vv   MUC5B MUTATED MUC5B WILD-TYPE
  M0             4              59
  M1             2               4
  MX             8              72
[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
  MUC5B MUTATED     5   9
  MUC5B WILD-TYPE  42 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED      5    9
  MUC5B WILD-TYPE   42  105
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  FEMALE             5              42
  MALE               9             105
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUC5B MUTATED                                  0     0
  MUC5B WILD-TYPE                                2     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MUC5B MUTATED                           3    11
  MUC5B WILD-TYPE                        39    91
D7V10, multiclass
                                  clus
vv                                 MUC5B MUTATED MUC5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    3              39
  WHITE                                       11              91
[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, binary
                 cls
clus                0   1
  MUC5B MUTATED     0  11
  MUC5B WILD-TYPE   6 109
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED      0   11
  MUC5B WILD-TYPE    6  109
                        clus
vv                       MUC5B MUTATED MUC5B WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            11             109
[1] 2 2
[1] FALSE

Clustering(8) Variable = ZNF814 MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2                0   1
  ZNF814 MUTATED     7   1
  ZNF814 WILD-TYPE 128   4
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               8              132 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               1                4 
$`ZNF814 MUTATED`
TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-DW-7840 TCGA-G7-A4TM TCGA-GL-A4EM TCGA-IZ-8195 
          87           64          114          194           32          677 
TCGA-KV-A6GE TCGA-P4-A5EB 
         885         2584 

$`ZNF814 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
         709          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 
        1968            2          118            4         1778          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
         763         1357           67          595          659          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
         930         1049          379         1536          857          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
         627           14         1338          671          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
           5          452         2639          586          270         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1454         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         403          233           29          364           84         3760 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2948         2839         1864         1533         1516          799 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 
        3950         1142          744          419          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
         578          757           97          208         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 
        1194         1059          765          446          786         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
         393          112          841          378          546         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
         408          360         1726         2228          167          511 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
         608           62          649          146          376            4 
TCGA-KV-A6GD TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         364         1043          845          924          841          616 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        3035         2653         2816          391          540          428 

  ZNF814 MUTATED ZNF814 WILD-TYPE 
              32                2 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
            2584             5925 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
           154.0            598.5 
[1] "32.0 - 2584.0 (154.0)" "2.0 - 5925.0 (598.5)" 
[1] "hr=" "6.3"
D8V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF814 MUTATED         5        1         2        0
  ZNF814 WILD-TYPE      90        8        34       10
D8V3, multiclass
           clus
vv          ZNF814 MUTATED ZNF814 WILD-TYPE
  STAGE I                5               90
  STAGE II               1                8
  STAGE III              2               34
  STAGE IV               0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF814 MUTATED    6  1     1
  ZNF814 WILD-TYPE 97 15    41
D8V4, multiclass
       clus
vv      ZNF814 MUTATED ZNF814 WILD-TYPE
  T1                 6               97
  T2                 1               15
  T3+T4              1               41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2
  ZNF814 MUTATED    0  1  0
  ZNF814 WILD-TYPE 28 16  4
D8V5, multiclass
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               1               48 
      TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473       TCGA-AL-7173 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B1-5398       TCGA-B1-A655       TCGA-B1-A656       TCGA-B1-A657 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885       TCGA-BQ-5887 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-5888       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-5892       TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-7048       TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7058 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-7963       TCGA-DZ-6131       TCGA-G7-6789       TCGA-G7-6793 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-6846       TCGA-GL-7966 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-GL-A59R       TCGA-IA-A40U       TCGA-IA-A40Y       TCGA-J7-6720 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-J7-8537       TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
                  vv
clus               M0 M1 MX
  ZNF814 MUTATED    0  0  7
  ZNF814 WILD-TYPE 63  6 73
D8V6, multiclass
    clus
vv   ZNF814 MUTATED ZNF814 WILD-TYPE
  M0              0               63
  M1              0                6
  MX              7               73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     0   8
  ZNF814 WILD-TYPE  47 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0    8
  ZNF814 WILD-TYPE   47  106
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  FEMALE              0               47
  MALE                8              106
[1] 2 2
[1] FALSE
D8V8, continuous
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               36 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8310       TCGA-A4-8311 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-8312       TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A4ZT 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-AL-3466       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7841 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-7842       TCGA-DW-7963       TCGA-EV-5901       TCGA-EV-5902 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-EV-5903       TCGA-G7-6790       TCGA-G7-6793       TCGA-G7-6796 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502       TCGA-IA-A40U 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-IA-A40X       TCGA-IA-A40Y       TCGA-J7-8537       TCGA-Q2-A5QZ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
D8V9, continuous
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               15 
      TCGA-A4-A48D       TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-B1-A654 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B9-A69E       TCGA-GL-7773       TCGA-GL-A59T       TCGA-HE-A5NI 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-HE-A5NJ       TCGA-HE-A5NK       TCGA-IA-A40U       TCGA-IZ-A6M8 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-P4-A5E7       TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF814 MUTATED                                  0     0
  ZNF814 WILD-TYPE                                2     2
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF814 MUTATED                           3     5
  ZNF814 WILD-TYPE                        39    97
D8V10, multiclass
                                  clus
vv                                 ZNF814 MUTATED ZNF814 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0                2
  BLACK OR AFRICAN AMERICAN                     3               39
  WHITE                                         5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     0   8
  ZNF814 WILD-TYPE   6 112
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0    8
  ZNF814 WILD-TYPE    6  112
                        clus
vv                       ZNF814 MUTATED ZNF814 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              8              112
[1] 2 2
[1] FALSE

Clustering(9) Variable = MET MUTATION ANALYSIS
D9V1, survival
               sevent
clus2             0   1
  MET MUTATED    14   0
  MET WILD-TYPE 121   5
  MET MUTATED MET WILD-TYPE 
           14           126 
  MET MUTATED MET WILD-TYPE 
            0             5 
$`MET MUTATED`
TCGA-A4-7734 TCGA-A4-7997 TCGA-AL-3472 TCGA-AL-7173 TCGA-B1-A654 TCGA-B9-4117 
          27            2          923         1357          108           14 
TCGA-BQ-7059 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-GL-A59R TCGA-HE-A5NH TCGA-IA-A40U 
         232         2460         1670          378          408          511 
TCGA-IZ-8196 TCGA-MH-A561 
         649          841 

$`MET WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7915 
         554           21          493            3          582            7 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8517 
          49          140          780          729          709          597 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ 
         600          436          379          516         1968            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3473 TCGA-AT-A5NU 
         118           87            4         1778          763           67 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         595          659          747          510           14          200 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        1029          307          930         1049          379         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
         857          803          627         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
         585          207            5          452         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         792          771          403          233           29          364 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
          84         3760         2948         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
        1516          799          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
         414         3950         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6134 TCGA-EV-5901 
         445           92         1240         2429         1856         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
         578          757           97          208         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1194         1059          765          446          786          194 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59T 
        5925          393          112          841           32          546 
TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X 
        2072          360         1726         2228          167          608 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
          62          677          146          376            4          364 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-P4-A5E6 
         885         1043          845          924          616         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2584         2816          391          540          428 

  MET MUTATED MET WILD-TYPE 
            2             2 
  MET MUTATED MET WILD-TYPE 
         2460          5925 
  MET MUTATED MET WILD-TYPE 
        459.5         598.5 
[1] "2.0 - 2460.0 (459.5)" "2.0 - 5925.0 (598.5)"
[1] "hr="     "7.6e+07"
D9V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  MET MUTATED         9        0         3        1
  MET WILD-TYPE      86        9        33        9
D9V3, multiclass
           clus
vv          MET MUTATED MET WILD-TYPE
  STAGE I             9            86
  STAGE II            0             9
  STAGE III           3            33
  STAGE IV            1             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  MET MUTATED    9  2     4
  MET WILD-TYPE 94 14    38
D9V4, multiclass
       clus
vv      MET MUTATED MET WILD-TYPE
  T1              9            94
  T2              2            14
  T3+T4           4            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2
  MET MUTATED    4  0  1
  MET WILD-TYPE 24 17  3
D9V5, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  N0           4            24
  N1           0            17
  N2           1             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            M0 M1 MX
  MET MUTATED    6  0  7
  MET WILD-TYPE 57  6 73
D9V6, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  M0           6            57
  M1           0             6
  MX           7            73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
               cls
clus              0   1
  MET MUTATED     4  11
  MET WILD-TYPE  43 103
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      4   11
  MET WILD-TYPE   43  103
        clus
vv       MET MUTATED MET WILD-TYPE
  FEMALE           4            43
  MALE            11           103
[1] 2 2
[1] FALSE
D9V8, continuous
[1] "Remove cluster labels:" "MET MUTATED"           
clus
  MET MUTATED MET WILD-TYPE 
            1            37 
   TCGA-A4-7286    TCGA-A4-7828    TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8312 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A4ZT    TCGA-A4-A57E    TCGA-A4-A5DU 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-A4-A5XZ    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-DW-5560    TCGA-DW-5561 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839    TCGA-DW-7840 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-DW-7841    TCGA-DW-7842    TCGA-DW-7963    TCGA-EV-5901    TCGA-EV-5902 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-EV-5903    TCGA-G7-6790    TCGA-G7-6793    TCGA-G7-6796    TCGA-G7-6797 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-G7-7501    TCGA-G7-7502    TCGA-G7-A4TM    TCGA-IA-A40X    TCGA-IA-A40Y 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-J7-8537    TCGA-Q2-A5QZ 
"MET WILD-TYPE" "MET WILD-TYPE" 
D9V9, continuous
[1] "Remove cluster labels:" "MET MUTATED"           
clus
  MET MUTATED MET WILD-TYPE 
            2            15 
   TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0    TCGA-B9-A44B    TCGA-B9-A69E 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-GL-7773    TCGA-GL-A59T    TCGA-HE-A5NI    TCGA-HE-A5NJ    TCGA-HE-A5NK 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-IZ-A6M8    TCGA-P4-A5E7    TCGA-P4-A5EB    TCGA-PJ-A5Z9    TCGA-Q2-A5QZ 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MET MUTATED                                  0     0
  MET WILD-TYPE                                2     2
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MET MUTATED                           3     8
  MET WILD-TYPE                        39    94
D9V10, multiclass
                                  clus
vv                                 MET MUTATED MET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0             2
  BLACK OR AFRICAN AMERICAN                  3            39
  WHITE                                      8            94
[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, binary
               cls
clus              0   1
  MET MUTATED     1  10
  MET WILD-TYPE   5 110
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      1   10
  MET WILD-TYPE    5  110
                        clus
vv                       MET MUTATED MET WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO          10           110
[1] 2 2
[1] FALSE

Clustering(10) Variable = SMARCB1 MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  SMARCB1 MUTATED     4   0
  SMARCB1 WILD-TYPE 131   5
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                4               136 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                0                 5 
$`SMARCB1 MUTATED`
TCGA-B1-A47M TCGA-BQ-5876 TCGA-BQ-7048 TCGA-GL-6846 
         659          586         2839         5925 

$`SMARCB1 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
         709          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
        1968            2          118           87            4         1778 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N 
         923          763         1357           67          595          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
         930         1049          379         1536          857          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
         627           14         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 
         207            5          452         2639          270         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1454         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         403          233           29          364           84         3760 
TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 
        2948         1864         1533         1516          799          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
         578          757           97          208         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1194         1059          765          446          786          194 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          378          546 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
        2072          408          360         1726         2228          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
         376            4          364          885         1043          845 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         924          841          616         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2816          391          540          428 

  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
              586                 2 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
             5925              3950 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
             1749               590 
[1] "586.0 - 5925.0 (1749.0)" "2.0 - 3950.0 (590.0)"   
[1] "hr="     "2.6e+07"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  SMARCB1 MUTATED         1        0         2        1
  SMARCB1 WILD-TYPE      94        9        34        9
D10V3, multiclass
           clus
vv          SMARCB1 MUTATED SMARCB1 WILD-TYPE
  STAGE I                 1                94
  STAGE II                0                 9
  STAGE III               2                34
  STAGE IV                1                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  SMARCB1 MUTATED     1   0     3
  SMARCB1 WILD-TYPE 102  16    39
D10V4, multiclass
       clus
vv      SMARCB1 MUTATED SMARCB1 WILD-TYPE
  T1                  1               102
  T2                  0                16
  T3+T4               3                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  SMARCB1 MUTATED    1  1  0
  SMARCB1 WILD-TYPE 27 16  4
D10V5, multiclass
[1] "Remove cluster labels:" "SMARCB1 MUTATED"       
clus
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                2                47 
       TCGA-A4-7583        TCGA-A4-7585        TCGA-A4-7915        TCGA-A4-A57E 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-A4-A5Y1        TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-3473 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-A655        TCGA-B1-A656 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-B1-A657        TCGA-B9-7268        TCGA-BQ-5877        TCGA-BQ-5878 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5882        TCGA-BQ-5885 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7058 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-G7-6789        TCGA-G7-6793 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-7966        TCGA-GL-A59R 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40Y        TCGA-J7-6720        TCGA-J7-8537 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-A5E8        TCGA-P4-A5EA 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
                   vv
clus                M0 M1 MX
  SMARCB1 MUTATED    2  0  2
  SMARCB1 WILD-TYPE 61  6 78
D10V6, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  M0               2                61
  M1               0                 6
  MX               2                78
[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
  SMARCB1 MUTATED     0   4
  SMARCB1 WILD-TYPE  47 110
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      0    4
  SMARCB1 WILD-TYPE   47  110
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  FEMALE               0                47
  MALE                 4               110
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCB1 MUTATED                                  0     0
  SMARCB1 WILD-TYPE                                2     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCB1 MUTATED                           1     3
  SMARCB1 WILD-TYPE                        41    99
D10V10, multiclass
                                  clus
vv                                 SMARCB1 MUTATED SMARCB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      1                41
  WHITE                                          3                99
[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, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     0   3
  SMARCB1 WILD-TYPE   6 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      0    3
  SMARCB1 WILD-TYPE    6  117
                        clus
vv                       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               3               117
[1] 2 2
[1] FALSE

Clustering(11) Variable = KDM6A MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED     4   0
  KDM6A WILD-TYPE 131   5
  KDM6A MUTATED KDM6A WILD-TYPE 
              4             136 
  KDM6A MUTATED KDM6A WILD-TYPE 
              0               5 
$`KDM6A MUTATED`
TCGA-A4-A48D TCGA-BQ-5886 TCGA-BQ-7060 TCGA-IZ-A6M8 
         379          792          214          146 

$`KDM6A WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A57E 
         709          597          600          436          516         1968 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 
           2          118           87            4         1778          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
         763         1357           67          595          659          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
         930         1049          379         1536          857          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
         627           14         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         207            5          452         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
        1938         1454         1242          792          921          771 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         403          233           29          364           84         3760 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2948         2839         1864         1533         1516          799 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         232          218          116          353          414         3950 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
         578          757           97          208         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1194         1059          765          446          786          194 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          378 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         546         2072          408          360         1726         2228 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         167          511          608           62          677          649 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
         376            4          364          885         1043          845 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         924          841          616         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2816          391          540          428 

  KDM6A MUTATED KDM6A WILD-TYPE 
            146               2 
  KDM6A MUTATED KDM6A WILD-TYPE 
            792            5925 
  KDM6A MUTATED KDM6A WILD-TYPE 
          296.5           598.5 
[1] "146.0 - 792.0 (296.5)" "2.0 - 5925.0 (598.5)" 
[1] "hr="     "9300000"
D11V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KDM6A MUTATED         5        0         2        0
  KDM6A WILD-TYPE      90        9        34       10
D11V3, multiclass
           clus
vv          KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I               5              90
  STAGE II              0               9
  STAGE III             2              34
  STAGE IV              0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  KDM6A MUTATED    4  1     2
  KDM6A WILD-TYPE 99 15    40
D11V4, multiclass
       clus
vv      KDM6A MUTATED KDM6A WILD-TYPE
  T1                4              99
  T2                1              15
  T3+T4             2              40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2
  KDM6A MUTATED    0  0  0
  KDM6A WILD-TYPE 28 17  4
D11V5, multiclass
                 vv
clus              M0 M1 MX
  KDM6A MUTATED    4  0  3
  KDM6A WILD-TYPE 59  6 77
D11V6, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  M0             4              59
  M1             0               6
  MX             3              77
[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
  KDM6A MUTATED     1   6
  KDM6A WILD-TYPE  46 108
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      1    6
  KDM6A WILD-TYPE   46  108
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE             1              46
  MALE               6             108
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              2              15 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-B1-A654      TCGA-B9-A44B 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B9-A69E      TCGA-GL-7773      TCGA-GL-A59T      TCGA-HE-A5NI 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-HE-A5NJ      TCGA-HE-A5NK      TCGA-IA-A40U      TCGA-P4-A5E7 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-P4-A5EB      TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM6A MUTATED                                  1     0
  KDM6A WILD-TYPE                                1     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED                           3     1
  KDM6A WILD-TYPE                        39   101
D11V10, multiclass
                                  clus
vv                                 KDM6A MUTATED KDM6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    3              39
  WHITE                                        1             101
[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, binary
                 cls
clus                0   1
  KDM6A MUTATED     0   4
  KDM6A WILD-TYPE   6 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      0    4
  KDM6A WILD-TYPE    6  116
                        clus
vv                       KDM6A MUTATED KDM6A WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             4             116
[1] 2 2
[1] FALSE

Clustering(12) Variable = SETD2 MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED     7   2
  SETD2 WILD-TYPE 128   3
  SETD2 MUTATED SETD2 WILD-TYPE 
              9             131 
  SETD2 MUTATED SETD2 WILD-TYPE 
              2               3 
$`SETD2 MUTATED`
TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-B1-A656 TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5876 
         140           87           14           64         2639          586 
TCGA-BQ-5877 TCGA-BQ-5890 TCGA-BQ-5891 
         270          233           29 

$`SETD2 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
           7           49            2          780          729          709 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
         597          600          436          379          516         1968 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
           2          118            4         1778          923          763 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
        1357           67          595          659          747          108 
TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
         510          200         1029          307          930         1049 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         379         1536          857          803          627           14 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1338          671          585          207            5          452 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         771          403          364           84         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 
        2839         1864         1533         1516          799          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
         578          757           97          208         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1194         1059          765          446          786          194 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          378 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         546         2072          408          360         1726         2228 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         167          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
         146          376            4          364          885         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
         845          924          841          616         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2584         2816          391          540          428 

  SETD2 MUTATED SETD2 WILD-TYPE 
             14               2 
  SETD2 MUTATED SETD2 WILD-TYPE 
           2639            5925 
  SETD2 MUTATED SETD2 WILD-TYPE 
            140             616 
[1] "14.0 - 2639.0 (140.0)" "2.0 - 5925.0 (616.0)" 
[1] "hr=" "16" 
D12V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SETD2 MUTATED         3        0         6        1
  SETD2 WILD-TYPE      92        9        30        9
D12V3, multiclass
           clus
vv          SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I               3              92
  STAGE II              0               9
  STAGE III             6              30
  STAGE IV              1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SETD2 MUTATED    4  0     6
  SETD2 WILD-TYPE 99 16    36
D12V4, multiclass
       clus
vv      SETD2 MUTATED SETD2 WILD-TYPE
  T1                4              99
  T2                0              16
  T3+T4             6              36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2
  SETD2 MUTATED    3  2  1
  SETD2 WILD-TYPE 25 15  3
D12V5, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  N0             3              25
  N1             2              15
  N2             1               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              M0 M1 MX
  SETD2 MUTATED    6  1  2
  SETD2 WILD-TYPE 57  5 78
D12V6, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  M0             6              57
  M1             1               5
  MX             2              78
[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
  SETD2 MUTATED     2   8
  SETD2 WILD-TYPE  45 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      2    8
  SETD2 WILD-TYPE   45  106
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE             2              45
  MALE               8             106
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
[1] "Remove cluster labels:" "SETD2 MUTATED"         
clus
  SETD2 MUTATED SETD2 WILD-TYPE 
              1              16 
     TCGA-A4-A48D      TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-B1-A654 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-B9-A69E      TCGA-GL-7773      TCGA-GL-A59T      TCGA-HE-A5NI 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-HE-A5NJ      TCGA-HE-A5NK      TCGA-IA-A40U      TCGA-IZ-A6M8 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETD2 MUTATED                                  0     0
  SETD2 WILD-TYPE                                2     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED                           3     7
  SETD2 WILD-TYPE                        39    95
D12V10, multiclass
                                  clus
vv                                 SETD2 MUTATED SETD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    3              39
  WHITE                                        7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, binary
                 cls
clus                0   1
  SETD2 MUTATED     0   7
  SETD2 WILD-TYPE   6 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      0    7
  SETD2 WILD-TYPE    6  113
                        clus
vv                       SETD2 MUTATED SETD2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             7             113
[1] 2 2
[1] FALSE

Clustering(13) Variable = AHNAK2 MUTATION ANALYSIS
D13V1, survival
                  sevent
clus2                0   1
  AHNAK2 MUTATED     6   0
  AHNAK2 WILD-TYPE 129   5
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               6              134 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               0                5 
$`AHNAK2 MUTATED`
TCGA-B1-5398 TCGA-B9-4117 TCGA-BQ-7060 TCGA-DZ-6135 TCGA-EV-5901 TCGA-GL-7773 
         595           14          214         1670         1040          393 

$`AHNAK2 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
         709          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
        1968            2          118           87            4         1778 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N 
         923          763         1357           67          659          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
         930         1049          379         1536          857          803 
TCGA-B9-4116 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         627         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
           5          452         2639          586          270         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1454         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         403          233           29          364           84         3760 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2948         2839         1864         1533         1516          799 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         232          218          116          353          414         3950 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 
        1240         2429         2460         1856          578          757 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          97          208         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7966 
         765          446          786          194         5925          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         841           32          378          546         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         360         1726         2228          167          511          608 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
          62          677          649          146          376            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         364          885         1043          845          924          841 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         616         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         540          428 

  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
              14                2 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
            1670             5925 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
           494.0            598.5 
[1] "14.0 - 1670.0 (494.0)" "2.0 - 5925.0 (598.5)" 
[1] "hr="     "2.6e+07"
D13V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  AHNAK2 MUTATED         4        0         2        0
  AHNAK2 WILD-TYPE      91        9        34       10
D13V3, multiclass
           clus
vv          AHNAK2 MUTATED AHNAK2 WILD-TYPE
  STAGE I                4               91
  STAGE II               0                9
  STAGE III              2               34
  STAGE IV               0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  AHNAK2 MUTATED    4  1     2
  AHNAK2 WILD-TYPE 99 15    40
D13V4, multiclass
       clus
vv      AHNAK2 MUTATED AHNAK2 WILD-TYPE
  T1                 4               99
  T2                 1               15
  T3+T4              2               40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2
  AHNAK2 MUTATED    2  0  0
  AHNAK2 WILD-TYPE 26 17  4
D13V5, multiclass
[1] "Remove cluster labels:" "AHNAK2 MUTATED"        
clus
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               2               47 
      TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-A4-A5Y1       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A655       TCGA-B1-A656       TCGA-B1-A657 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-BQ-5880       TCGA-BQ-5885       TCGA-BQ-5887       TCGA-BQ-5888 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891       TCGA-BQ-5892 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7058       TCGA-DW-7963 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-DZ-6131       TCGA-G7-6789       TCGA-G7-6793       TCGA-G7-6795 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-G7-7501       TCGA-GL-6846       TCGA-GL-7966       TCGA-GL-A59R 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A40Y       TCGA-J7-6720       TCGA-J7-8537 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
                  vv
clus               M0 M1 MX
  AHNAK2 MUTATED    4  0  2
  AHNAK2 WILD-TYPE 59  6 78
D13V6, multiclass
    clus
vv   AHNAK2 MUTATED AHNAK2 WILD-TYPE
  M0              4               59
  M1              0                6
  MX              2               78
[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
  AHNAK2 MUTATED     2   5
  AHNAK2 WILD-TYPE  45 109
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHNAK2 MUTATED      2    5
  AHNAK2 WILD-TYPE   45  109
        clus
vv       AHNAK2 MUTATED AHNAK2 WILD-TYPE
  FEMALE              2               45
  MALE                5              109
[1] 2 2
[1] FALSE
D13V8, continuous
[1] "Remove cluster labels:" "AHNAK2 MUTATED"        
clus
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               1               37 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8310       TCGA-A4-8311 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-A4-8312       TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A4ZT 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-AL-3466       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-DW-7841       TCGA-DW-7842       TCGA-DW-7963       TCGA-EV-5902 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-EV-5903       TCGA-G7-6790       TCGA-G7-6793       TCGA-G7-6796 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502       TCGA-G7-A4TM 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y       TCGA-J7-8537 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-Q2-A5QZ 
"AHNAK2 WILD-TYPE" 
D13V9, continuous
[1] "Remove cluster labels:" "AHNAK2 MUTATED"        
clus
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               1               16 
      TCGA-A4-A48D       TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-B1-A654 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-B9-A44B       TCGA-B9-A69E       TCGA-GL-A59T       TCGA-HE-A5NI 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-HE-A5NJ       TCGA-HE-A5NK       TCGA-IA-A40U       TCGA-IZ-A6M8 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AHNAK2 MUTATED                                  1     0
  AHNAK2 WILD-TYPE                                1     2
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  AHNAK2 MUTATED                           1     3
  AHNAK2 WILD-TYPE                        41    99
D13V10, multiclass
                                  clus
vv                                 AHNAK2 MUTATED AHNAK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                1
  ASIAN                                         0                2
  BLACK OR AFRICAN AMERICAN                     1               41
  WHITE                                         3               99
[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, binary
                  cls
clus                 0   1
  AHNAK2 MUTATED     0   4
  AHNAK2 WILD-TYPE   6 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHNAK2 MUTATED      0    4
  AHNAK2 WILD-TYPE    6  116
                        clus
vv                       AHNAK2 MUTATED AHNAK2 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              4              116
[1] 2 2
[1] FALSE

Clustering(14) Variable = AHCY MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  AHCY MUTATED     3   0
  AHCY WILD-TYPE 132   5
  AHCY MUTATED AHCY WILD-TYPE 
             3            137 
  AHCY MUTATED AHCY WILD-TYPE 
             0              5 
$`AHCY MUTATED`
TCGA-A4-A6HP TCGA-B9-4117 TCGA-IA-A40Y 
           4           14           62 

$`AHCY WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
         709          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3472 
        1968            2          118           87         1778          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
         763         1357           67          595          659          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
         930         1049          379         1536          857          803 
TCGA-B9-4116 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         627         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
           5          452         2639          586          270         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1454         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         403          233           29          364           84         3760 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2948         2839         1864         1533         1516          799 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        3950         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
          92         1240         2429         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
        1040          578          757           97          208         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
        1479         1194         1059          765          446          786 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
         194         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         378          546         2072          408          360         1726 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 
        2228          167          511          608          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
         146          376            4          364          885         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
         845          924          841          616         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2584         2816          391          540          428 

  AHCY MUTATED AHCY WILD-TYPE 
             4              2 
  AHCY MUTATED AHCY WILD-TYPE 
            62           5925 
  AHCY MUTATED AHCY WILD-TYPE 
            14            600 
[1] "4.0 - 62.0 (14.0)"    "2.0 - 5925.0 (600.0)"
[1] "hr=" NA   
D14V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  AHCY MUTATED         1        0         2        0
  AHCY WILD-TYPE      94        9        34       10
D14V3, multiclass
           clus
vv          AHCY MUTATED AHCY WILD-TYPE
  STAGE I              1             94
  STAGE II             0              9
  STAGE III            2             34
  STAGE IV             0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  AHCY MUTATED     1   1     2
  AHCY WILD-TYPE 102  15    40
D14V4, multiclass
       clus
vv      AHCY MUTATED AHCY WILD-TYPE
  T1               1            102
  T2               1             15
  T3+T4            2             40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2
  AHCY MUTATED    1  1  0
  AHCY WILD-TYPE 27 16  4
D14V5, multiclass
[1] "Remove cluster labels:" "AHCY MUTATED"          
clus
  AHCY MUTATED AHCY WILD-TYPE 
             2             47 
    TCGA-A4-7583     TCGA-A4-7585     TCGA-A4-7915     TCGA-A4-A57E 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-A4-A5Y1     TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-B1-A657     TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5885     TCGA-BQ-5887 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7058 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-DW-7963     TCGA-DZ-6131     TCGA-G7-6789     TCGA-G7-6793 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-GL-6846     TCGA-GL-7966 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-GL-A59R     TCGA-IA-A40U     TCGA-J7-6720     TCGA-J7-8537 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
                vv
clus             M0 M1 MX
  AHCY MUTATED    1  0  2
  AHCY WILD-TYPE 62  6 78
D14V6, multiclass
    clus
vv   AHCY MUTATED AHCY WILD-TYPE
  M0            1             62
  M1            0              6
  MX            2             78
[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
  AHCY MUTATED     2   2
  AHCY WILD-TYPE  45 112
[1] "tbl2"
                cls
clus             [,1] [,2]
  AHCY MUTATED      2    2
  AHCY WILD-TYPE   45  112
        clus
vv       AHCY MUTATED AHCY WILD-TYPE
  FEMALE            2             45
  MALE              2            112
[1] 2 2
[1] FALSE
D14V8, continuous
[1] "Remove cluster labels:" "AHCY MUTATED"          
clus
  AHCY MUTATED AHCY WILD-TYPE 
             2             36 
    TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8310     TCGA-A4-8311 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-A4-8312     TCGA-A4-8518     TCGA-A4-8630     TCGA-A4-A4ZT 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-AL-3466 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-DW-7842     TCGA-DW-7963     TCGA-EV-5901     TCGA-EV-5902 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-EV-5903     TCGA-G7-6790     TCGA-G7-6793     TCGA-G7-6796 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A40X     TCGA-J7-8537     TCGA-Q2-A5QZ 
"AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" "AHCY WILD-TYPE" 
D14V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AHCY MUTATED                                  0     0
  AHCY WILD-TYPE                                2     2
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AHCY MUTATED                           1     2
  AHCY WILD-TYPE                        41   100
D14V10, multiclass
                                  clus
vv                                 AHCY MUTATED AHCY WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0              2
  BLACK OR AFRICAN AMERICAN                   1             41
  WHITE                                       2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, binary
                cls
clus               0   1
  AHCY MUTATED     0   3
  AHCY WILD-TYPE   6 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  AHCY MUTATED      0    3
  AHCY WILD-TYPE    6  117
                        clus
vv                       AHCY MUTATED AHCY WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            3            117
[1] 2 2
[1] FALSE

Clustering(15) Variable = IDUA MUTATION ANALYSIS
D15V1, survival
                sevent
clus2              0   1
  IDUA MUTATED     4   0
  IDUA WILD-TYPE 131   5
  IDUA MUTATED IDUA WILD-TYPE 
             4            136 
  IDUA MUTATED IDUA WILD-TYPE 
             0              5 
$`IDUA MUTATED`
TCGA-BQ-5883 TCGA-G7-6792 TCGA-GL-7773 TCGA-P4-A5EB 
        1242         1479          393         2584 

$`IDUA WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
         709          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
        1968            2          118           87            4         1778 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         923          763         1357           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         747          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
         307          930         1049          379         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
         803          627           14         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
         585          207            5          452         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
         270         1938         1454          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
         771          403          233           29          364           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         799          232          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
         414         3950         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
         445           92         1240         2429         2460         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
        1670         1040          578          757           97          208 
TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
        1575         1194         1059          765          446          786 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
         194         5925          112          841           32          378 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         546         2072          408          360         1726         2228 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         167          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
         146          376            4          364          885         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
         845          924          841          616         3035         2653 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2816          391          540          428 

  IDUA MUTATED IDUA WILD-TYPE 
           393              2 
  IDUA MUTATED IDUA WILD-TYPE 
          2584           5925 
  IDUA MUTATED IDUA WILD-TYPE 
        1360.5          590.5 
[1] "393.0 - 2584.0 (1360.5)" "2.0 - 5925.0 (590.5)"   
[1] "hr="     "2.6e+07"
D15V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  IDUA MUTATED         4        0         1        0
  IDUA WILD-TYPE      91        9        35       10
D15V3, multiclass
           clus
vv          IDUA MUTATED IDUA WILD-TYPE
  STAGE I              4             91
  STAGE II             0              9
  STAGE III            1             35
  STAGE IV             0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  IDUA MUTATED    4  0     1
  IDUA WILD-TYPE 99 16    41
D15V4, multiclass
       clus
vv      IDUA MUTATED IDUA WILD-TYPE
  T1               4             99
  T2               0             16
  T3+T4            1             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2
  IDUA MUTATED    1  0  0
  IDUA WILD-TYPE 27 17  4
D15V5, multiclass
[1] "Remove cluster labels:" "IDUA MUTATED"          
clus
  IDUA MUTATED IDUA WILD-TYPE 
             1             48 
    TCGA-A4-7583     TCGA-A4-7915     TCGA-A4-A57E     TCGA-A4-A5Y1 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656     TCGA-B1-A657 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7058 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-DW-7963     TCGA-DZ-6131     TCGA-G7-6789     TCGA-G7-6793 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-GL-6846     TCGA-GL-7966 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-GL-A59R     TCGA-IA-A40U     TCGA-IA-A40Y     TCGA-J7-6720 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-J7-8537     TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
                vv
clus             M0 M1 MX
  IDUA MUTATED    2  0  3
  IDUA WILD-TYPE 61  6 77
D15V6, multiclass
    clus
vv   IDUA MUTATED IDUA WILD-TYPE
  M0            2             61
  M1            0              6
  MX            3             77
[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
  IDUA MUTATED     1   4
  IDUA WILD-TYPE  46 110
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      1    4
  IDUA WILD-TYPE   46  110
        clus
vv       IDUA MUTATED IDUA WILD-TYPE
  FEMALE            1             46
  MALE              4            110
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
[1] "Remove cluster labels:" "IDUA MUTATED"          
clus
  IDUA MUTATED IDUA WILD-TYPE 
             2             15 
    TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-B1-A654 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B9-A44B     TCGA-B9-A69E     TCGA-GL-A59T     TCGA-HE-A5NI 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-HE-A5NJ     TCGA-HE-A5NK     TCGA-IA-A40U     TCGA-IZ-A6M8 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-P4-A5E7     TCGA-PJ-A5Z9     TCGA-Q2-A5QZ 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IDUA MUTATED                                  0     0
  IDUA WILD-TYPE                                2     2
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IDUA MUTATED                           2     3
  IDUA WILD-TYPE                        40    99
D15V10, multiclass
                                  clus
vv                                 IDUA MUTATED IDUA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0              2
  BLACK OR AFRICAN AMERICAN                   2             40
  WHITE                                       3             99
[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, binary
                cls
clus               0   1
  IDUA MUTATED     0   4
  IDUA WILD-TYPE   6 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      0    4
  IDUA WILD-TYPE    6  116
                        clus
vv                       IDUA MUTATED IDUA WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            4            116
[1] 2 2
[1] FALSE

Clustering(16) Variable = OR2L8 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  OR2L8 MUTATED     2   0
  OR2L8 WILD-TYPE 133   5
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              2             138 
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              0               5 
$`OR2L8 MUTATED`
TCGA-EV-5903 TCGA-IZ-8196 
         757          649 

$`OR2L8 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
         709          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
        1968            2          118           87            4         1778 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         923          763         1357           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         747          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
         307          930         1049          379         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
         803          627           14         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
         585          207            5          452         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         792          771          403          233           29          364 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
          84         3760         2948         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
        1516          799          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         353          414         3950         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-G7-6789 
        1856         1670         1040          578           97          208 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        1575         1479         1194         1059          765          446 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
         786          194         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          378          546         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
        1726         2228          167          511          608           62 
TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
         677          146          376            4          364          885 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
        1043          845          924          841          616         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2584         2816          391          540          428 

  OR2L8 MUTATED OR2L8 WILD-TYPE 
            649               2 
  OR2L8 MUTATED OR2L8 WILD-TYPE 
            757            5925 
  OR2L8 MUTATED OR2L8 WILD-TYPE 
          703.0           590.5 
[1] "649.0 - 757.0 (703.0)" "2.0 - 5925.0 (590.5)" 
[1] "Remove cluster labels:" "OR2L8 MUTATED"         
D16V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  OR2L8 MUTATED         3        0         0        1
  OR2L8 WILD-TYPE      92        9        36        9
D16V3, multiclass
           clus
vv          OR2L8 MUTATED OR2L8 WILD-TYPE
  STAGE I               3              92
  STAGE II              0               9
  STAGE III             0              36
  STAGE IV              1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  OR2L8 MUTATED     3   0     1
  OR2L8 WILD-TYPE 100  16    41
D16V4, multiclass
       clus
vv      OR2L8 MUTATED OR2L8 WILD-TYPE
  T1                3             100
  T2                0              16
  T3+T4             1              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2
  OR2L8 MUTATED    0  1  0
  OR2L8 WILD-TYPE 28 16  4
D16V5, multiclass
[1] "Remove cluster labels:" "OR2L8 MUTATED"         
clus
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              1              48 
     TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-A4-A5Y1      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B1-A657      TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-5887      TCGA-BQ-5888      TCGA-BQ-5890      TCGA-BQ-5891 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7058 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6789      TCGA-G7-6793 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846      TCGA-GL-7966 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-GL-A59R      TCGA-IA-A40U      TCGA-IA-A40Y      TCGA-J7-6720 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-J7-8537      TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
                 vv
clus              M0 M1 MX
  OR2L8 MUTATED    1  1  2
  OR2L8 WILD-TYPE 62  5 78
D16V6, multiclass
    clus
vv   OR2L8 MUTATED OR2L8 WILD-TYPE
  M0             1              62
  M1             1               5
  MX             2              78
[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
  OR2L8 MUTATED     1   3
  OR2L8 WILD-TYPE  46 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2L8 MUTATED      1    3
  OR2L8 WILD-TYPE   46  111
        clus
vv       OR2L8 MUTATED OR2L8 WILD-TYPE
  FEMALE             1              46
  MALE               3             111
[1] 2 2
[1] FALSE
D16V8, continuous
[1] "Remove cluster labels:" "OR2L8 MUTATED"         
clus
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              1              37 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8310      TCGA-A4-8311 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A4ZT 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-AL-3466      TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-DW-7841      TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-EV-5902      TCGA-G7-6790      TCGA-G7-6793      TCGA-G7-6796 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-Q2-A5QZ 
"OR2L8 WILD-TYPE" 
D16V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2L8 MUTATED                                  0     0
  OR2L8 WILD-TYPE                                2     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR2L8 MUTATED                           0     4
  OR2L8 WILD-TYPE                        42    98
D16V10, multiclass
                                  clus
vv                                 OR2L8 MUTATED OR2L8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    0              42
  WHITE                                        4              98
[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, binary
                 cls
clus                0   1
  OR2L8 MUTATED     0   3
  OR2L8 WILD-TYPE   6 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2L8 MUTATED      0    3
  OR2L8 WILD-TYPE    6  117
                        clus
vv                       OR2L8 MUTATED OR2L8 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3             117
[1] 2 2
[1] FALSE

Clustering(17) Variable = HOXD8 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  HOXD8 MUTATED     4   0
  HOXD8 WILD-TYPE 131   5
  HOXD8 MUTATED HOXD8 WILD-TYPE 
              4             136 
  HOXD8 MUTATED HOXD8 WILD-TYPE 
              0               5 
$`HOXD8 MUTATED`
TCGA-AL-3472 TCGA-B1-A47N TCGA-BQ-5878 TCGA-IZ-8196 
         923          747         1938          649 

$`HOXD8 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
         709          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
        1968            2          118           87            4         1778 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A654 
         763         1357           67          595          659          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         510           14          200         1029          307          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
        1049          379         1536          857          803          627 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
          14         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5881 
           5          452         2639          586          270         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1242          792          921          792          771          403 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         233           29          364           84         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 
        2839         1864         1533         1516          799          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
         578          757           97          208         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1194         1059          765          446          786          194 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          378 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         546         2072          408          360         1726         2228 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-A6M8 
         167          511          608           62          677          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
         376            4          364          885         1043          845 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         924          841          616         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2816          391          540          428 

  HOXD8 MUTATED HOXD8 WILD-TYPE 
            649               2 
  HOXD8 MUTATED HOXD8 WILD-TYPE 
           1938            5925 
  HOXD8 MUTATED HOXD8 WILD-TYPE 
          835.0           585.5 
[1] "649.0 - 1938.0 (835.0)" "2.0 - 5925.0 (585.5)"  
[1] "hr="     "2.6e+07"
D17V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  HOXD8 MUTATED         2        0         1        0
  HOXD8 WILD-TYPE      93        9        35       10
D17V3, multiclass
           clus
vv          HOXD8 MUTATED HOXD8 WILD-TYPE
  STAGE I               2              93
  STAGE II              0               9
  STAGE III             1              35
  STAGE IV              0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  HOXD8 MUTATED     2   1     1
  HOXD8 WILD-TYPE 101  15    41
D17V4, multiclass
       clus
vv      HOXD8 MUTATED HOXD8 WILD-TYPE
  T1                2             101
  T2                1              15
  T3+T4             1              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2
  HOXD8 MUTATED    1  1  0
  HOXD8 WILD-TYPE 27 16  4
D17V5, multiclass
[1] "Remove cluster labels:" "HOXD8 MUTATED"         
clus
  HOXD8 MUTATED HOXD8 WILD-TYPE 
              2              47 
     TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-A4-A5Y1      TCGA-AL-3466      TCGA-AL-3473      TCGA-AL-7173 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656      TCGA-B1-A657 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5879      TCGA-BQ-5880 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-BQ-5882      TCGA-BQ-5885      TCGA-BQ-5887      TCGA-BQ-5888 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891      TCGA-BQ-5892 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045      TCGA-BQ-7048 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7058      TCGA-DW-7963 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-DZ-6131      TCGA-G7-6789      TCGA-G7-6793      TCGA-G7-6795 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-G7-7501      TCGA-GL-6846      TCGA-GL-7966      TCGA-GL-A59R 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A40Y      TCGA-J7-6720      TCGA-J7-8537 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
                 vv
clus              M0 M1 MX
  HOXD8 MUTATED    2  0  2
  HOXD8 WILD-TYPE 61  6 78
D17V6, multiclass
    clus
vv   HOXD8 MUTATED HOXD8 WILD-TYPE
  M0             2              61
  M1             0               6
  MX             2              78
[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
  HOXD8 MUTATED     1   3
  HOXD8 WILD-TYPE  46 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD8 MUTATED      1    3
  HOXD8 WILD-TYPE   46  111
        clus
vv       HOXD8 MUTATED HOXD8 WILD-TYPE
  FEMALE             1              46
  MALE               3             111
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HOXD8 MUTATED                                  0     0
  HOXD8 WILD-TYPE                                2     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HOXD8 MUTATED                           1     3
  HOXD8 WILD-TYPE                        41    99
D17V10, multiclass
                                  clus
vv                                 HOXD8 MUTATED HOXD8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    1              41
  WHITE                                        3              99
[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, binary
                 cls
clus                0   1
  HOXD8 MUTATED     0   3
  HOXD8 WILD-TYPE   6 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD8 MUTATED      0    3
  HOXD8 WILD-TYPE    6  117
                        clus
vv                       HOXD8 MUTATED HOXD8 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3             117
[1] 2 2
[1] FALSE

Clustering(18) Variable = PAM MUTATION ANALYSIS
D18V1, survival
               sevent
clus2             0   1
  PAM MUTATED     3   0
  PAM WILD-TYPE 132   5
  PAM MUTATED PAM WILD-TYPE 
            3           137 
  PAM MUTATED PAM WILD-TYPE 
            0             5 
$`PAM MUTATED`
TCGA-HE-A5NI TCGA-IA-A40U TCGA-P4-A5E6 
         360          511         3035 

$`PAM WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
         709          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
        1968            2          118           87            4         1778 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         923          763         1357           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         747          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
         307          930         1049          379         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
         803          627           14         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
         585          207            5          452         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         792          771          403          233           29          364 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
          84         3760         2948         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
        1516          799          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         353          414         3950         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
        1856         1670         1040          578          757           97 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
         208         1575         1479         1194         1059          765 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         446          786          194         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         841           32          378          546         2072          408 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        1726         2228          167          608           62          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
         649          146          376            4          364          885 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E7 
        1043          845          924          841          616         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2584         2816          391          540          428 

  PAM MUTATED PAM WILD-TYPE 
          360             2 
  PAM MUTATED PAM WILD-TYPE 
         3035          5925 
  PAM MUTATED PAM WILD-TYPE 
          511           597 
[1] "360.0 - 3035.0 (511.0)" "2.0 - 5925.0 (597.0)"  
[1] "hr="     "2.5e+07"
D18V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  PAM MUTATED         1        0         2        0
  PAM WILD-TYPE      94        9        34       10
D18V3, multiclass
           clus
vv          PAM MUTATED PAM WILD-TYPE
  STAGE I             1            94
  STAGE II            0             9
  STAGE III           2            34
  STAGE IV            0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2 T3+T4
  PAM MUTATED     2   0     1
  PAM WILD-TYPE 101  16    41
D18V4, multiclass
       clus
vv      PAM MUTATED PAM WILD-TYPE
  T1              2           101
  T2              0            16
  T3+T4           1            41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2
  PAM MUTATED    1  1  0
  PAM WILD-TYPE 27 16  4
D18V5, multiclass
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            2            47 
   TCGA-A4-7583    TCGA-A4-7585    TCGA-A4-7915    TCGA-A4-A57E    TCGA-A4-A5Y1 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-AL-3466    TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173    TCGA-B1-5398 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B1-A655    TCGA-B1-A656    TCGA-B1-A657    TCGA-B9-7268    TCGA-BQ-5877 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5878    TCGA-BQ-5879    TCGA-BQ-5880    TCGA-BQ-5882    TCGA-BQ-5885 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889    TCGA-BQ-5890    TCGA-BQ-5891 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894    TCGA-BQ-7045    TCGA-BQ-7048 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-7050    TCGA-BQ-7051    TCGA-BQ-7058    TCGA-DW-7963    TCGA-DZ-6131 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-6789    TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-7501    TCGA-GL-6846 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-GL-7966    TCGA-GL-A59R    TCGA-IA-A40Y    TCGA-J7-6720    TCGA-J7-8537 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-P4-A5E8    TCGA-P4-A5EA 
"PAM WILD-TYPE" "PAM WILD-TYPE" 
               vv
clus            M0 M1 MX
  PAM MUTATED    1  0  2
  PAM WILD-TYPE 62  6 78
D18V6, multiclass
    clus
vv   PAM MUTATED PAM WILD-TYPE
  M0           1            62
  M1           0             6
  MX           2            78
[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
  PAM MUTATED     0   3
  PAM WILD-TYPE  47 111
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      0    3
  PAM WILD-TYPE   47  111
        clus
vv       PAM MUTATED PAM WILD-TYPE
  FEMALE           0            47
  MALE             3           111
[1] 2 2
[1] FALSE
D18V8, continuous
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            1            37 
   TCGA-A4-7286    TCGA-A4-7828    TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8312 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A4ZT    TCGA-A4-A57E    TCGA-A4-A5DU 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-A5XZ    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-DW-5560    TCGA-DW-5561 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839    TCGA-DW-7840 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-7841    TCGA-DW-7842    TCGA-DW-7963    TCGA-EV-5901    TCGA-EV-5902 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-EV-5903    TCGA-G7-6790    TCGA-G7-6793    TCGA-G7-6796    TCGA-G7-6797 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-7501    TCGA-G7-7502    TCGA-G7-A4TM    TCGA-IA-A40X    TCGA-IA-A40Y 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-J7-8537    TCGA-Q2-A5QZ 
"PAM WILD-TYPE" "PAM WILD-TYPE" 
D18V9, continuous
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            2            15 
   TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0    TCGA-B1-A654    TCGA-B9-A44B 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B9-A69E    TCGA-GL-7773    TCGA-GL-A59T    TCGA-HE-A5NJ    TCGA-HE-A5NK 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-IZ-A6M8    TCGA-P4-A5E7    TCGA-P4-A5EB    TCGA-PJ-A5Z9    TCGA-Q2-A5QZ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAM MUTATED                                  0     0
  PAM WILD-TYPE                                2     2
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  PAM MUTATED                           1     1
  PAM WILD-TYPE                        41   101
D18V10, multiclass
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            2           146 
   TCGA-A4-7286    TCGA-A4-7287    TCGA-A4-7288    TCGA-A4-7583    TCGA-A4-7584 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-7585    TCGA-A4-7732    TCGA-A4-7734    TCGA-A4-7828    TCGA-A4-7915 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-7996    TCGA-A4-7997    TCGA-A4-8098    TCGA-A4-8310    TCGA-A4-8311 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-8312    TCGA-A4-8515    TCGA-A4-8517    TCGA-A4-8518    TCGA-A4-8630 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-A48D    TCGA-A4-A4ZT    TCGA-A4-A57E    TCGA-A4-A5DU    TCGA-A4-A5XZ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-A5Y0    TCGA-A4-A5Y1    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-AL-3467 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173    TCGA-AT-A5NU    TCGA-B1-5398 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B1-A47M    TCGA-B1-A47N    TCGA-B1-A654    TCGA-B1-A655    TCGA-B1-A656 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B1-A657    TCGA-B3-3925    TCGA-B3-3926    TCGA-B3-4103    TCGA-B3-4104 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B3-8121    TCGA-B9-4113    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4116 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B9-4117    TCGA-B9-5156    TCGA-B9-7268    TCGA-B9-A44B    TCGA-B9-A5W7 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B9-A5W8    TCGA-B9-A5W9    TCGA-B9-A69E    TCGA-BQ-5875    TCGA-BQ-5876 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879    TCGA-BQ-5880    TCGA-BQ-5881 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5883    TCGA-BQ-5884    TCGA-BQ-5885    TCGA-BQ-5886    TCGA-BQ-5887 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5888    TCGA-BQ-5889    TCGA-BQ-5890    TCGA-BQ-5891    TCGA-BQ-5892 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-5893    TCGA-BQ-7044    TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-7050    TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7058 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-BQ-7062    TCGA-DW-5560 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DW-7963    TCGA-DZ-6131 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DZ-6133    TCGA-DZ-6134    TCGA-EV-5901    TCGA-EV-5902    TCGA-EV-5903 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-F9-A4JJ    TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792    TCGA-G7-6793 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7501    TCGA-G7-7502 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-A4TM    TCGA-GL-6846    TCGA-GL-7773    TCGA-GL-7966    TCGA-GL-8500 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-GL-A4EM    TCGA-GL-A59R    TCGA-GL-A59T    TCGA-IA-A40X    TCGA-IA-A40Y 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-IZ-8195    TCGA-IZ-8196    TCGA-IZ-A6M8    TCGA-IZ-A6M9    TCGA-J7-6720 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-J7-8537    TCGA-KV-A6GD    TCGA-KV-A6GE    TCGA-MH-A55W    TCGA-MH-A55Z 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-MH-A560    TCGA-MH-A561    TCGA-MH-A562    TCGA-P4-A5E7    TCGA-P4-A5E8 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-P4-A5EA    TCGA-P4-A5EB    TCGA-P4-A5ED    TCGA-PJ-A5Z8    TCGA-PJ-A5Z9 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-Q2-A5QZ 
"PAM WILD-TYPE" 
D18V11, binary
               cls
clus              0   1
  PAM MUTATED     0   2
  PAM WILD-TYPE   6 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      0    2
  PAM WILD-TYPE    6  118
                        clus
vv                       PAM MUTATED PAM WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           2           118
[1] 2 2
[1] FALSE

Clustering(19) Variable = CSGALNACT2 MUTATION ANALYSIS
D19V1, survival
                      sevent
clus2                    0   1
  CSGALNACT2 MUTATED     4   0
  CSGALNACT2 WILD-TYPE 131   5
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   4                  136 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   0                    5 
$`CSGALNACT2 MUTATED`
TCGA-A4-A4ZT TCGA-HE-A5NK TCGA-KV-A6GD TCGA-MH-A560 
         516         2228          364          924 

$`CSGALNACT2 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A57E 
         709          597          600          436          379         1968 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 
           2          118           87            4         1778          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
         763         1357           67          595          659          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
         930         1049          379         1536          857          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
         627           14         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         207            5          452         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
         771          403          233           29          364           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         799          232          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
         414         3950         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
         445           92         1240         2429         2460         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
        1670         1040          578          757           97          208 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        1575         1479         1194         1059          765          446 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
         786          194         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          378          546         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        1726          167          511          608           62          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GE TCGA-MH-A55W 
         649          146          376            4          885         1043 
TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         845          841          616         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2816          391          540          428 

  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                 364                    2 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                2228                 5925 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                 720                  596 
[1] "364.0 - 2228.0 (720.0)" "2.0 - 5925.0 (596.0)"  
[1] "hr="     "2.6e+07"
D19V2, continuous
                      vv
clus                   STAGE I STAGE II STAGE III STAGE IV
  CSGALNACT2 MUTATED         3        0         1        0
  CSGALNACT2 WILD-TYPE      92        9        35       10
D19V3, multiclass
           clus
vv          CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  STAGE I                    3                   92
  STAGE II                   0                    9
  STAGE III                  1                   35
  STAGE IV                   0                   10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                   T1 T2 T3+T4
  CSGALNACT2 MUTATED    4  0     1
  CSGALNACT2 WILD-TYPE 99 16    41
D19V4, multiclass
       clus
vv      CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  T1                     4                   99
  T2                     0                   16
  T3+T4                  1                   41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                   N0 N1 N2
  CSGALNACT2 MUTATED    0  0  0
  CSGALNACT2 WILD-TYPE 28 17  4
D19V5, multiclass
                      vv
clus                   M0 M1 MX
  CSGALNACT2 MUTATED    3  0  2
  CSGALNACT2 WILD-TYPE 60  6 78
D19V6, multiclass
    clus
vv   CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  M0                  3                   60
  M1                  0                    6
  MX                  2                   78
[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
  CSGALNACT2 MUTATED     2   3
  CSGALNACT2 WILD-TYPE  45 111
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      2    3
  CSGALNACT2 WILD-TYPE   45  111
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  FEMALE                  2                   45
  MALE                    3                  111
[1] 2 2
[1] FALSE
D19V8, continuous
[1] "Remove cluster labels:" "CSGALNACT2 MUTATED"    
clus
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   1                   37 
          TCGA-A4-7286           TCGA-A4-7828           TCGA-A4-8310 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-8311           TCGA-A4-8312           TCGA-A4-8518 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-8630           TCGA-A4-A57E           TCGA-A4-A5DU 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-A5XZ           TCGA-A4-A6HP           TCGA-AL-3466 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-5560           TCGA-DW-5561           TCGA-DW-7834 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-7837           TCGA-DW-7838           TCGA-DW-7839 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-7840           TCGA-DW-7841           TCGA-DW-7842 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-7963           TCGA-EV-5901           TCGA-EV-5902 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-EV-5903           TCGA-G7-6790           TCGA-G7-6793 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-G7-6796           TCGA-G7-6797           TCGA-G7-7501 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-G7-7502           TCGA-G7-A4TM           TCGA-IA-A40U 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-IA-A40X           TCGA-IA-A40Y           TCGA-J7-8537 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-Q2-A5QZ 
"CSGALNACT2 WILD-TYPE" 
D19V9, continuous
[1] "Remove cluster labels:" "CSGALNACT2 MUTATED"    
clus
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   1                   16 
          TCGA-A4-A48D           TCGA-A4-A57E           TCGA-A4-A5Y0 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-B1-A654           TCGA-B9-A44B           TCGA-B9-A69E 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-GL-7773           TCGA-GL-A59T           TCGA-HE-A5NI 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-HE-A5NJ           TCGA-IA-A40U           TCGA-IZ-A6M8 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-P4-A5E7           TCGA-P4-A5EB           TCGA-PJ-A5Z9 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-Q2-A5QZ 
"CSGALNACT2 WILD-TYPE" 
                      vv
clus                   AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSGALNACT2 MUTATED                                  0     0
  CSGALNACT2 WILD-TYPE                                2     2
                      vv
clus                   BLACK OR AFRICAN AMERICAN WHITE
  CSGALNACT2 MUTATED                           0     3
  CSGALNACT2 WILD-TYPE                        42    99
D19V10, multiclass
                                  clus
vv                                 CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                  0                    2
  ASIAN                                             0                    2
  BLACK OR AFRICAN AMERICAN                         0                   42
  WHITE                                             3                   99
[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, binary
                      cls
clus                     0   1
  CSGALNACT2 MUTATED     0   3
  CSGALNACT2 WILD-TYPE   6 117
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      0    3
  CSGALNACT2 WILD-TYPE    6  117
                        clus
vv                       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  HISPANIC OR LATINO                      0                    6
  NOT HISPANIC OR LATINO                  3                  117
[1] 2 2
[1] FALSE
