[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/10005964/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/10686704/transformed.cor.cli.txt"

nPatients in clinical file=202, in cluster file=168, common to both=165
[1]  28 165
[1] "HNRNPM MUTATION ANALYSIS"
[1] 3
  HNRNPM MUTATED HNRNPM WILD-TYPE 
              11              154 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
              11              154 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
           12           153 
  NF2 MUTATED NF2 WILD-TYPE 
           12           153 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
             9            156 
  NEFH MUTATED NEFH WILD-TYPE 
             9            156 
[1] "TDG MUTATION ANALYSIS"
[1] 3
  TDG MUTATED TDG WILD-TYPE 
            5           160 
  TDG MUTATED TDG WILD-TYPE 
            5           160 
[1] "ZNF598 MUTATION ANALYSIS"
[1] 3
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              13              152 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              13              152 
[1] "SKI MUTATION ANALYSIS"
[1] 3
  SKI MUTATED SKI WILD-TYPE 
            6           159 
  SKI MUTATED SKI WILD-TYPE 
            6           159 
[1] "CSGALNACT2 MUTATION ANALYSIS"
[1] 3
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   5                  160 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   5                  160 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             15             150 
  SETD2 MUTATED SETD2 WILD-TYPE 
             15             150 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
           15           150 
  MET MUTATED MET WILD-TYPE 
           15           150 
[1] "MUC5B MUTATION ANALYSIS"
[1] 3
  MUC5B MUTATED MUC5B WILD-TYPE 
             18             147 
  MUC5B MUTATED MUC5B WILD-TYPE 
             18             147 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
              9             156 
  KDM6A MUTATED KDM6A WILD-TYPE 
              9             156 
[1] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               8              157 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               8              157 
[1] "OR2L8 MUTATION ANALYSIS"
[1] 3
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              4             161 
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              4             161 
[1] "MYH6 MUTATION ANALYSIS"
[1] 3
  MYH6 MUTATED MYH6 WILD-TYPE 
             8            157 
  MYH6 MUTATED MYH6 WILD-TYPE 
             8            157 
[1] "UNC13A MUTATION ANALYSIS"
[1] 3
  UNC13A MUTATED UNC13A WILD-TYPE 
               9              156 
  UNC13A MUTATED UNC13A WILD-TYPE 
               9              156 
[1] "MED16 MUTATION ANALYSIS"
[1] 3
  MED16 MUTATED MED16 WILD-TYPE 
              4             161 
  MED16 MUTATED MED16 WILD-TYPE 
              4             161 
[1] "GLUD2 MUTATION ANALYSIS"
[1] 3
  GLUD2 MUTATED GLUD2 WILD-TYPE 
             11             154 
  GLUD2 MUTATED GLUD2 WILD-TYPE 
             11             154 
[1] "BMS1 MUTATION ANALYSIS"
[1] 3
  BMS1 MUTATED BMS1 WILD-TYPE 
            13            152 
  BMS1 MUTATED BMS1 WILD-TYPE 
            13            152 
[1] "FUS MUTATION ANALYSIS"
[1] 3
  FUS MUTATED FUS WILD-TYPE 
            3           162 
  FUS MUTATED FUS WILD-TYPE 
            3           162 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             7            158 
  TP53 MUTATED TP53 WILD-TYPE 
             7            158 
[1] "ACADL MUTATION ANALYSIS"
[1] 3
  ACADL MUTATED ACADL WILD-TYPE 
              4             161 
  ACADL MUTATED ACADL WILD-TYPE 
              4             161 
[1] "AHNAK2 MUTATION ANALYSIS"
[1] 3
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
              10              155 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
              10              155 
[1] "SMARCB1 MUTATION ANALYSIS"
[1] 3
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                5               160 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                5               160 
[1] "TEKT1 MUTATION ANALYSIS"
[1] 3
  TEKT1 MUTATED TEKT1 WILD-TYPE 
              4             161 
  TEKT1 MUTATED TEKT1 WILD-TYPE 
              4             161 
[1] "MKL1 MUTATION ANALYSIS"
[1] 3
  MKL1 MUTATED MKL1 WILD-TYPE 
             9            156 
  MKL1 MUTATED MKL1 WILD-TYPE 
             9            156 
[1] "MYH7 MUTATION ANALYSIS"
[1] 3
  MYH7 MUTATED MYH7 WILD-TYPE 
             6            159 
  MYH7 MUTATED MYH7 WILD-TYPE 
             6            159 
[1] "MAP4K3 MUTATION ANALYSIS"
[1] 3
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
               5              160 
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
               5              160 
[1] "NEK2 MUTATION ANALYSIS"
[1] 3
  NEK2 MUTATED NEK2 WILD-TYPE 
             3            162 
  NEK2 MUTATED NEK2 WILD-TYPE 
             3            162 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 165 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-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
        1636          923          763         1357           26           67 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         595          659          747          108          510           14 
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-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
         857          803          627           14           35          460 
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-5877 TCGA-BQ-5878 TCGA-BQ-5879 
         102         2639          586          270         1938           NA 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
          NA         1454           NA         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
         792          771          403           NA          233           29 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
         364           NA           84         3760           NA         2948 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2839           NA         1864         1533         1516          799 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         612           NA          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-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
          NA         1856         1670         1040          578          757 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
          97          208         1575         1479           NA         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
        1059          765          446          786          279         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          178           91 
TCGA-HE-7128 TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          NA           NA           NA         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-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD 
         649          146            2           NA            4          160 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         885         1043          391          543          438          292 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
        3035         2653           NA           NA         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         391          174           57 
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=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=136,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=8,	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=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=9,	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=11,	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 165 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  17  44   1 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  103    17    45 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
103  17  44   1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  103    17    45 
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=11, 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    11   0
  HNRNPM WILD-TYPE 126   5
  HNRNPM MUTATED HNRNPM WILD-TYPE 
              11              131 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
               0                5 
$`HNRNPM MUTATED`
TCGA-B9-5155 TCGA-BQ-5887 TCGA-BQ-7055 TCGA-BQ-7062 TCGA-DW-7841 TCGA-DZ-6132 
         460          771          799          116          445         2460 
TCGA-EV-5902 TCGA-G7-7502 TCGA-GL-6846 TCGA-IA-A40X TCGA-PJ-A5Z8 
         578          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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
         803          627           14           35         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
          64          585          207            5          102         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
         586          270         1938         1454         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         921          792          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-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-5560 
        1516          612          232          214          218          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-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
          92         1240         2429         1856         1670         1040 
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-A4TM TCGA-GL-7773 TCGA-GL-7966 
        1059          765          446          279          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         841           32          178           91         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 
         360         1726          167          511           62          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
         649          146            2            4          160          885 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
        1043          391          543          438          292         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2584         2816          174           57 

  HNRNPM MUTATED HNRNPM WILD-TYPE 
             116                2 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
            5925             3950 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
             608              543 
[1] "116.0 - 5925.0 (608.0)" "2.0 - 3950.0 (543.0)"  
[1] "hr="     "7.7e+07"
D1V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  HNRNPM MUTATED         8        0         2        1
  HNRNPM WILD-TYPE      87       10        37        9
D1V3, multiclass
           clus
vv          HNRNPM MUTATED HNRNPM WILD-TYPE
  STAGE I                8               87
  STAGE II               0               10
  STAGE III              2               37
  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     3
  HNRNPM WILD-TYPE 95 17    42
D1V4, multiclass
       clus
vv      HNRNPM MUTATED HNRNPM WILD-TYPE
  T1                 8               95
  T2                 0               17
  T3+T4              3               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
  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-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885       TCGA-BQ-5888 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891       TCGA-BQ-5892 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048 
"HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" "HNRNPM WILD-TYPE" 
      TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7056       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 60  6 76
D1V6, multiclass
    clus
vv   HNRNPM MUTATED HNRNPM WILD-TYPE
  M0              5               60
  M1              0                6
  MX              5               76
[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   9
  HNRNPM WILD-TYPE  48 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPM MUTATED      2    9
  HNRNPM WILD-TYPE   48  106
        clus
vv       HNRNPM MUTATED HNRNPM WILD-TYPE
  FEMALE              2               48
  MALE                9              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     7
  HNRNPM WILD-TYPE                        40    99
D1V10, multiclass
                                  clus
vv                                 HNRNPM MUTATED HNRNPM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0                2
  BLACK OR AFRICAN AMERICAN                     3               40
  WHITE                                         7               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"
D1V11, binary
                  cls
clus                 0   1
  HNRNPM MUTATED     0   7
  HNRNPM WILD-TYPE   6 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPM MUTATED      0    7
  HNRNPM WILD-TYPE    6  117
                        clus
vv                       HNRNPM MUTATED HNRNPM WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              7              117
[1] 2 2
[1] FALSE

Clustering(2) Variable = NF2 MUTATION ANALYSIS
D2V1, survival
               sevent
clus2             0   1
  NF2 MUTATED     9   1
  NF2 WILD-TYPE 128   4
  NF2 MUTATED NF2 WILD-TYPE 
           10           132 
  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-BQ-7044 TCGA-EV-5902 TCGA-G7-6797 TCGA-GL-7966 
        3760          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-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
         118           87            4         1778         1636          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N 
         763         1357           26           67          595          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 
         207            5          102          586         1938         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-7046 TCGA-BQ-7048 TCGA-BQ-7050 
         233           29          364         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
         218          116          353          414         3950         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
        2429         2460         1856         1670         1040          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-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
         446          786          279         5925          393          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          178           91         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-A6GD TCGA-KV-A6GE 
         649          146            2            4          160          885 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
        1043          391          543          438          292         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2584         2816          391          174           57 

  NF2 MUTATED NF2 WILD-TYPE 
           14             2 
  NF2 MUTATED NF2 WILD-TYPE 
         3760          5925 
  NF2 MUTATED NF2 WILD-TYPE 
          424           568 
[1] "14.0 - 3760.0 (424.0)" "2.0 - 5925.0 (568.0)" 
[1] "hr=" "3.4"
D2V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NF2 MUTATED         3        0         6        2
  NF2 WILD-TYPE      92       10        33        8
D2V3, multiclass
           clus
vv          NF2 MUTATED NF2 WILD-TYPE
  STAGE I             3            92
  STAGE II            0            10
  STAGE III           6            33
  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    4  1     7
  NF2 WILD-TYPE 99 16    38
D2V4, multiclass
       clus
vv      NF2 MUTATED NF2 WILD-TYPE
  T1              4            99
  T2              1            16
  T3+T4           7            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
  NF2 MUTATED    0  4  0
  NF2 WILD-TYPE 28 13  4
D2V5, 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    3  2  6
  NF2 WILD-TYPE 62  4 75
D2V6, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  M0           3            62
  M1           2             4
  MX           6            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"
D2V7, binary
               cls
clus              0   1
  NF2 MUTATED     5   7
  NF2 WILD-TYPE  45 108
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      5    7
  NF2 WILD-TYPE   45  108
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  FEMALE           5            45
  MALE             7           108
[1] 2 2
[1] FALSE
D2V8, 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" 
D2V9, 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     7
  NF2 WILD-TYPE                        39    99
D2V10, multiclass
                                  clus
vv                                 NF2 MUTATED NF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0             2
  BLACK OR AFRICAN AMERICAN                  4            39
  WHITE                                      7            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"
D2V11, binary
               cls
clus              0   1
  NF2 MUTATED     1   6
  NF2 WILD-TYPE   5 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      1    6
  NF2 WILD-TYPE    5  118
                        clus
vv                       NF2 MUTATED NF2 WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO           6           118
[1] 2 2
[1] FALSE

Clustering(3) Variable = NEFH MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  NEFH MUTATED     8   0
  NEFH WILD-TYPE 129   5
  NEFH MUTATED NEFH WILD-TYPE 
             8            134 
  NEFH MUTATED NEFH WILD-TYPE 
             0              5 
$`NEFH MUTATED`
TCGA-B9-4117 TCGA-B9-A5W8 TCGA-GL-A59T TCGA-HE-A5NL TCGA-IA-A40X TCGA-MH-A55Z 
          14          207           91          167          608          391 
TCGA-MH-A560 TCGA-P4-A5EB 
         543         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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         803          627           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
          64          585            5          102         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-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799          612          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-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          279         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-HE-A5NF TCGA-HE-A5NH 
         112          841           32          178         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         360         1726          511           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
         146            2            4          160          885         1043 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 
         438          292         3035         2653         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         174           57 

  NEFH MUTATED NEFH WILD-TYPE 
            14              2 
  NEFH MUTATED NEFH WILD-TYPE 
          2584           5925 
  NEFH MUTATED NEFH WILD-TYPE 
         299.0          583.5 
[1] "14.0 - 2584.0 (299.0)" "2.0 - 5925.0 (583.5)" 
[1] "hr="     "2.6e+07"
D3V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NEFH MUTATED         7        1         0        0
  NEFH WILD-TYPE      88        9        39       10
D3V3, multiclass
           clus
vv          NEFH MUTATED NEFH WILD-TYPE
  STAGE I              7             88
  STAGE II             1              9
  STAGE III            0             39
  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    7  2     0
  NEFH WILD-TYPE 96 15    45
D3V4, multiclass
       clus
vv      NEFH MUTATED NEFH WILD-TYPE
  T1               7             96
  T2               2             15
  T3+T4            0             45
[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
D3V5, multiclass
                vv
clus             M0 M1 MX
  NEFH MUTATED    1  0  7
  NEFH WILD-TYPE 64  6 74
D3V6, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  M0            1             64
  M1            0              6
  MX            7             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
  NEFH MUTATED     3   6
  NEFH WILD-TYPE  47 109
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      3    6
  NEFH WILD-TYPE   47  109
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  FEMALE            3             47
  MALE              6            109
[1] 2 2
[1] FALSE
D3V8, 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" 
D3V9, continuous
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             2             11 
    TCGA-A4-A48D     TCGA-B1-A654     TCGA-B9-A44B     TCGA-B9-A69E 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-GL-7773     TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-IA-A40U 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-P4-A5E7     TCGA-PJ-A5Z9     TCGA-Q2-A5QZ 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
                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                        39   102
D3V10, multiclass
                                  clus
vv                                 NEFH MUTATED NEFH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0              2
  BLACK OR AFRICAN AMERICAN                   4             39
  WHITE                                       4            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
                cls
clus               0   1
  NEFH MUTATED     0   8
  NEFH WILD-TYPE   6 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      0    8
  NEFH WILD-TYPE    6  116
                        clus
vv                       NEFH MUTATED NEFH WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            8            116
[1] 2 2
[1] FALSE

Clustering(4) Variable = TDG MUTATION ANALYSIS
D4V1, survival
               sevent
clus2             0   1
  TDG MUTATED     5   0
  TDG WILD-TYPE 132   5
  TDG MUTATED TDG WILD-TYPE 
            5           137 
  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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         671           64          585          207            5          102 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         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-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
          84         3760         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          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-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-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
         786          279          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
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            2            4          160          885         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
         391          543          438          292         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2584         2816          391          174           57 

  TDG MUTATED TDG WILD-TYPE 
           29             2 
  TDG MUTATED TDG WILD-TYPE 
         5925          3950 
  TDG MUTATED TDG WILD-TYPE 
          364           578 
[1] "29.0 - 5925.0 (364.0)" "2.0 - 3950.0 (578.0)" 
[1] "hr="     "2.7e+07"
D4V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  TDG MUTATED         3        0         1        1
  TDG WILD-TYPE      92       10        38        9
D4V3, multiclass
           clus
vv          TDG MUTATED TDG WILD-TYPE
  STAGE I             3            92
  STAGE II            0            10
  STAGE III           1            38
  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  17    43
D4V4, multiclass
       clus
vv      TDG MUTATED TDG WILD-TYPE
  T1              3           100
  T2              0            17
  T3+T4           2            43
[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
D4V5, 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 62  6 79
D4V6, multiclass
    clus
vv   TDG MUTATED TDG WILD-TYPE
  M0           3            62
  M1           0             6
  MX           2            79
[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
  TDG MUTATED     1   4
  TDG WILD-TYPE  49 111
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      1    4
  TDG WILD-TYPE   49  111
        clus
vv       TDG MUTATED TDG WILD-TYPE
  FEMALE           1            49
  MALE             4           111
[1] 2 2
[1] FALSE
D4V8, 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" 
D4V9, 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                        42   102
D4V10, multiclass
                                  clus
vv                                 TDG MUTATED TDG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0             2
  BLACK OR AFRICAN AMERICAN                  1            42
  WHITE                                      4           102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
               cls
clus              0   1
  TDG MUTATED     0   4
  TDG WILD-TYPE   6 120
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      0    4
  TDG WILD-TYPE    6  120
                        clus
vv                       TDG MUTATED TDG WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           4           120
[1] 2 2
[1] FALSE

Clustering(5) Variable = ZNF598 MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2                0   1
  ZNF598 MUTATED     9   1
  ZNF598 WILD-TYPE 128   4
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              10              132 
  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-DZ-6131 TCGA-EV-5903 TCGA-G7-7501 TCGA-G7-7502 
        2429          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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
         923         1357           26          595          659          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
         207            5          102         2639          586         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-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         612          232          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
         414         1142          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        1240         2460         1856         1670         1040          578 
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-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
         765          279         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          178           91         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-A6GD TCGA-KV-A6GE 
         649          146            2            4          160          885 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
        1043          391          543          438          292         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2584         2816          391          174           57 

  ZNF598 MUTATED ZNF598 WILD-TYPE 
              67                2 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
            3950             5925 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
           750.5            548.5 
[1] "67.0 - 3950.0 (750.5)" "2.0 - 5925.0 (548.5)" 
[1] "hr=" "2.7"
D5V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF598 MUTATED         7        1         3        2
  ZNF598 WILD-TYPE      88        9        36        8
D5V3, multiclass
           clus
vv          ZNF598 MUTATED ZNF598 WILD-TYPE
  STAGE I                7               88
  STAGE II               1                9
  STAGE III              3               36
  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    7  1     5
  ZNF598 WILD-TYPE 96 16    40
D5V4, multiclass
       clus
vv      ZNF598 MUTATED ZNF598 WILD-TYPE
  T1                 7               96
  T2                 1               16
  T3+T4              5               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
  ZNF598 MUTATED    2  3  0
  ZNF598 WILD-TYPE 26 14  4
D5V5, multiclass
    clus
vv   ZNF598 MUTATED ZNF598 WILD-TYPE
  N0              2               26
  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    4  2  7
  ZNF598 WILD-TYPE 61  4 74
D5V6, multiclass
    clus
vv   ZNF598 MUTATED ZNF598 WILD-TYPE
  M0              4               61
  M1              2                4
  MX              7               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"
D5V7, binary
                  cls
clus                 0   1
  ZNF598 MUTATED     4   9
  ZNF598 WILD-TYPE  46 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      4    9
  ZNF598 WILD-TYPE   46  106
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  FEMALE              4               46
  MALE                9              106
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, 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     9
  ZNF598 WILD-TYPE                        40    97
D5V10, multiclass
                                  clus
vv                                 ZNF598 MUTATED ZNF598 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0                2
  BLACK OR AFRICAN AMERICAN                     3               40
  WHITE                                         9               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"
D5V11, binary
                  cls
clus                 0   1
  ZNF598 MUTATED     1   8
  ZNF598 WILD-TYPE   5 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      1    8
  ZNF598 WILD-TYPE    5  116
                        clus
vv                       ZNF598 MUTATED ZNF598 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO              8              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 132   5
  SKI MUTATED SKI WILD-TYPE 
            5           137 
  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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
          64          585          207            5          102         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5885 
         586          270         1938         1454         1242          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-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799          612          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-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 
         279         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
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            2            4          160          885         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
         391          543          438          292         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2584         2816          391          174           57 

  SKI MUTATED SKI WILD-TYPE 
          671             2 
  SKI MUTATED SKI WILD-TYPE 
         2460          5925 
  SKI MUTATED SKI WILD-TYPE 
         1670           516 
[1] "671.0 - 2460.0 (1670.0)" "2.0 - 5925.0 (516.0)"   
[1] "hr="     "7.6e+07"
D6V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  SKI MUTATED         4        1         1        0
  SKI WILD-TYPE      91        9        38       10
D6V3, multiclass
           clus
vv          SKI MUTATED SKI WILD-TYPE
  STAGE I             4            91
  STAGE II            1             9
  STAGE III           1            38
  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 16    44
D6V4, multiclass
       clus
vv      SKI MUTATED SKI WILD-TYPE
  T1              4            99
  T2              1            16
  T3+T4           1            44
[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-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879    TCGA-BQ-5880 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-BQ-5882    TCGA-BQ-5885    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-BQ-5890    TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-BQ-7045    TCGA-BQ-7048    TCGA-BQ-7050    TCGA-BQ-7051    TCGA-BQ-7056 
"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 62  6 78
D6V6, multiclass
    clus
vv   SKI MUTATED SKI WILD-TYPE
  M0           3            62
  M1           0             6
  MX           3            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"
D6V7, binary
               cls
clus              0   1
  SKI MUTATED     1   5
  SKI WILD-TYPE  49 110
[1] "tbl2"
               cls
clus            [,1] [,2]
  SKI MUTATED      1    5
  SKI WILD-TYPE   49  110
        clus
vv       SKI MUTATED SKI WILD-TYPE
  FEMALE           1            49
  MALE             5           110
[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                        42   103
D6V10, multiclass
                                  clus
vv                                 SKI MUTATED SKI WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0             2
  BLACK OR AFRICAN AMERICAN                  1            42
  WHITE                                      3           103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
               cls
clus              0   1
  SKI MUTATED     0   2
  SKI WILD-TYPE   6 122
[1] "tbl2"
               cls
clus            [,1] [,2]
  SKI MUTATED      0    2
  SKI WILD-TYPE    6  122
                        clus
vv                       SKI MUTATED SKI WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           2           122
[1] 2 2
[1] FALSE

Clustering(7) Variable = CSGALNACT2 MUTATION ANALYSIS
D7V1, survival
                      sevent
clus2                    0   1
  CSGALNACT2 MUTATED     3   0
  CSGALNACT2 WILD-TYPE 134   5
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   3                  139 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   0                    5 
$`CSGALNACT2 MUTATED`
TCGA-A4-A4ZT TCGA-KV-A6GD TCGA-MH-A560 
         516          160          543 

$`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-A5XZ 
         709          597          600          436          379            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
         118           87            4         1778         1636          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         763         1357           26           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
         747          108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         627           14           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
          64          585          207            5          102         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
         586          270         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-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
         364           84         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
         218          116          353          414         3950         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          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-6846 
        1059          765          446          786          279         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          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            2 
TCGA-J7-8537 TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 
           4          885         1043          391          438          292 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3035         2653         2584         2816          391          174 
TCGA-Q2-A5QZ 
          57 

  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                 160                    2 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                 543                 5925 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                 516                  582 
[1] "160.0 - 543.0 (516.0)" "2.0 - 5925.0 (582.0)" 
[1] "hr="     "9200000"
D7V2, continuous
                      vv
clus                   STAGE I STAGE II STAGE III STAGE IV
  CSGALNACT2 MUTATED         4        0         1        0
  CSGALNACT2 WILD-TYPE      91       10        38       10
D7V3, multiclass
           clus
vv          CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  STAGE I                    4                   91
  STAGE II                   0                   10
  STAGE III                  1                   38
  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 17    44
D7V4, multiclass
       clus
vv      CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  T1                     4                   99
  T2                     0                   17
  T3+T4                  1                   44
[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
D7V5, multiclass
                      vv
clus                   M0 M1 MX
  CSGALNACT2 MUTATED    2  0  3
  CSGALNACT2 WILD-TYPE 63  6 78
D7V6, multiclass
    clus
vv   CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  M0                  2                   63
  M1                  0                    6
  MX                  3                   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"
D7V7, binary
                      cls
clus                     0   1
  CSGALNACT2 MUTATED     3   2
  CSGALNACT2 WILD-TYPE  47 113
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      3    2
  CSGALNACT2 WILD-TYPE   47  113
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  FEMALE                  3                   47
  MALE                    2                  113
[1] 2 2
[1] FALSE
D7V8, 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" 
D7V9, continuous
                      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     4
  CSGALNACT2 WILD-TYPE                        43   102
D7V10, multiclass
                                  clus
vv                                 CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                  0                    2
  ASIAN                                             0                    2
  BLACK OR AFRICAN AMERICAN                         0                   43
  WHITE                                             4                  102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
                      cls
clus                     0   1
  CSGALNACT2 MUTATED     0   3
  CSGALNACT2 WILD-TYPE   6 121
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      0    3
  CSGALNACT2 WILD-TYPE    6  121
                        clus
vv                       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  HISPANIC OR LATINO                      0                    6
  NOT HISPANIC OR LATINO                  3                  121
[1] 2 2
[1] FALSE

Clustering(8) Variable = SETD2 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED     9   2
  SETD2 WILD-TYPE 128   3
  SETD2 MUTATED SETD2 WILD-TYPE 
             11             131 
  SETD2 MUTATED SETD2 WILD-TYPE 
              2               3 
$`SETD2 MUTATED`
TCGA-A4-7583 TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-B1-A656 TCGA-B9-5155 TCGA-B9-A44B 
           3          140           87           14          460           64 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5890 TCGA-BQ-5891 
        2639          586          270          233           29 

$`SETD2 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554           21          493          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8517 
          49            2          780          729          709          597 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 
         600          436          379          516            2          118 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
           4         1778         1636          923          763         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
          26           67          595          659          747          108 
TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
         510         1029          307          930         1049          379 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1338          671          585          207            5          102 
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-7056 
        2839         1864         1533         1516          799          612 
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 
         279         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
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            2            4          160          885         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
         391          543          438          292         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2584         2816          391          174           57 

  SETD2 MUTATED SETD2 WILD-TYPE 
              3               2 
  SETD2 MUTATED SETD2 WILD-TYPE 
           2639            5925 
  SETD2 MUTATED SETD2 WILD-TYPE 
            140             595 
[1] "3.0 - 2639.0 (140.0)" "2.0 - 5925.0 (595.0)"
[1] "hr=" "13" 
D8V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SETD2 MUTATED         5        0         8        2
  SETD2 WILD-TYPE      90       10        31        8
D8V3, multiclass
           clus
vv          SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I               5              90
  STAGE II              0              10
  STAGE III             8              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
  SETD2 MUTATED    6  0     9
  SETD2 WILD-TYPE 97 17    36
D8V4, multiclass
       clus
vv      SETD2 MUTATED SETD2 WILD-TYPE
  T1                6              97
  T2                0              17
  T3+T4             9              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    4  2  2
  SETD2 WILD-TYPE 24 15  2
D8V5, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  N0             4              24
  N1             2              15
  N2             2               2
[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    8  1  4
  SETD2 WILD-TYPE 57  5 77
D8V6, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  M0             8              57
  M1             1               5
  MX             4              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"
D8V7, binary
                 cls
clus                0   1
  SETD2 MUTATED     5  10
  SETD2 WILD-TYPE  45 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      5   10
  SETD2 WILD-TYPE   45  105
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE             5              45
  MALE              10             105
[1] 2 2
[1] FALSE
D8V8, continuous
[1] "Remove cluster labels:" "SETD2 MUTATED"         
clus
  SETD2 MUTATED SETD2 WILD-TYPE 
              1              37 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8310      TCGA-A4-8311 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A4ZT 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-AL-3466      TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-DW-7841      TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-EV-5902      TCGA-EV-5903      TCGA-G7-6790      TCGA-G7-6796 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-Q2-A5QZ 
"SETD2 WILD-TYPE" 
D8V9, continuous
[1] "Remove cluster labels:" "SETD2 MUTATED"         
clus
  SETD2 MUTATED SETD2 WILD-TYPE 
              1              12 
     TCGA-A4-A48D      TCGA-B1-A654      TCGA-B9-A69E      TCGA-GL-7773 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-GL-A59T      TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-IA-A40U 
"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                           4    10
  SETD2 WILD-TYPE                        39    96
D8V10, multiclass
                                  clus
vv                                 SETD2 MUTATED SETD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    4              39
  WHITE                                       10              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"
D8V11, binary
                 cls
clus                0   1
  SETD2 MUTATED     0  10
  SETD2 WILD-TYPE   6 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      0   10
  SETD2 WILD-TYPE    6  114
                        clus
vv                       SETD2 MUTATED SETD2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            10             114
[1] 2 2
[1] FALSE

Clustering(9) Variable = MET MUTATION ANALYSIS
D9V1, survival
               sevent
clus2             0   1
  MET MUTATED    14   0
  MET WILD-TYPE 123   5
  MET MUTATED MET WILD-TYPE 
           14           128 
  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          178          408          511 
TCGA-IZ-8196 TCGA-MH-A561 
         649          438 

$`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-A5XZ TCGA-A4-A5Y0 
         600          436          379          516            2          118 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3473 TCGA-AL-A5DJ 
          87            4         1778         1636          763           26 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A655 TCGA-B1-A656 
          67          595          659          747          510           14 
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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         857          803          627           35          460         1338 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         671           64          585          207            5          102 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         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-7056 TCGA-BQ-7060 
        1864         1533         1516          799          612          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
         218          116          353          414         3950         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
        2429         1856         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          279         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ 
         841           32           91         2072          360         1726 
TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         167          608           62          677          146            2 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
           4          160          885         1043          391          543 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         292         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         174           57 

  MET MUTATED MET WILD-TYPE 
            2             2 
  MET MUTATED MET WILD-TYPE 
         2460          5925 
  MET MUTATED MET WILD-TYPE 
        423.0         583.5 
[1] "2.0 - 2460.0 (423.0)" "2.0 - 5925.0 (583.5)"
[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       10        36        9
D9V3, multiclass
           clus
vv          MET MUTATED MET WILD-TYPE
  STAGE I             9            86
  STAGE II            0            10
  STAGE III           3            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
  MET MUTATED    9  2     4
  MET WILD-TYPE 94 15    41
D9V4, multiclass
       clus
vv      MET MUTATED MET WILD-TYPE
  T1              9            94
  T2              2            15
  T3+T4           4            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
  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 59  6 74
D9V6, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  M0           6            59
  M1           0             6
  MX           7            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"
D9V7, binary
               cls
clus              0   1
  MET MUTATED     4  11
  MET WILD-TYPE  46 104
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      4   11
  MET WILD-TYPE   46  104
        clus
vv       MET MUTATED MET WILD-TYPE
  FEMALE           4            46
  MALE            11           104
[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            11 
   TCGA-A4-A48D    TCGA-B9-A44B    TCGA-B9-A69E    TCGA-GL-7773    TCGA-GL-A59T 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-HE-A5NI    TCGA-HE-A5NJ    TCGA-P4-A5E7    TCGA-P4-A5EB    TCGA-PJ-A5Z9 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-Q2-A5QZ 
"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                        40    98
D9V10, multiclass
                                  clus
vv                                 MET MUTATED MET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0             2
  BLACK OR AFRICAN AMERICAN                  3            40
  WHITE                                      8            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"
D9V11, binary
               cls
clus              0   1
  MET MUTATED     1  10
  MET WILD-TYPE   5 114
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      1   10
  MET WILD-TYPE    5  114
                        clus
vv                       MET MUTATED MET WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO          10           114
[1] 2 2
[1] FALSE

Clustering(10) Variable = MUC5B MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2               0   1
  MUC5B MUTATED    13   1
  MUC5B WILD-TYPE 124   4
  MUC5B MUTATED MUC5B WILD-TYPE 
             14             128 
  MUC5B MUTATED MUC5B WILD-TYPE 
              1               4 
$`MUC5B MUTATED`
TCGA-A4-7288 TCGA-A4-8311 TCGA-A4-8518 TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-B1-A47N 
         493          729          600          118           87          747 
TCGA-BQ-5888 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
         403         3760         2839          218          116         1240 
TCGA-G7-7502 TCGA-P4-A5E7 
         786         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-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
        1636          923          763         1357           26           67 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         595          659          108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         671           64          585          207            5          102 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
         792          921          792          771          233           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
         364           84         2948         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-DW-5560 TCGA-DW-5561 
         799          612          232          214          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-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
          92         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-A4TM TCGA-GL-6846 
        1194         1059          765          446          279         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          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            2 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
           4          160          885         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         438          292         3035         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         174           57 

  MUC5B MUTATED MUC5B WILD-TYPE 
             87               2 
  MUC5B MUTATED MUC5B WILD-TYPE 
           3760            5925 
  MUC5B MUTATED MUC5B WILD-TYPE 
          664.5           548.5 
[1] "87.0 - 3760.0 (664.5)" "2.0 - 5925.0 (548.5)" 
[1] "hr=" "1.9"
D10V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MUC5B MUTATED        11        1         3        2
  MUC5B WILD-TYPE      84        9        36        8
D10V3, multiclass
           clus
vv          MUC5B MUTATED MUC5B WILD-TYPE
  STAGE I              11              84
  STAGE II              1               9
  STAGE III             3              36
  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   14  1     3
  MUC5B WILD-TYPE 89 16    42
D10V4, multiclass
       clus
vv      MUC5B MUTATED MUC5B WILD-TYPE
  T1               14              89
  T2                1              16
  T3+T4             3              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
  MUC5B MUTATED    4  2  0
  MUC5B WILD-TYPE 24 15  4
D10V5, multiclass
    clus
vv   MUC5B MUTATED MUC5B WILD-TYPE
  N0             4              24
  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    6  2 10
  MUC5B WILD-TYPE 59  4 71
D10V6, multiclass
    clus
vv   MUC5B MUTATED MUC5B WILD-TYPE
  M0             6              59
  M1             2               4
  MX            10              71
[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
  MUC5B MUTATED     7  11
  MUC5B WILD-TYPE  43 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED      7   11
  MUC5B WILD-TYPE   43  104
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  FEMALE             7              43
  MALE              11             104
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
[1] "Remove cluster labels:" "MUC5B MUTATED"         
clus
  MUC5B MUTATED MUC5B WILD-TYPE 
              1              12 
     TCGA-A4-A48D      TCGA-B1-A654      TCGA-B9-A44B      TCGA-B9-A69E 
"MUC5B WILD-TYPE" "MUC5B WILD-TYPE" "MUC5B WILD-TYPE" "MUC5B WILD-TYPE" 
     TCGA-GL-7773      TCGA-GL-A59T      TCGA-HE-A5NI      TCGA-HE-A5NJ 
"MUC5B WILD-TYPE" "MUC5B WILD-TYPE" "MUC5B WILD-TYPE" "MUC5B WILD-TYPE" 
     TCGA-IA-A40U      TCGA-P4-A5EB      TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"MUC5B WILD-TYPE" "MUC5B WILD-TYPE" "MUC5B WILD-TYPE" "MUC5B WILD-TYPE" 
                 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    15
  MUC5B WILD-TYPE                        40    91
D10V10, multiclass
                                  clus
vv                                 MUC5B MUTATED MUC5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    3              40
  WHITE                                       15              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"
D10V11, binary
                 cls
clus                0   1
  MUC5B MUTATED     0  14
  MUC5B WILD-TYPE   6 110
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED      0   14
  MUC5B WILD-TYPE    6  110
                        clus
vv                       MUC5B MUTATED MUC5B WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            14             110
[1] 2 2
[1] FALSE

Clustering(11) Variable = KDM6A MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED     6   0
  KDM6A WILD-TYPE 131   5
  KDM6A MUTATED KDM6A WILD-TYPE 
              6             136 
  KDM6A MUTATED KDM6A WILD-TYPE 
              0               5 
$`KDM6A MUTATED`
TCGA-A4-A48D TCGA-BQ-5886 TCGA-BQ-7060 TCGA-DZ-6131 TCGA-G7-6797 TCGA-IZ-A6M8 
         379          792          214         2429          765          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-A5XZ 
         709          597          600          436          516            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
         118           87            4         1778         1636          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         763         1357           26           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
         747          108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         627           14           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
          64          585          207            5          102         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
         586          270         1938         1454         1242          792 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         921          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-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 
        1516          799          612          232          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-6132 TCGA-DZ-6134 
         114          445           92         1240         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-G7-7501 TCGA-G7-7502 
        1575         1479         1194         1059          446          786 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
         279         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
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 
           2            4          160          885         1043          391 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         543          438          292         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2816          391          174           57 

  KDM6A MUTATED KDM6A WILD-TYPE 
            146               2 
  KDM6A MUTATED KDM6A WILD-TYPE 
           2429            5925 
  KDM6A MUTATED KDM6A WILD-TYPE 
            572             566 
[1] "146.0 - 2429.0 (572.0)" "2.0 - 5925.0 (566.0)"  
[1] "hr="     "2.6e+07"
D11V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KDM6A MUTATED         5        0         4        0
  KDM6A WILD-TYPE      90       10        35       10
D11V3, multiclass
           clus
vv          KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I               5              90
  STAGE II              0              10
  STAGE III             4              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
  KDM6A MUTATED    5  1     3
  KDM6A WILD-TYPE 98 16    42
D11V4, multiclass
       clus
vv      KDM6A MUTATED KDM6A WILD-TYPE
  T1                5              98
  T2                1              16
  T3+T4             3              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
  KDM6A MUTATED    1  0  0
  KDM6A WILD-TYPE 27 17  4
D11V5, multiclass
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              1              48 
     TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-A5Y1      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878      TCGA-BQ-5879 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885      TCGA-BQ-5887 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7056 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BQ-7058      TCGA-DW-7963      TCGA-G7-6789      TCGA-G7-6793 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846      TCGA-GL-7966 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-GL-A59R      TCGA-IA-A40U      TCGA-IA-A40Y      TCGA-J7-6720 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-J7-8537      TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
                 vv
clus              M0 M1 MX
  KDM6A MUTATED    4  0  5
  KDM6A WILD-TYPE 61  6 76
D11V6, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  M0             4              61
  M1             0               6
  MX             5              76
[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   8
  KDM6A WILD-TYPE  49 107
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      1    8
  KDM6A WILD-TYPE   49  107
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE             1              49
  MALE               8             107
[1] 2 2
[1] FALSE
D11V8, continuous
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              1              37 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8310      TCGA-A4-8311 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A4ZT 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AL-3466      TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-7841      TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-EV-5902      TCGA-EV-5903      TCGA-G7-6790      TCGA-G7-6793 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-Q2-A5QZ 
"KDM6A WILD-TYPE" 
D11V9, continuous
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              1              12 
     TCGA-B1-A654      TCGA-B9-A44B      TCGA-B9-A69E      TCGA-GL-7773 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-GL-A59T      TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-IA-A40U 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"KDM6A WILD-TYPE" "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     3
  KDM6A WILD-TYPE                        40   103
D11V10, multiclass
                                  clus
vv                                 KDM6A MUTATED KDM6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    3              40
  WHITE                                        3             103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, binary
                 cls
clus                0   1
  KDM6A MUTATED     0   5
  KDM6A WILD-TYPE   6 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      0    5
  KDM6A WILD-TYPE    6  119
                        clus
vv                       KDM6A MUTATED KDM6A WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             119
[1] 2 2
[1] FALSE

Clustering(12) Variable = ZNF814 MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2                0   1
  ZNF814 MUTATED     7   1
  ZNF814 WILD-TYPE 130   4
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               8              134 
  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          279           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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
           2          118            4         1778         1636          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         763         1357           26           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
         747          108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         627           14           35          460         1338          671 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
         585          207            5          102         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-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799          612          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-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         419          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-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
         446          786         5925          393          112          841 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8196 TCGA-IZ-A6M8 
         167          511          608           62          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
           2            4          160         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 
         438          292         3035         2653         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         174           57 

  ZNF814 MUTATED ZNF814 WILD-TYPE 
              32                2 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
            2584             5925 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
           196.5            580.0 
[1] "32.0 - 2584.0 (196.5)" "2.0 - 5925.0 (580.0)" 
[1] "hr=" "5.5"
D12V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF814 MUTATED         5        1         2        0
  ZNF814 WILD-TYPE      90        9        37       10
D12V3, multiclass
           clus
vv          ZNF814 MUTATED ZNF814 WILD-TYPE
  STAGE I                5               90
  STAGE II               1                9
  STAGE III              2               37
  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 16    44
D12V4, multiclass
       clus
vv      ZNF814 MUTATED ZNF814 WILD-TYPE
  T1                 6               97
  T2                 1               16
  T3+T4              1               44
[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
D12V5, 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-B9-7268 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879       TCGA-BQ-5880 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-5882       TCGA-BQ-5885       TCGA-BQ-5887       TCGA-BQ-5888 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891       TCGA-BQ-5892 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7056       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 65  6 74
D12V6, multiclass
    clus
vv   ZNF814 MUTATED ZNF814 WILD-TYPE
  M0              0               65
  M1              0                6
  MX              7               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"
D12V7, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     0   8
  ZNF814 WILD-TYPE  50 107
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0    8
  ZNF814 WILD-TYPE   50  107
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  FEMALE              0               50
  MALE                8              107
[1] 2 2
[1] FALSE
D12V8, 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" 
D12V9, continuous
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               11 
      TCGA-A4-A48D       TCGA-B1-A654       TCGA-B9-A69E       TCGA-GL-7773 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-GL-A59T       TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-IA-A40U 
"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                        40   101
D12V10, multiclass
                                  clus
vv                                 ZNF814 MUTATED ZNF814 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0                2
  BLACK OR AFRICAN AMERICAN                     3               40
  WHITE                                         5              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"
D12V11, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     0   8
  ZNF814 WILD-TYPE   6 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0    8
  ZNF814 WILD-TYPE    6  116
                        clus
vv                       ZNF814 MUTATED ZNF814 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              8              116
[1] 2 2
[1] FALSE

Clustering(13) Variable = OR2L8 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  OR2L8 MUTATED     2   0
  OR2L8 WILD-TYPE 135   5
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              2             140 
  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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         671           64          585          207            5          102 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         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-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          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-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
         578           97          208         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
        1059          765          446          786          279         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          167          511 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
         608           62          677          146            2            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         160          885         1043          391          543          438 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         292         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         174           57 

  OR2L8 MUTATED OR2L8 WILD-TYPE 
            649               2 
  OR2L8 MUTATED OR2L8 WILD-TYPE 
            757            5925 
  OR2L8 MUTATED OR2L8 WILD-TYPE 
          703.0           548.5 
[1] "649.0 - 757.0 (703.0)" "2.0 - 5925.0 (548.5)" 
[1] "Remove cluster labels:" "OR2L8 MUTATED"         
D13V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  OR2L8 MUTATED         3        0         0        1
  OR2L8 WILD-TYPE      92       10        39        9
D13V3, multiclass
           clus
vv          OR2L8 MUTATED OR2L8 WILD-TYPE
  STAGE I               3              92
  STAGE II              0              10
  STAGE III             0              39
  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  17    44
D13V4, multiclass
       clus
vv      OR2L8 MUTATED OR2L8 WILD-TYPE
  T1                3             100
  T2                0              17
  T3+T4             1              44
[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
D13V5, 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-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878      TCGA-BQ-5879 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885      TCGA-BQ-5887 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5890      TCGA-BQ-5891      TCGA-BQ-5892 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045      TCGA-BQ-7048 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7056      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 64  5 79
D13V6, multiclass
    clus
vv   OR2L8 MUTATED OR2L8 WILD-TYPE
  M0             1              64
  M1             1               5
  MX             2              79
[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
  OR2L8 MUTATED     1   3
  OR2L8 WILD-TYPE  49 112
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2L8 MUTATED      1    3
  OR2L8 WILD-TYPE   49  112
        clus
vv       OR2L8 MUTATED OR2L8 WILD-TYPE
  FEMALE             1              49
  MALE               3             112
[1] 2 2
[1] FALSE
D13V8, 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" 
D13V9, 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                        43   102
D13V10, multiclass
                                  clus
vv                                 OR2L8 MUTATED OR2L8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    0              43
  WHITE                                        4             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, binary
                 cls
clus                0   1
  OR2L8 MUTATED     0   3
  OR2L8 WILD-TYPE   6 121
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2L8 MUTATED      0    3
  OR2L8 WILD-TYPE    6  121
                        clus
vv                       OR2L8 MUTATED OR2L8 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3             121
[1] 2 2
[1] FALSE

Clustering(14) Variable = MYH6 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  MYH6 MUTATED     5   0
  MYH6 WILD-TYPE 132   5
  MYH6 MUTATED MYH6 WILD-TYPE 
             5            137 
  MYH6 MUTATED MYH6 WILD-TYPE 
             0              5 
$`MYH6 MUTATED`
TCGA-B9-5156 TCGA-BQ-7059 TCGA-DZ-6132 TCGA-G7-6795 TCGA-G7-6797 
        1338          232         2460         1194          765 

$`MYH6 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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-7268 
         803          627           14           35          460          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
          64          585          207            5          102         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
         586          270         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-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
         364           84         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7060 TCGA-BQ-7061 
        1533         1516          799          612          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-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-G7-6796 TCGA-G7-7501 TCGA-G7-7502 
         208         1575         1479         1059          446          786 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
         279         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
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            2            4          160          885         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
         391          543          438          292         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2584         2816          391          174           57 

  MYH6 MUTATED MYH6 WILD-TYPE 
           232              2 
  MYH6 MUTATED MYH6 WILD-TYPE 
          2460           5925 
  MYH6 MUTATED MYH6 WILD-TYPE 
          1194            543 
[1] "232.0 - 2460.0 (1194.0)" "2.0 - 5925.0 (543.0)"   
[1] "hr="     "2.6e+07"
D14V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MYH6 MUTATED         4        1         2        0
  MYH6 WILD-TYPE      91        9        37       10
D14V3, multiclass
           clus
vv          MYH6 MUTATED MYH6 WILD-TYPE
  STAGE I              4             91
  STAGE II             1              9
  STAGE III            2             37
  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
  MYH6 MUTATED    7  0     1
  MYH6 WILD-TYPE 96 17    44
D14V4, multiclass
       clus
vv      MYH6 MUTATED MYH6 WILD-TYPE
  T1               7             96
  T2               0             17
  T3+T4            1             44
[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
  MYH6 MUTATED    1  0  0
  MYH6 WILD-TYPE 27 17  4
D14V5, multiclass
[1] "Remove cluster labels:" "MYH6 MUTATED"          
clus
  MYH6 MUTATED MYH6 WILD-TYPE 
             1             48 
    TCGA-A4-7583     TCGA-A4-7585     TCGA-A4-7915     TCGA-A4-A57E 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-A4-A5Y1     TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7056 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-BQ-7058     TCGA-DW-7963     TCGA-DZ-6131     TCGA-G7-6789 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-7501     TCGA-GL-6846     TCGA-GL-7966 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-GL-A59R     TCGA-IA-A40U     TCGA-IA-A40Y     TCGA-J7-6720 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-J7-8537     TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
                vv
clus             M0 M1 MX
  MYH6 MUTATED    4  0  3
  MYH6 WILD-TYPE 61  6 78
D14V6, multiclass
    clus
vv   MYH6 MUTATED MYH6 WILD-TYPE
  M0            4             61
  M1            0              6
  MX            3             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
  MYH6 MUTATED     3   5
  MYH6 WILD-TYPE  47 110
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH6 MUTATED      3    5
  MYH6 WILD-TYPE   47  110
        clus
vv       MYH6 MUTATED MYH6 WILD-TYPE
  FEMALE            3             47
  MALE              5            110
[1] 2 2
[1] FALSE
D14V8, continuous
[1] "Remove cluster labels:" "MYH6 MUTATED"          
clus
  MYH6 MUTATED MYH6 WILD-TYPE 
             2             36 
    TCGA-A4-7286     TCGA-A4-8310     TCGA-A4-8311     TCGA-A4-8312 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-A4-8518     TCGA-A4-8630     TCGA-A4-A4ZT     TCGA-A4-A57E 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP     TCGA-AL-3466 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-DW-7842     TCGA-DW-7963     TCGA-EV-5901     TCGA-EV-5902 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-EV-5903     TCGA-G7-6790     TCGA-G7-6793     TCGA-G7-6796 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM     TCGA-IA-A40U 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
    TCGA-IA-A40X     TCGA-IA-A40Y     TCGA-J7-8537     TCGA-Q2-A5QZ 
"MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" "MYH6 WILD-TYPE" 
D14V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYH6 MUTATED                                  0     0
  MYH6 WILD-TYPE                                2     2
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYH6 MUTATED                           1     5
  MYH6 WILD-TYPE                        42   101
D14V10, multiclass
                                  clus
vv                                 MYH6 MUTATED MYH6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0              2
  BLACK OR AFRICAN AMERICAN                   1             42
  WHITE                                       5            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"
D14V11, binary
                cls
clus               0   1
  MYH6 MUTATED     0   5
  MYH6 WILD-TYPE   6 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH6 MUTATED      0    5
  MYH6 WILD-TYPE    6  119
                        clus
vv                       MYH6 MUTATED MYH6 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            5            119
[1] 2 2
[1] FALSE

Clustering(15) Variable = UNC13A MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2                0   1
  UNC13A MUTATED     8   0
  UNC13A WILD-TYPE 129   5
  UNC13A MUTATED UNC13A WILD-TYPE 
               8              134 
  UNC13A MUTATED UNC13A WILD-TYPE 
               0                5 
$`UNC13A MUTATED`
TCGA-A4-7583 TCGA-BQ-5878 TCGA-BQ-5885 TCGA-BQ-7048 TCGA-BQ-7059 TCGA-DZ-6132 
           3         1938          921         2839          232         2460 
TCGA-G7-6795 TCGA-GL-6846 
        1194         5925 

$`UNC13A WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554           21          493          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
         118           87            4         1778         1636          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         763         1357           26           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
         747          108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         627           14           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
          64          585          207            5          102         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 
         586          270         1454         1242          792          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-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        3760         2948         1864         1533         1516          799 
TCGA-BQ-7056 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         612          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-6134 TCGA-DZ-6135 TCGA-EV-5901 
          92         1240         2429         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-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-7773 
        1059          765          446          786          279          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
         112          841           32          178           91         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         408          360         1726          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            2            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         160          885         1043          391          543          438 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         292         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         174           57 

  UNC13A MUTATED UNC13A WILD-TYPE 
               3                2 
  UNC13A MUTATED UNC13A WILD-TYPE 
            5925             3950 
  UNC13A MUTATED UNC13A WILD-TYPE 
          1566.0            529.5 
[1] "3.0 - 5925.0 (1566.0)" "2.0 - 3950.0 (529.5)" 
[1] "hr="   "8e+07"
D15V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  UNC13A MUTATED         5        0         3        1
  UNC13A WILD-TYPE      90       10        36        9
D15V3, multiclass
           clus
vv          UNC13A MUTATED UNC13A WILD-TYPE
  STAGE I                5               90
  STAGE II               0               10
  STAGE III              3               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
  UNC13A MUTATED    5  0     4
  UNC13A WILD-TYPE 98 17    41
D15V4, multiclass
       clus
vv      UNC13A MUTATED UNC13A WILD-TYPE
  T1                 5               98
  T2                 0               17
  T3+T4              4               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
  UNC13A MUTATED    4  2  0
  UNC13A WILD-TYPE 24 15  4
D15V5, multiclass
    clus
vv   UNC13A MUTATED UNC13A WILD-TYPE
  N0              4               24
  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
  UNC13A MUTATED    6  0  3
  UNC13A WILD-TYPE 59  6 78
D15V6, multiclass
    clus
vv   UNC13A MUTATED UNC13A WILD-TYPE
  M0              6               59
  M1              0                6
  MX              3               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"
D15V7, binary
                  cls
clus                 0   1
  UNC13A MUTATED     2   7
  UNC13A WILD-TYPE  48 108
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UNC13A MUTATED      2    7
  UNC13A WILD-TYPE   48  108
        clus
vv       UNC13A MUTATED UNC13A WILD-TYPE
  FEMALE              2               48
  MALE                7              108
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UNC13A MUTATED                                  0     0
  UNC13A WILD-TYPE                                2     2
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UNC13A MUTATED                           1     7
  UNC13A WILD-TYPE                        42    99
D15V10, multiclass
                                  clus
vv                                 UNC13A MUTATED UNC13A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0                2
  BLACK OR AFRICAN AMERICAN                     1               42
  WHITE                                         7               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
  UNC13A MUTATED     0   6
  UNC13A WILD-TYPE   6 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UNC13A MUTATED      0    6
  UNC13A WILD-TYPE    6  118
                        clus
vv                       UNC13A MUTATED UNC13A WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              6              118
[1] 2 2
[1] FALSE

Clustering(16) Variable = MED16 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  MED16 MUTATED     2   1
  MED16 WILD-TYPE 135   4
  MED16 MUTATED MED16 WILD-TYPE 
              3             139 
  MED16 MUTATED MED16 WILD-TYPE 
              1               4 
$`MED16 MUTATED`
TCGA-BQ-5890 TCGA-DZ-6132 TCGA-G7-6789 
         233         2460          208 

$`MED16 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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         671           64          585          207            5          102 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 
         792          921          792          771          403           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
         364           84         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
         218          116          353          414         3950         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2429         1856         1670         1040          578          757 
TCGA-F9-A4JJ TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
          97         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          279         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         841           32          178           91         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
         360         1726          167          511          608           62 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
         677          649          146            2            4          160 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         885         1043          391          543          438          292 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3035         2653         2584         2816          391          174 
TCGA-Q2-A5QZ 
          57 

  MED16 MUTATED MED16 WILD-TYPE 
            208               2 
  MED16 MUTATED MED16 WILD-TYPE 
           2460            5925 
  MED16 MUTATED MED16 WILD-TYPE 
            233             578 
[1] "208.0 - 2460.0 (233.0)" "2.0 - 5925.0 (578.0)"  
[1] "hr=" "9.3"
D16V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MED16 MUTATED         1        0         2        1
  MED16 WILD-TYPE      94       10        37        9
D16V3, multiclass
           clus
vv          MED16 MUTATED MED16 WILD-TYPE
  STAGE I               1              94
  STAGE II              0              10
  STAGE III             2              37
  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
  MED16 MUTATED     1   0     3
  MED16 WILD-TYPE 102  17    42
D16V4, multiclass
       clus
vv      MED16 MUTATED MED16 WILD-TYPE
  T1                1             102
  T2                0              17
  T3+T4             3              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
  MED16 MUTATED    1  0  1
  MED16 WILD-TYPE 27 17  3
D16V5, multiclass
[1] "Remove cluster labels:" "MED16 MUTATED"         
clus
  MED16 MUTATED MED16 WILD-TYPE 
              2              47 
     TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-A4-A5Y1      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878      TCGA-BQ-5879 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885      TCGA-BQ-5887 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5889      TCGA-BQ-5891      TCGA-BQ-5892 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045      TCGA-BQ-7048 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7056      TCGA-BQ-7058 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6793      TCGA-G7-6795 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-G7-7501      TCGA-GL-6846      TCGA-GL-7966      TCGA-GL-A59R 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A40Y      TCGA-J7-6720      TCGA-J7-8537 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
                 vv
clus              M0 M1 MX
  MED16 MUTATED    2  0  2
  MED16 WILD-TYPE 63  6 79
D16V6, multiclass
    clus
vv   MED16 MUTATED MED16 WILD-TYPE
  M0             2              63
  M1             0               6
  MX             2              79
[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
  MED16 MUTATED     2   2
  MED16 WILD-TYPE  48 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED16 MUTATED      2    2
  MED16 WILD-TYPE   48  113
        clus
vv       MED16 MUTATED MED16 WILD-TYPE
  FEMALE             2              48
  MALE               2             113
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MED16 MUTATED                                  0     0
  MED16 WILD-TYPE                                2     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MED16 MUTATED                           0     2
  MED16 WILD-TYPE                        43   104
D16V10, multiclass
[1] "Remove cluster labels:" "MED16 MUTATED"         
clus
  MED16 MUTATED MED16 WILD-TYPE 
              2             151 
     TCGA-A4-7286      TCGA-A4-7287      TCGA-A4-7288      TCGA-A4-7583 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-A4-7584      TCGA-A4-7585      TCGA-A4-7732      TCGA-A4-7734 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-A4-7828      TCGA-A4-7915      TCGA-A4-7996      TCGA-A4-7997 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-A4-8098      TCGA-A4-8310      TCGA-A4-8311      TCGA-A4-8312 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-A4-8515      TCGA-A4-8517      TCGA-A4-8518      TCGA-A4-8630 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-A4-A5XZ      TCGA-A4-A5Y0      TCGA-A4-A5Y1      TCGA-A4-A6HP 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-AL-3466      TCGA-AL-3467      TCGA-AL-3468      TCGA-AL-3472 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-AL-3473      TCGA-AL-7173      TCGA-AL-A5DJ      TCGA-AT-A5NU 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-B1-5398      TCGA-B1-A47M      TCGA-B1-A47N      TCGA-B1-A654 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-B1-A655      TCGA-B1-A656      TCGA-B3-3925      TCGA-B3-3926 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-B3-4103      TCGA-B3-4104      TCGA-B3-8121      TCGA-B9-4113 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-B9-4114      TCGA-B9-4115      TCGA-B9-4116      TCGA-B9-4117 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-B9-4617      TCGA-B9-5155      TCGA-B9-5156      TCGA-B9-7268 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-B9-A44B      TCGA-B9-A5W7      TCGA-B9-A5W8      TCGA-B9-A5W9 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-B9-A69E      TCGA-BQ-5875      TCGA-BQ-5876      TCGA-BQ-5877 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-BQ-5878      TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5881 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-BQ-5883      TCGA-BQ-5884      TCGA-BQ-5885      TCGA-BQ-5886 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-BQ-5887      TCGA-BQ-5888      TCGA-BQ-5889      TCGA-BQ-5891 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-7044      TCGA-BQ-7045 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-BQ-7046      TCGA-BQ-7048      TCGA-BQ-7049      TCGA-BQ-7050 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-BQ-7051      TCGA-BQ-7053      TCGA-BQ-7055      TCGA-BQ-7056 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-BQ-7058      TCGA-BQ-7059      TCGA-BQ-7060      TCGA-BQ-7061 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-BQ-7062      TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-DW-7841      TCGA-DW-7842      TCGA-DW-7963      TCGA-DZ-6131 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-DZ-6133      TCGA-DZ-6134      TCGA-EV-5901      TCGA-EV-5902 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-EV-5903      TCGA-F9-A4JJ      TCGA-G7-6790      TCGA-G7-6792 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM      TCGA-GL-6846 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-GL-7773      TCGA-GL-7966      TCGA-GL-8500      TCGA-GL-A4EM 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-GL-A59R      TCGA-GL-A59T      TCGA-IA-A40U      TCGA-IA-A40X 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-IZ-8195      TCGA-IZ-8196      TCGA-IZ-A6M8 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-IZ-A6M9      TCGA-J7-6720      TCGA-J7-8537      TCGA-KV-A6GD 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-KV-A6GE      TCGA-MH-A55W      TCGA-MH-A55Z      TCGA-MH-A560 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-MH-A561      TCGA-MH-A562      TCGA-P4-A5E6      TCGA-P4-A5E7 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-P4-A5E8      TCGA-P4-A5EA      TCGA-P4-A5EB      TCGA-P4-A5ED 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-PJ-A5Z8      TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
D16V11, binary
                 cls
clus                0   1
  MED16 MUTATED     0   2
  MED16 WILD-TYPE   6 122
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED16 MUTATED      0    2
  MED16 WILD-TYPE    6  122
                        clus
vv                       MED16 MUTATED MED16 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             2             122
[1] 2 2
[1] FALSE

Clustering(17) Variable = GLUD2 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  GLUD2 MUTATED     8   0
  GLUD2 WILD-TYPE 129   5
  GLUD2 MUTATED GLUD2 WILD-TYPE 
              8             134 
  GLUD2 MUTATED GLUD2 WILD-TYPE 
              0               5 
$`GLUD2 MUTATED`
TCGA-A4-7288 TCGA-A4-7996 TCGA-A4-A5Y0 TCGA-B9-A5W8 TCGA-BQ-5878 TCGA-BQ-7046 
         493           49          118          207         1938         2948 
TCGA-BQ-7050 TCGA-BQ-7053 
        1864         1516 

$`GLUD2 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-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8517 
           2          140          780          729          709          597 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y1 
         600          436          379          516            2           87 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
           4         1778         1636          923          763         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
          26           67          595          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
         510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5881 
           5          102         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-7048 
         233           29          364           84         3760         2839 
TCGA-BQ-7051 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1533          799          612          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-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          279         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
         112          841           32          178           91         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         408          360         1726          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            2            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         160          885         1043          391          543          438 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         292         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         174           57 

  GLUD2 MUTATED GLUD2 WILD-TYPE 
             49               2 
  GLUD2 MUTATED GLUD2 WILD-TYPE 
           2948            5925 
  GLUD2 MUTATED GLUD2 WILD-TYPE 
         1004.5           566.0 
[1] "49.0 - 2948.0 (1004.5)" "2.0 - 5925.0 (566.0)"  
[1] "hr="     "7.6e+07"
D17V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  GLUD2 MUTATED         7        1         2        0
  GLUD2 WILD-TYPE      88        9        37       10
D17V3, multiclass
           clus
vv          GLUD2 MUTATED GLUD2 WILD-TYPE
  STAGE I               7              88
  STAGE II              1               9
  STAGE III             2              37
  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
  GLUD2 MUTATED    7  2     2
  GLUD2 WILD-TYPE 96 15    43
D17V4, multiclass
       clus
vv      GLUD2 MUTATED GLUD2 WILD-TYPE
  T1                7              96
  T2                2              15
  T3+T4             2              43
[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
  GLUD2 MUTATED    2  1  0
  GLUD2 WILD-TYPE 26 16  4
D17V5, multiclass
    clus
vv   GLUD2 MUTATED GLUD2 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
  GLUD2 MUTATED    7  0  4
  GLUD2 WILD-TYPE 58  6 77
D17V6, multiclass
    clus
vv   GLUD2 MUTATED GLUD2 WILD-TYPE
  M0             7              58
  M1             0               6
  MX             4              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"
D17V7, binary
                 cls
clus                0   1
  GLUD2 MUTATED     6   5
  GLUD2 WILD-TYPE  44 110
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLUD2 MUTATED      6    5
  GLUD2 WILD-TYPE   44  110
        clus
vv       GLUD2 MUTATED GLUD2 WILD-TYPE
  FEMALE             6              44
  MALE               5             110
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLUD2 MUTATED                                  0     0
  GLUD2 WILD-TYPE                                2     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GLUD2 MUTATED                           3     6
  GLUD2 WILD-TYPE                        40   100
D17V10, multiclass
                                  clus
vv                                 GLUD2 MUTATED GLUD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    3              40
  WHITE                                        6             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"
D17V11, binary
                 cls
clus                0   1
  GLUD2 MUTATED     2   3
  GLUD2 WILD-TYPE   4 121
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLUD2 MUTATED      2    3
  GLUD2 WILD-TYPE    4  121
                        clus
vv                       GLUD2 MUTATED GLUD2 WILD-TYPE
  HISPANIC OR LATINO                 2               4
  NOT HISPANIC OR LATINO             3             121
[1] 2 2
[1] FALSE

Clustering(18) Variable = BMS1 MUTATION ANALYSIS
D18V1, survival
                sevent
clus2              0   1
  BMS1 MUTATED    13   0
  BMS1 WILD-TYPE 124   5
  BMS1 MUTATED BMS1 WILD-TYPE 
            13            129 
  BMS1 MUTATED BMS1 WILD-TYPE 
             0              5 
$`BMS1 MUTATED`
TCGA-A4-7915 TCGA-A4-A6HP TCGA-B9-4114 TCGA-B9-4116 TCGA-BQ-7044 TCGA-BQ-7060 
           7            4          857          627         3760          214 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DZ-6135 TCGA-G7-6790 TCGA-G7-6796 
        1142          744          419         1670         1575         1059 
TCGA-G7-6797 
         765 

$`BMS1 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-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 
         118           87         1778         1636          923          763 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
        1357           26           67          595          659          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         108          510           14         1029          307          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
        1049          379         1536          803           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
           5          102         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-7046 
         403          233           29          364           84         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
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-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-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
        1856         1040          578          757           97          208 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
        1479         1194          446          786          279         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          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            2 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
           4          160          885         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         438          292         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         391          174           57 

  BMS1 MUTATED BMS1 WILD-TYPE 
             4              2 
  BMS1 MUTATED BMS1 WILD-TYPE 
          3760           5925 
  BMS1 MUTATED BMS1 WILD-TYPE 
           765            516 
[1] "4.0 - 3760.0 (765.0)" "2.0 - 5925.0 (516.0)"
[1] "hr="     "7.9e+07"
D18V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  BMS1 MUTATED         8        1         2        0
  BMS1 WILD-TYPE      87        9        37       10
D18V3, multiclass
           clus
vv          BMS1 MUTATED BMS1 WILD-TYPE
  STAGE I              8             87
  STAGE II             1              9
  STAGE III            2             37
  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
  BMS1 MUTATED    9  3     1
  BMS1 WILD-TYPE 94 14    44
D18V4, multiclass
       clus
vv      BMS1 MUTATED BMS1 WILD-TYPE
  T1               9             94
  T2               3             14
  T3+T4            1             44
[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
  BMS1 MUTATED    1  0  0
  BMS1 WILD-TYPE 27 17  4
D18V5, multiclass
[1] "Remove cluster labels:" "BMS1 MUTATED"          
clus
  BMS1 MUTATED BMS1 WILD-TYPE 
             1             48 
    TCGA-A4-7583     TCGA-A4-7585     TCGA-A4-A57E     TCGA-A4-A5Y1 
"BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" 
    TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173 
"BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" 
    TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656     TCGA-B9-7268 
"BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" 
    TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880 
"BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" 
    TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887     TCGA-BQ-5888 
"BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" 
    TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5892 
"BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" 
    TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045     TCGA-BQ-7048 
"BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" 
    TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7056     TCGA-BQ-7058 
"BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" 
    TCGA-DW-7963     TCGA-DZ-6131     TCGA-G7-6789     TCGA-G7-6793 
"BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-GL-6846     TCGA-GL-7966 
"BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" 
    TCGA-GL-A59R     TCGA-IA-A40U     TCGA-IA-A40Y     TCGA-J7-6720 
"BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" 
    TCGA-J7-8537     TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" "BMS1 WILD-TYPE" 
                vv
clus             M0 M1 MX
  BMS1 MUTATED    2  0  9
  BMS1 WILD-TYPE 63  6 72
D18V6, multiclass
    clus
vv   BMS1 MUTATED BMS1 WILD-TYPE
  M0            2             63
  M1            0              6
  MX            9             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"
D18V7, binary
                cls
clus               0   1
  BMS1 MUTATED     3  10
  BMS1 WILD-TYPE  47 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  BMS1 MUTATED      3   10
  BMS1 WILD-TYPE   47  105
        clus
vv       BMS1 MUTATED BMS1 WILD-TYPE
  FEMALE            3             47
  MALE             10            105
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BMS1 MUTATED                                  1     0
  BMS1 WILD-TYPE                                1     2
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BMS1 MUTATED                           4     7
  BMS1 WILD-TYPE                        39    99
D18V10, multiclass
                                  clus
vv                                 BMS1 MUTATED BMS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              1
  ASIAN                                       0              2
  BLACK OR AFRICAN AMERICAN                   4             39
  WHITE                                       7             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"
D18V11, binary
                cls
clus               0   1
  BMS1 MUTATED     0  11
  BMS1 WILD-TYPE   6 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  BMS1 MUTATED      0   11
  BMS1 WILD-TYPE    6  113
                        clus
vv                       BMS1 MUTATED BMS1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           11            113
[1] 2 2
[1] FALSE

Clustering(19) Variable = FUS MUTATION ANALYSIS
D19V1, survival
               sevent
clus2             0   1
  FUS MUTATED     1   0
  FUS WILD-TYPE 136   5
  FUS MUTATED FUS WILD-TYPE 
            1           141 
  FUS MUTATED FUS WILD-TYPE 
            0             5 
$`FUS MUTATED`
TCGA-BQ-7062 
         116 

$`FUS 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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         671           64          585          207            5          102 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         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-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          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-DW-7963 
         744          419          114          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-6846 
        1059          765          446          786          279         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          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            2 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
           4          160          885         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         438          292         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         391          174           57 

  FUS MUTATED FUS WILD-TYPE 
          116             2 
  FUS MUTATED FUS WILD-TYPE 
          116          5925 
  FUS MUTATED FUS WILD-TYPE 
          116           578 
[1] "116.0 - 116.0 (116.0)" "2.0 - 5925.0 (578.0)" 
[1] "Remove cluster labels:" "FUS MUTATED"           
D19V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  FUS MUTATED         1        0         1        1
  FUS WILD-TYPE      94       10        38        9
D19V3, multiclass
           clus
vv          FUS MUTATED FUS WILD-TYPE
  STAGE I             1            94
  STAGE II            0            10
  STAGE III           1            38
  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
  FUS MUTATED     1   0     2
  FUS WILD-TYPE 102  17    43
D19V4, multiclass
       clus
vv      FUS MUTATED FUS WILD-TYPE
  T1              1           102
  T2              0            17
  T3+T4           2            43
[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
  FUS MUTATED    1  0  1
  FUS WILD-TYPE 27 17  3
D19V5, multiclass
[1] "Remove cluster labels:" "FUS MUTATED"           
clus
  FUS MUTATED FUS WILD-TYPE 
            2            47 
   TCGA-A4-7583    TCGA-A4-7585    TCGA-A4-7915    TCGA-A4-A57E    TCGA-A4-A5Y1 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-AL-3466    TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173    TCGA-B1-5398 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-B1-A655    TCGA-B1-A656    TCGA-B9-7268    TCGA-BQ-5877    TCGA-BQ-5878 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-BQ-5879    TCGA-BQ-5880    TCGA-BQ-5885    TCGA-BQ-5887    TCGA-BQ-5888 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-BQ-5889    TCGA-BQ-5890    TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-BQ-5894    TCGA-BQ-7045    TCGA-BQ-7048    TCGA-BQ-7050    TCGA-BQ-7051 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-BQ-7056    TCGA-BQ-7058    TCGA-DW-7963    TCGA-DZ-6131    TCGA-G7-6789 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-G7-6795    TCGA-G7-7501    TCGA-GL-6846    TCGA-GL-7966    TCGA-GL-A59R 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-IA-A40U    TCGA-IA-A40Y    TCGA-J7-6720    TCGA-J7-8537    TCGA-P4-A5E6 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-P4-A5E8    TCGA-P4-A5EA 
"FUS WILD-TYPE" "FUS WILD-TYPE" 
               vv
clus            M0 M1 MX
  FUS MUTATED    2  0  1
  FUS WILD-TYPE 63  6 80
D19V6, multiclass
    clus
vv   FUS MUTATED FUS WILD-TYPE
  M0           2            63
  M1           0             6
  MX           1            80
[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
  FUS MUTATED     1   2
  FUS WILD-TYPE  49 113
[1] "tbl2"
               cls
clus            [,1] [,2]
  FUS MUTATED      1    2
  FUS WILD-TYPE   49  113
        clus
vv       FUS MUTATED FUS WILD-TYPE
  FEMALE           1            49
  MALE             2           113
[1] 2 2
[1] FALSE
D19V8, continuous
[1] "Remove cluster labels:" "FUS MUTATED"           
clus
  FUS MUTATED FUS WILD-TYPE 
            1            37 
   TCGA-A4-7286    TCGA-A4-7828    TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8312 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A4ZT    TCGA-A4-A57E    TCGA-A4-A5DU 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-A4-A5XZ    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-DW-5560    TCGA-DW-5561 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839    TCGA-DW-7840 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-DW-7841    TCGA-DW-7842    TCGA-DW-7963    TCGA-EV-5901    TCGA-EV-5902 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-EV-5903    TCGA-G7-6790    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7501 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-G7-7502    TCGA-G7-A4TM    TCGA-IA-A40U    TCGA-IA-A40X    TCGA-IA-A40Y 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-J7-8537    TCGA-Q2-A5QZ 
"FUS WILD-TYPE" "FUS WILD-TYPE" 
D19V9, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FUS MUTATED                                  0     0
  FUS WILD-TYPE                                2     2
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FUS MUTATED                           1     1
  FUS WILD-TYPE                        42   105
D19V10, multiclass
[1] "Remove cluster labels:" "FUS MUTATED"           
clus
  FUS MUTATED FUS WILD-TYPE 
            2           151 
   TCGA-A4-7286    TCGA-A4-7287    TCGA-A4-7288    TCGA-A4-7583    TCGA-A4-7584 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-A4-7585    TCGA-A4-7732    TCGA-A4-7734    TCGA-A4-7828    TCGA-A4-7915 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-A4-7996    TCGA-A4-7997    TCGA-A4-8098    TCGA-A4-8310    TCGA-A4-8311 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-A4-8312    TCGA-A4-8515    TCGA-A4-8517    TCGA-A4-8518    TCGA-A4-8630 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-A4-A48D    TCGA-A4-A4ZT    TCGA-A4-A57E    TCGA-A4-A5DU    TCGA-A4-A5XZ 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-A4-A5Y0    TCGA-A4-A5Y1    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-AL-3467 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-AL-3468    TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173    TCGA-AL-A5DJ 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-AT-A5NU    TCGA-B1-5398    TCGA-B1-A47M    TCGA-B1-A47N    TCGA-B1-A654 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-B1-A655    TCGA-B1-A656    TCGA-B3-3925    TCGA-B3-3926    TCGA-B3-4103 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-B3-4104    TCGA-B3-8121    TCGA-B9-4113    TCGA-B9-4114    TCGA-B9-4115 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-B9-4116    TCGA-B9-4117    TCGA-B9-4617    TCGA-B9-5155    TCGA-B9-5156 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-B9-7268    TCGA-B9-A44B    TCGA-B9-A5W7    TCGA-B9-A5W8    TCGA-B9-A5W9 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-B9-A69E    TCGA-BQ-5875    TCGA-BQ-5876    TCGA-BQ-5877    TCGA-BQ-5878 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-BQ-5879    TCGA-BQ-5880    TCGA-BQ-5881    TCGA-BQ-5883    TCGA-BQ-5884 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-BQ-5885    TCGA-BQ-5886    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-BQ-5890    TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-7044 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048    TCGA-BQ-7049    TCGA-BQ-7050 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7056    TCGA-BQ-7058 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-DW-5560    TCGA-DW-5561 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839    TCGA-DW-7840 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-DW-7841    TCGA-DW-7842    TCGA-DW-7963    TCGA-DZ-6131    TCGA-DZ-6133 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-DZ-6134    TCGA-EV-5901    TCGA-EV-5902    TCGA-EV-5903    TCGA-F9-A4JJ 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792    TCGA-G7-6795    TCGA-G7-6796 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-G7-6797    TCGA-G7-7501    TCGA-G7-7502    TCGA-G7-A4TM    TCGA-GL-6846 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-GL-7773    TCGA-GL-7966    TCGA-GL-8500    TCGA-GL-A4EM    TCGA-GL-A59R 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-GL-A59T    TCGA-IA-A40U    TCGA-IA-A40X    TCGA-IA-A40Y    TCGA-IZ-8195 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-IZ-8196    TCGA-IZ-A6M8    TCGA-IZ-A6M9    TCGA-J7-6720    TCGA-J7-8537 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-KV-A6GD    TCGA-KV-A6GE    TCGA-MH-A55W    TCGA-MH-A55Z    TCGA-MH-A560 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-MH-A561    TCGA-MH-A562    TCGA-P4-A5E6    TCGA-P4-A5E7    TCGA-P4-A5E8 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-P4-A5EA    TCGA-P4-A5EB    TCGA-P4-A5ED    TCGA-PJ-A5Z8    TCGA-PJ-A5Z9 
"FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" "FUS WILD-TYPE" 
   TCGA-Q2-A5QZ 
"FUS WILD-TYPE" 
D19V11, binary
               cls
clus              0   1
  FUS MUTATED     0   2
  FUS WILD-TYPE   6 122
[1] "tbl2"
               cls
clus            [,1] [,2]
  FUS MUTATED      0    2
  FUS WILD-TYPE    6  122
                        clus
vv                       FUS MUTATED FUS WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           2           122
[1] 2 2
[1] FALSE

Clustering(20) Variable = TP53 MUTATION ANALYSIS
D20V1, survival
                sevent
clus2              0   1
  TP53 MUTATED     4   0
  TP53 WILD-TYPE 133   5
  TP53 MUTATED TP53 WILD-TYPE 
             4            138 
  TP53 MUTATED TP53 WILD-TYPE 
             0              5 
$`TP53 MUTATED`
TCGA-A4-7287 TCGA-B1-A655 TCGA-B3-4104 TCGA-BQ-5881 
          21          510         1049         1454 

$`TP53 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
         118           87            4         1778         1636          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         763         1357           26           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         747          108           14         1029          307          930 
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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         207            5          102         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1938         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-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         612          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          279         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          178           91         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-A6GD TCGA-KV-A6GE 
         649          146            2            4          160          885 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
        1043          391          543          438          292         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2584         2816          391          174           57 

  TP53 MUTATED TP53 WILD-TYPE 
            21              2 
  TP53 MUTATED TP53 WILD-TYPE 
          1454           5925 
  TP53 MUTATED TP53 WILD-TYPE 
         779.5          566.0 
[1] "21.0 - 1454.0 (779.5)" "2.0 - 5925.0 (566.0)" 
[1] "hr="     "9300000"
D20V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED         4        1         0        2
  TP53 WILD-TYPE      91        9        39        8
D20V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              4             91
  STAGE II             1              9
  STAGE III            0             39
  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
  TP53 MUTATED    4  2     1
  TP53 WILD-TYPE 99 15    44
D20V4, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T1               4             99
  T2               2             15
  T3+T4            1             44
[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
  TP53 MUTATED    2  1  0
  TP53 WILD-TYPE 26 16  4
D20V5, multiclass
    clus
vv   TP53 MUTATED TP53 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
  TP53 MUTATED    4  2  1
  TP53 WILD-TYPE 61  4 80
D20V6, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  M0            4             61
  M1            2              4
  MX            1             80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                cls
clus               0   1
  TP53 MUTATED     3   4
  TP53 WILD-TYPE  47 111
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      3    4
  TP53 WILD-TYPE   47  111
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            3             47
  MALE              4            111
[1] 2 2
[1] FALSE
D20V8, continuous
[1] "Remove cluster labels:" "TP53 MUTATED"          
clus
  TP53 MUTATED TP53 WILD-TYPE 
             1             37 
    TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8310     TCGA-A4-8311 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A4-8312     TCGA-A4-8518     TCGA-A4-8630     TCGA-A4-A4ZT 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP     TCGA-AL-3466 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DW-7842     TCGA-DW-7963     TCGA-EV-5901     TCGA-EV-5902 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-EV-5903     TCGA-G7-6790     TCGA-G7-6793     TCGA-G7-6796 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A40X     TCGA-IA-A40Y     TCGA-J7-8537 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-Q2-A5QZ 
"TP53 WILD-TYPE" 
D20V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  0     0
  TP53 WILD-TYPE                                2     2
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                           0     7
  TP53 WILD-TYPE                        43    99
D20V10, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0              2
  BLACK OR AFRICAN AMERICAN                   0             43
  WHITE                                       7             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"
D20V11, binary
                cls
clus               0   1
  TP53 MUTATED     0   6
  TP53 WILD-TYPE   6 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      0    6
  TP53 WILD-TYPE    6  118
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            118
[1] 2 2
[1] FALSE

Clustering(21) Variable = ACADL MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  ACADL MUTATED     3   0
  ACADL WILD-TYPE 134   5
  ACADL MUTATED ACADL WILD-TYPE 
              3             139 
  ACADL MUTATED ACADL WILD-TYPE 
              0               5 
$`ACADL MUTATED`
TCGA-A4-8310 TCGA-AL-3468 TCGA-BQ-5891 
         780         1636           29 

$`ACADL 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-A4-8311 TCGA-A4-8515 
           7           49            2          140          729          709 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
         118           87            4         1778          923          763 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
        1357           26           67          595          659          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
          14           35          460         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
         585          207            5          102         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-5892 TCGA-BQ-5894 
         792          771          403          233          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-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          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          279         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         841           32          178           91         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
         360         1726          167          511          608           62 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
         677          649          146            2            4          160 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         885         1043          391          543          438          292 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3035         2653         2584         2816          391          174 
TCGA-Q2-A5QZ 
          57 

  ACADL MUTATED ACADL WILD-TYPE 
             29               2 
  ACADL MUTATED ACADL WILD-TYPE 
           1636            5925 
  ACADL MUTATED ACADL WILD-TYPE 
            780             554 
[1] "29.0 - 1636.0 (780.0)" "2.0 - 5925.0 (554.0)" 
[1] "hr="     "2.5e+07"
D21V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ACADL MUTATED         0        1         3        0
  ACADL WILD-TYPE      95        9        36       10
D21V3, multiclass
           clus
vv          ACADL MUTATED ACADL WILD-TYPE
  STAGE I               0              95
  STAGE II              1               9
  STAGE III             3              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
  ACADL MUTATED     0   1     3
  ACADL WILD-TYPE 103  16    42
D21V4, multiclass
       clus
vv      ACADL MUTATED ACADL WILD-TYPE
  T1                0             103
  T2                1              16
  T3+T4             3              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
  ACADL MUTATED    2  0  0
  ACADL WILD-TYPE 26 17  4
D21V5, multiclass
[1] "Remove cluster labels:" "ACADL MUTATED"         
clus
  ACADL MUTATED ACADL WILD-TYPE 
              2              47 
     TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-A4-A5Y1      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878      TCGA-BQ-5879 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-BQ-5880      TCGA-BQ-5885      TCGA-BQ-5887      TCGA-BQ-5888 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5892      TCGA-BQ-5893 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-BQ-5894      TCGA-BQ-7045      TCGA-BQ-7048      TCGA-BQ-7050 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-BQ-7051      TCGA-BQ-7056      TCGA-BQ-7058      TCGA-DW-7963 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-DZ-6131      TCGA-G7-6789      TCGA-G7-6793      TCGA-G7-6795 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-G7-7501      TCGA-GL-6846      TCGA-GL-7966      TCGA-GL-A59R 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A40Y      TCGA-J7-6720      TCGA-J7-8537 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
                 vv
clus              M0 M1 MX
  ACADL MUTATED    3  0  1
  ACADL WILD-TYPE 62  6 80
D21V6, multiclass
    clus
vv   ACADL MUTATED ACADL WILD-TYPE
  M0             3              62
  M1             0               6
  MX             1              80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                 cls
clus                0   1
  ACADL MUTATED     1   3
  ACADL WILD-TYPE  49 112
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACADL MUTATED      1    3
  ACADL WILD-TYPE   49  112
        clus
vv       ACADL MUTATED ACADL WILD-TYPE
  FEMALE             1              49
  MALE               3             112
[1] 2 2
[1] FALSE
D21V8, continuous
[1] "Remove cluster labels:" "ACADL MUTATED"         
clus
  ACADL MUTATED ACADL WILD-TYPE 
              1              37 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8311      TCGA-A4-8312 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A4ZT      TCGA-A4-A57E 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-EV-5903      TCGA-G7-6790      TCGA-G7-6793      TCGA-G7-6796 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537 
"ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" "ACADL WILD-TYPE" 
     TCGA-Q2-A5QZ 
"ACADL WILD-TYPE" 
D21V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACADL MUTATED                                  0     0
  ACADL WILD-TYPE                                2     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACADL MUTATED                           0     3
  ACADL WILD-TYPE                        43   103
D21V10, multiclass
                                  clus
vv                                 ACADL MUTATED ACADL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    0              43
  WHITE                                        3             103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, binary
                 cls
clus                0   1
  ACADL MUTATED     0   3
  ACADL WILD-TYPE   6 121
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACADL MUTATED      0    3
  ACADL WILD-TYPE    6  121
                        clus
vv                       ACADL MUTATED ACADL WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3             121
[1] 2 2
[1] FALSE

Clustering(22) Variable = AHNAK2 MUTATION ANALYSIS
D22V1, survival
                  sevent
clus2                0   1
  AHNAK2 MUTATED     7   0
  AHNAK2 WILD-TYPE 130   5
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               7              135 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               0                5 
$`AHNAK2 MUTATED`
TCGA-B1-5398 TCGA-B9-4117 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-DZ-6135 TCGA-EV-5901 
         595           14          232          214         1670         1040 
TCGA-GL-7773 
         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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47M 
         923          763         1357           26           67          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
         747          108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
         627           35          460         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
         585          207            5          102         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-7056 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
        1516          799          612          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-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          279 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
        5925          112          841           32          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          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            2 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
           4          160          885         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         438          292         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         391          174           57 

  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
              14                2 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
            1670             5925 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
             393              578 
[1] "14.0 - 1670.0 (393.0)" "2.0 - 5925.0 (578.0)" 
[1] "hr="     "2.6e+07"
D22V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  AHNAK2 MUTATED         7        0         2        0
  AHNAK2 WILD-TYPE      88       10        37       10
D22V3, multiclass
           clus
vv          AHNAK2 MUTATED AHNAK2 WILD-TYPE
  STAGE I                7               88
  STAGE II               0               10
  STAGE III              2               37
  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    7  1     2
  AHNAK2 WILD-TYPE 96 16    43
D22V4, multiclass
       clus
vv      AHNAK2 MUTATED AHNAK2 WILD-TYPE
  T1                 7               96
  T2                 1               16
  T3+T4              2               43
[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
D22V5, 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-B9-7268 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879       TCGA-BQ-5880 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-BQ-5885       TCGA-BQ-5887       TCGA-BQ-5888       TCGA-BQ-5889 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-BQ-5890       TCGA-BQ-5891       TCGA-BQ-5892       TCGA-BQ-5893 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048       TCGA-BQ-7050 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-BQ-7051       TCGA-BQ-7056       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    5  0  4
  AHNAK2 WILD-TYPE 60  6 77
D22V6, multiclass
    clus
vv   AHNAK2 MUTATED AHNAK2 WILD-TYPE
  M0              5               60
  M1              0                6
  MX              4               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"
D22V7, binary
                  cls
clus                 0   1
  AHNAK2 MUTATED     3   7
  AHNAK2 WILD-TYPE  47 108
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHNAK2 MUTATED      3    7
  AHNAK2 WILD-TYPE   47  108
        clus
vv       AHNAK2 MUTATED AHNAK2 WILD-TYPE
  FEMALE              3               47
  MALE                7              108
[1] 2 2
[1] FALSE
D22V8, 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" 
D22V9, continuous
[1] "Remove cluster labels:" "AHNAK2 MUTATED"        
clus
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
               1               12 
      TCGA-A4-A48D       TCGA-B1-A654       TCGA-B9-A44B       TCGA-B9-A69E 
"AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" "AHNAK2 WILD-TYPE" 
      TCGA-GL-A59T       TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-IA-A40U 
"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     5
  AHNAK2 WILD-TYPE                        42   101
D22V10, multiclass
                                  clus
vv                                 AHNAK2 MUTATED AHNAK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                1
  ASIAN                                         0                2
  BLACK OR AFRICAN AMERICAN                     1               42
  WHITE                                         5              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"
D22V11, binary
                  cls
clus                 0   1
  AHNAK2 MUTATED     0   5
  AHNAK2 WILD-TYPE   6 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHNAK2 MUTATED      0    5
  AHNAK2 WILD-TYPE    6  119
                        clus
vv                       AHNAK2 MUTATED AHNAK2 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              5              119
[1] 2 2
[1] FALSE

Clustering(23) Variable = SMARCB1 MUTATION ANALYSIS
D23V1, survival
                   sevent
clus2                 0   1
  SMARCB1 MUTATED     5   0
  SMARCB1 WILD-TYPE 132   5
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                5               137 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                0                 5 
$`SMARCB1 MUTATED`
TCGA-B1-A47M TCGA-BQ-5876 TCGA-BQ-7048 TCGA-BQ-7061 TCGA-GL-6846 
         659          586         2839          218         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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
         747          108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         627           14           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
          64          585          207            5          102         2639 
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-7050 TCGA-BQ-7051 TCGA-BQ-7053 
          84         3760         2948         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 
         799          612          232          214          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-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
         786          279          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
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            2            4          160          885         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
         391          543          438          292         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2584         2816          391          174           57 

  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
              218                 2 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
             5925              3950 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
              659               543 
[1] "218.0 - 5925.0 (659.0)" "2.0 - 3950.0 (543.0)"  
[1] "hr="     "2.7e+07"
D23V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  SMARCB1 MUTATED         2        0         2        1
  SMARCB1 WILD-TYPE      93       10        37        9
D23V3, multiclass
           clus
vv          SMARCB1 MUTATED SMARCB1 WILD-TYPE
  STAGE I                 2                93
  STAGE II                0                10
  STAGE III               2                37
  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     2   0     3
  SMARCB1 WILD-TYPE 101  17    42
D23V4, multiclass
       clus
vv      SMARCB1 MUTATED SMARCB1 WILD-TYPE
  T1                  2               101
  T2                  0                17
  T3+T4               3                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
  SMARCB1 MUTATED    1  1  0
  SMARCB1 WILD-TYPE 27 16  4
D23V5, 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-B9-7268        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5882        TCGA-BQ-5885        TCGA-BQ-5887 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7045 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7056        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    3  0  2
  SMARCB1 WILD-TYPE 62  6 79
D23V6, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  M0               3                62
  M1               0                 6
  MX               2                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     1   4
  SMARCB1 WILD-TYPE  49 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      1    4
  SMARCB1 WILD-TYPE   49  111
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  FEMALE               1                49
  MALE                 4               111
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, 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     4
  SMARCB1 WILD-TYPE                        42   102
D23V10, multiclass
                                  clus
vv                                 SMARCB1 MUTATED SMARCB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      1                42
  WHITE                                          4               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     0   4
  SMARCB1 WILD-TYPE   6 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      0    4
  SMARCB1 WILD-TYPE    6  120
                        clus
vv                       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               4               120
[1] 2 2
[1] FALSE

Clustering(24) Variable = TEKT1 MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2               0   1
  TEKT1 MUTATED     2   0
  TEKT1 WILD-TYPE 135   5
  TEKT1 MUTATED TEKT1 WILD-TYPE 
              2             140 
  TEKT1 MUTATED TEKT1 WILD-TYPE 
              0               5 
$`TEKT1 MUTATED`
TCGA-A4-8630 TCGA-G7-6796 
         436         1059 

$`TEKT1 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-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         709          597          600          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
         118           87            4         1778         1636          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         763         1357           26           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
         747          108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         627           14           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
          64          585          207            5          102         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
         586          270         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-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
         364           84         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
         218          116          353          414         3950         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          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-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
         765          446          786          279         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
         112          841           32          178           91         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         408          360         1726          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            2            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         160          885         1043          391          543          438 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         292         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         174           57 

  TEKT1 MUTATED TEKT1 WILD-TYPE 
            436               2 
  TEKT1 MUTATED TEKT1 WILD-TYPE 
           1059            5925 
  TEKT1 MUTATED TEKT1 WILD-TYPE 
          747.5           566.0 
[1] "436.0 - 1059.0 (747.5)" "2.0 - 5925.0 (566.0)"  
[1] "Remove cluster labels:" "TEKT1 MUTATED"         
D24V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TEKT1 MUTATED         3        0         1        0
  TEKT1 WILD-TYPE      92       10        38       10
D24V3, multiclass
           clus
vv          TEKT1 MUTATED TEKT1 WILD-TYPE
  STAGE I               3              92
  STAGE II              0              10
  STAGE III             1              38
  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
  TEKT1 MUTATED     3   0     1
  TEKT1 WILD-TYPE 100  17    44
D24V4, multiclass
       clus
vv      TEKT1 MUTATED TEKT1 WILD-TYPE
  T1                3             100
  T2                0              17
  T3+T4             1              44
[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
  TEKT1 MUTATED    0  0  0
  TEKT1 WILD-TYPE 28 17  4
D24V5, multiclass
                 vv
clus              M0 M1 MX
  TEKT1 MUTATED    2  0  2
  TEKT1 WILD-TYPE 63  6 79
D24V6, multiclass
    clus
vv   TEKT1 MUTATED TEKT1 WILD-TYPE
  M0             2              63
  M1             0               6
  MX             2              79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                 cls
clus                0   1
  TEKT1 MUTATED     3   1
  TEKT1 WILD-TYPE  47 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEKT1 MUTATED      3    1
  TEKT1 WILD-TYPE   47  114
        clus
vv       TEKT1 MUTATED TEKT1 WILD-TYPE
  FEMALE             3              47
  MALE               1             114
[1] 2 2
[1] FALSE
D24V8, continuous
[1] "Remove cluster labels:" "TEKT1 MUTATED"         
clus
  TEKT1 MUTATED TEKT1 WILD-TYPE 
              2              36 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8310      TCGA-A4-8311 
"TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8518      TCGA-A4-A4ZT      TCGA-A4-A57E 
"TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" 
     TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466 
"TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837 
"TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841 
"TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" 
     TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902 
"TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" 
     TCGA-EV-5903      TCGA-G7-6790      TCGA-G7-6793      TCGA-G7-6797 
"TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM      TCGA-IA-A40U 
"TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" 
     TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" "TEKT1 WILD-TYPE" 
D24V9, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TEKT1 MUTATED                                  0     0
  TEKT1 WILD-TYPE                                2     2
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TEKT1 MUTATED                           0     3
  TEKT1 WILD-TYPE                        43   103
D24V10, multiclass
                                  clus
vv                                 TEKT1 MUTATED TEKT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0               2
  BLACK OR AFRICAN AMERICAN                    0              43
  WHITE                                        3             103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, binary
                 cls
clus                0   1
  TEKT1 MUTATED     0   2
  TEKT1 WILD-TYPE   6 122
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEKT1 MUTATED      0    2
  TEKT1 WILD-TYPE    6  122
                        clus
vv                       TEKT1 MUTATED TEKT1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             2             122
[1] 2 2
[1] FALSE

Clustering(25) Variable = MKL1 MUTATION ANALYSIS
D25V1, survival
                sevent
clus2              0   1
  MKL1 MUTATED     7   0
  MKL1 WILD-TYPE 130   5
  MKL1 MUTATED MKL1 WILD-TYPE 
             7            135 
  MKL1 MUTATED MKL1 WILD-TYPE 
             0              5 
$`MKL1 MUTATED`
TCGA-A4-A48D TCGA-B3-4104 TCGA-B9-4116 TCGA-BQ-7048 TCGA-DW-7837 TCGA-DZ-6131 
         379         1049          627         2839         1142         2429 
TCGA-GL-7773 
         393 

$`MKL1 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-A5XZ 
         709          597          600          436          516            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
         118           87            4         1778         1636          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         763         1357           26           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
         747          108          510           14         1029          307 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
         930          379         1536          857          803           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         207            5          102         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-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        3760         2948         1864         1533         1516          799 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         612          232          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
         414         3950          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
          92         1240         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          279 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
        5925          112          841           32          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          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            2 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
           4          160          885         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         438          292         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         391          174           57 

  MKL1 MUTATED MKL1 WILD-TYPE 
           379              2 
  MKL1 MUTATED MKL1 WILD-TYPE 
          2839           5925 
  MKL1 MUTATED MKL1 WILD-TYPE 
          1049            543 
[1] "379.0 - 2839.0 (1049.0)" "2.0 - 5925.0 (543.0)"   
[1] "hr="     "7.4e+07"
D25V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MKL1 MUTATED         4        1         3        0
  MKL1 WILD-TYPE      91        9        36       10
D25V3, multiclass
           clus
vv          MKL1 MUTATED MKL1 WILD-TYPE
  STAGE I              4             91
  STAGE II             1              9
  STAGE III            3             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
  MKL1 MUTATED    4  2     3
  MKL1 WILD-TYPE 99 15    42
D25V4, multiclass
       clus
vv      MKL1 MUTATED MKL1 WILD-TYPE
  T1               4             99
  T2               2             15
  T3+T4            3             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
  MKL1 MUTATED    2  1  0
  MKL1 WILD-TYPE 26 16  4
D25V5, multiclass
    clus
vv   MKL1 MUTATED MKL1 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
  MKL1 MUTATED    4  0  4
  MKL1 WILD-TYPE 61  6 77
D25V6, multiclass
    clus
vv   MKL1 MUTATED MKL1 WILD-TYPE
  M0            4             61
  M1            0              6
  MX            4             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"
D25V7, binary
                cls
clus               0   1
  MKL1 MUTATED     2   7
  MKL1 WILD-TYPE  48 108
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL1 MUTATED      2    7
  MKL1 WILD-TYPE   48  108
        clus
vv       MKL1 MUTATED MKL1 WILD-TYPE
  FEMALE            2             48
  MALE              7            108
[1] 2 2
[1] FALSE
D25V8, continuous
[1] "Remove cluster labels:" "MKL1 MUTATED"          
clus
  MKL1 MUTATED MKL1 WILD-TYPE 
             1             37 
    TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8310     TCGA-A4-8311 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-A4-8312     TCGA-A4-8518     TCGA-A4-8630     TCGA-A4-A4ZT 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-AL-3466     TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-DW-7842     TCGA-DW-7963     TCGA-EV-5901     TCGA-EV-5902 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-EV-5903     TCGA-G7-6790     TCGA-G7-6793     TCGA-G7-6796 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A40X     TCGA-IA-A40Y     TCGA-J7-8537 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-Q2-A5QZ 
"MKL1 WILD-TYPE" 
D25V9, continuous
[1] "Remove cluster labels:" "MKL1 MUTATED"          
clus
  MKL1 MUTATED MKL1 WILD-TYPE 
             2             11 
    TCGA-B1-A654     TCGA-B9-A44B     TCGA-B9-A69E     TCGA-GL-A59T 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-IA-A40U     TCGA-P4-A5E7 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-P4-A5EB     TCGA-PJ-A5Z9     TCGA-Q2-A5QZ 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MKL1 MUTATED                                  0     0
  MKL1 WILD-TYPE                                2     2
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MKL1 MUTATED                           3     6
  MKL1 WILD-TYPE                        40   100
D25V10, multiclass
                                  clus
vv                                 MKL1 MUTATED MKL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0              2
  BLACK OR AFRICAN AMERICAN                   3             40
  WHITE                                       6            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"
D25V11, binary
                cls
clus               0   1
  MKL1 MUTATED     0   6
  MKL1 WILD-TYPE   6 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL1 MUTATED      0    6
  MKL1 WILD-TYPE    6  118
                        clus
vv                       MKL1 MUTATED MKL1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            118
[1] 2 2
[1] FALSE

Clustering(26) Variable = MYH7 MUTATION ANALYSIS
D26V1, survival
                sevent
clus2              0   1
  MYH7 MUTATED     4   1
  MYH7 WILD-TYPE 133   4
  MYH7 MUTATED MYH7 WILD-TYPE 
             5            137 
  MYH7 MUTATED MYH7 WILD-TYPE 
             1              4 
$`MYH7 MUTATED`
TCGA-A4-A5Y1 TCGA-B3-3925 TCGA-B9-5156 TCGA-BQ-7060 TCGA-P4-A5E6 
          87         1029         1338          214         3035 

$`MYH7 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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
           2          118            4         1778         1636          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         763         1357           26           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3926 TCGA-B3-4103 
         747          108          510           14          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-B9-4617 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          14           35          460          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         207            5          102         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-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         799          612          232          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          279         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          178           91         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-A6GD TCGA-KV-A6GE 
         649          146            2            4          160          885 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E7 
        1043          391          543          438          292         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2584         2816          391          174           57 

  MYH7 MUTATED MYH7 WILD-TYPE 
            87              2 
  MYH7 MUTATED MYH7 WILD-TYPE 
          3035           5925 
  MYH7 MUTATED MYH7 WILD-TYPE 
          1029            554 
[1] "87.0 - 3035.0 (1029.0)" "2.0 - 5925.0 (554.0)"  
[1] "hr=" "6.3"
D26V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MYH7 MUTATED         2        0         3        0
  MYH7 WILD-TYPE      93       10        36       10
D26V3, multiclass
           clus
vv          MYH7 MUTATED MYH7 WILD-TYPE
  STAGE I              2             93
  STAGE II             0             10
  STAGE III            3             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
  MYH7 MUTATED    5  0     1
  MYH7 WILD-TYPE 98 17    44
D26V4, multiclass
       clus
vv      MYH7 MUTATED MYH7 WILD-TYPE
  T1               5             98
  T2               0             17
  T3+T4            1             44
[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
  MYH7 MUTATED    0  2  0
  MYH7 WILD-TYPE 28 15  4
D26V5, multiclass
[1] "Remove cluster labels:" "MYH7 MUTATED"          
clus
  MYH7 MUTATED MYH7 WILD-TYPE 
             2             47 
    TCGA-A4-7583     TCGA-A4-7585     TCGA-A4-7915     TCGA-A4-A57E 
"MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" 
    TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173 
"MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" 
    TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656     TCGA-B9-7268 
"MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" 
    TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880 
"MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" 
    TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887     TCGA-BQ-5888 
"MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" 
    TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5892 
"MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" 
    TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045     TCGA-BQ-7048 
"MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" 
    TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7056     TCGA-BQ-7058 
"MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" 
    TCGA-DW-7963     TCGA-DZ-6131     TCGA-G7-6789     TCGA-G7-6793 
"MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-GL-6846     TCGA-GL-7966 
"MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" 
    TCGA-GL-A59R     TCGA-IA-A40U     TCGA-IA-A40Y     TCGA-J7-6720 
"MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" 
    TCGA-J7-8537     TCGA-P4-A5E8     TCGA-P4-A5EA 
"MYH7 WILD-TYPE" "MYH7 WILD-TYPE" "MYH7 WILD-TYPE" 
                vv
clus             M0 M1 MX
  MYH7 MUTATED    2  0  3
  MYH7 WILD-TYPE 63  6 78
D26V6, multiclass
    clus
vv   MYH7 MUTATED MYH7 WILD-TYPE
  M0            2             63
  M1            0              6
  MX            3             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"
D26V7, binary
                cls
clus               0   1
  MYH7 MUTATED     1   5
  MYH7 WILD-TYPE  49 110
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH7 MUTATED      1    5
  MYH7 WILD-TYPE   49  110
        clus
vv       MYH7 MUTATED MYH7 WILD-TYPE
  FEMALE            1             49
  MALE              5            110
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYH7 MUTATED                                  1     0
  MYH7 WILD-TYPE                                1     2
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYH7 MUTATED                           1     4
  MYH7 WILD-TYPE                        42   102
D26V10, multiclass
                                  clus
vv                                 MYH7 MUTATED MYH7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              1
  ASIAN                                       0              2
  BLACK OR AFRICAN AMERICAN                   1             42
  WHITE                                       4            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, binary
                cls
clus               0   1
  MYH7 MUTATED     0   5
  MYH7 WILD-TYPE   6 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH7 MUTATED      0    5
  MYH7 WILD-TYPE    6  119
                        clus
vv                       MYH7 MUTATED MYH7 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            5            119
[1] 2 2
[1] FALSE

Clustering(27) Variable = MAP4K3 MUTATION ANALYSIS
D27V1, survival
                  sevent
clus2                0   1
  MAP4K3 MUTATED     4   0
  MAP4K3 WILD-TYPE 133   5
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
               4              138 
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
               0                5 
$`MAP4K3 MUTATED`
TCGA-B9-4617 TCGA-BQ-5885 TCGA-BQ-7059 TCGA-GL-A59R 
          35          921          232          178 

$`MAP4K3 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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         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-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         803          627           14          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
          64          585          207            5          102         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
         586          270         1938         1454         1242          792 
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-7056 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
        1516          799          612          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          279         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
         841           32           91         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-A6GD TCGA-KV-A6GE 
         649          146            2            4          160          885 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
        1043          391          543          438          292         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2584         2816          391          174           57 

  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
              35                2 
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
             921             5925 
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
             205              580 
[1] "35.0 - 921.0 (205.0)" "2.0 - 5925.0 (580.0)"
[1] "hr="     "9200000"
D27V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  MAP4K3 MUTATED         2        0         2        0
  MAP4K3 WILD-TYPE      93       10        37       10
D27V3, multiclass
           clus
vv          MAP4K3 MUTATED MAP4K3 WILD-TYPE
  STAGE I                2               93
  STAGE II               0               10
  STAGE III              2               37
  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
  MAP4K3 MUTATED     3   0     2
  MAP4K3 WILD-TYPE 100  17    43
D27V4, multiclass
       clus
vv      MAP4K3 MUTATED MAP4K3 WILD-TYPE
  T1                 3              100
  T2                 0               17
  T3+T4              2               43
[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
  MAP4K3 MUTATED    2  0  0
  MAP4K3 WILD-TYPE 26 17  4
D27V5, multiclass
[1] "Remove cluster labels:" "MAP4K3 MUTATED"        
clus
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
               2               47 
      TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E 
"MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" 
      TCGA-A4-A5Y1       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473 
"MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-5398       TCGA-B1-A655       TCGA-B1-A656 
"MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" 
      TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879 
"MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" 
      TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5887       TCGA-BQ-5888 
"MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" 
      TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891       TCGA-BQ-5892 
"MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" 
      TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048 
"MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" 
      TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7056       TCGA-BQ-7058 
"MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" 
      TCGA-DW-7963       TCGA-DZ-6131       TCGA-G7-6789       TCGA-G7-6793 
"MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-6846       TCGA-GL-7966 
"MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A40Y       TCGA-J7-6720       TCGA-J7-8537 
"MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" "MAP4K3 WILD-TYPE" 
                  vv
clus               M0 M1 MX
  MAP4K3 MUTATED    3  0  2
  MAP4K3 WILD-TYPE 62  6 79
D27V6, multiclass
    clus
vv   MAP4K3 MUTATED MAP4K3 WILD-TYPE
  M0              3               62
  M1              0                6
  MX              2               79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                  cls
clus                 0   1
  MAP4K3 MUTATED     1   4
  MAP4K3 WILD-TYPE  49 111
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K3 MUTATED      1    4
  MAP4K3 WILD-TYPE   49  111
        clus
vv       MAP4K3 MUTATED MAP4K3 WILD-TYPE
  FEMALE              1               49
  MALE                4              111
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP4K3 MUTATED                                  0     0
  MAP4K3 WILD-TYPE                                2     2
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAP4K3 MUTATED                           1     4
  MAP4K3 WILD-TYPE                        42   102
D27V10, multiclass
                                  clus
vv                                 MAP4K3 MUTATED MAP4K3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0                2
  BLACK OR AFRICAN AMERICAN                     1               42
  WHITE                                         4              102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, binary
                  cls
clus                 0   1
  MAP4K3 MUTATED     0   4
  MAP4K3 WILD-TYPE   6 120
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K3 MUTATED      0    4
  MAP4K3 WILD-TYPE    6  120
                        clus
vv                       MAP4K3 MUTATED MAP4K3 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              4              120
[1] 2 2
[1] FALSE

Clustering(28) Variable = NEK2 MUTATION ANALYSIS
D28V1, survival
                sevent
clus2              0   1
  NEK2 MUTATED     1   0
  NEK2 WILD-TYPE 136   5
  NEK2 MUTATED NEK2 WILD-TYPE 
             1            141 
  NEK2 MUTATED NEK2 WILD-TYPE 
             0              5 
$`NEK2 MUTATED`
TCGA-G7-6795 
        1194 

$`NEK2 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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         671           64          585          207            5          102 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         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-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          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-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
        1059          765          446          786          279         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          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            2 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
           4          160          885         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         438          292         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         391          174           57 

  NEK2 MUTATED NEK2 WILD-TYPE 
          1194              2 
  NEK2 MUTATED NEK2 WILD-TYPE 
          1194           5925 
  NEK2 MUTATED NEK2 WILD-TYPE 
          1194            554 
[1] "1194.0 - 1194.0 (1194.0)" "2.0 - 5925.0 (554.0)"    
[1] "Remove cluster labels:" "NEK2 MUTATED"          
D28V2, continuous
[1] "Remove cluster labels:" "NEK2 MUTATED"          
clus
  NEK2 MUTATED NEK2 WILD-TYPE 
             2            160 
    TCGA-A4-7286     TCGA-A4-7287     TCGA-A4-7288     TCGA-A4-7583 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-A4-7584     TCGA-A4-7585     TCGA-A4-7732     TCGA-A4-7734 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-A4-7828     TCGA-A4-7915     TCGA-A4-7996     TCGA-A4-7997 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-A4-8098     TCGA-A4-8310     TCGA-A4-8311     TCGA-A4-8312 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-A4-8515     TCGA-A4-8517     TCGA-A4-8518     TCGA-A4-8630 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A4ZT     TCGA-A4-A57E     TCGA-A4-A5DU 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-A4-A5XZ     TCGA-A4-A5Y0     TCGA-A4-A5Y1     TCGA-A4-A6HP 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-AL-3466     TCGA-AL-3467     TCGA-AL-3468     TCGA-AL-3472 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-AL-3473     TCGA-AL-7173     TCGA-AL-A5DJ     TCGA-AT-A5NU 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-B1-5398     TCGA-B1-A47M     TCGA-B1-A47N     TCGA-B1-A654 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-B1-A655     TCGA-B1-A656     TCGA-B3-3925     TCGA-B3-3926 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-B3-4103     TCGA-B3-4104     TCGA-B3-8121     TCGA-B9-4113 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-B9-4114     TCGA-B9-4115     TCGA-B9-4116     TCGA-B9-4117 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-B9-4617     TCGA-B9-5155     TCGA-B9-5156     TCGA-B9-7268 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-B9-A44B     TCGA-B9-A5W7     TCGA-B9-A5W8     TCGA-B9-A5W9 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-B9-A69E     TCGA-BQ-5875     TCGA-BQ-5876     TCGA-BQ-5877 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5881 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-5882     TCGA-BQ-5883     TCGA-BQ-5884     TCGA-BQ-5885 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-5886     TCGA-BQ-5887     TCGA-BQ-5888     TCGA-BQ-5889 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5892     TCGA-BQ-5893 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-5894     TCGA-BQ-7044     TCGA-BQ-7045     TCGA-BQ-7046 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7049     TCGA-BQ-7050     TCGA-BQ-7051 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-7053     TCGA-BQ-7055     TCGA-BQ-7056     TCGA-BQ-7058 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-7059     TCGA-BQ-7060     TCGA-BQ-7061     TCGA-BQ-7062 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-DW-7842     TCGA-DW-7963     TCGA-DZ-6131     TCGA-DZ-6132 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-DZ-6133     TCGA-DZ-6134     TCGA-DZ-6135     TCGA-EV-5901 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-F9-A4JJ     TCGA-G7-6789 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-G7-6790     TCGA-G7-6792     TCGA-G7-6796     TCGA-G7-6797 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM     TCGA-GL-6846 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-7966     TCGA-GL-8500     TCGA-GL-A4EM 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-GL-A59R     TCGA-GL-A59T     TCGA-HE-A5NF     TCGA-HE-A5NH 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-HE-A5NL     TCGA-IA-A40U 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-IA-A40X     TCGA-IA-A40Y     TCGA-IZ-8195     TCGA-IZ-8196 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-IZ-A6M8     TCGA-IZ-A6M9     TCGA-J7-6720     TCGA-J7-8537 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-KV-A6GD     TCGA-KV-A6GE     TCGA-MH-A55W     TCGA-MH-A55Z 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-MH-A560     TCGA-MH-A561     TCGA-MH-A562     TCGA-P4-A5E6 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-P4-A5E7     TCGA-P4-A5E8     TCGA-P4-A5EA     TCGA-P4-A5EB 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-P4-A5ED     TCGA-PJ-A5Z8     TCGA-PJ-A5Z9     TCGA-Q2-A5QZ 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NEK2 MUTATED         2        0         0        1
  NEK2 WILD-TYPE      93       10        39        9
D28V3, multiclass
           clus
vv          NEK2 MUTATED NEK2 WILD-TYPE
  STAGE I              2             93
  STAGE II             0             10
  STAGE III            0             39
  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
  NEK2 MUTATED     1   1     1
  NEK2 WILD-TYPE 102  16    44
D28V4, multiclass
       clus
vv      NEK2 MUTATED NEK2 WILD-TYPE
  T1               1            102
  T2               1             16
  T3+T4            1             44
[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
  NEK2 MUTATED    1  0  1
  NEK2 WILD-TYPE 27 17  3
D28V5, multiclass
[1] "Remove cluster labels:" "NEK2 MUTATED"          
clus
  NEK2 MUTATED NEK2 WILD-TYPE 
             2             47 
    TCGA-A4-7583     TCGA-A4-7585     TCGA-A4-7915     TCGA-A4-A57E 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-A4-A5Y1     TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7056 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-7058     TCGA-DW-7963     TCGA-DZ-6131     TCGA-G7-6789 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-G7-7501     TCGA-GL-6846     TCGA-GL-7966     TCGA-GL-A59R 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A40Y     TCGA-J7-6720     TCGA-J7-8537 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
                vv
clus             M0 M1 MX
  NEK2 MUTATED    1  0  2
  NEK2 WILD-TYPE 64  6 79
D28V6, multiclass
    clus
vv   NEK2 MUTATED NEK2 WILD-TYPE
  M0            1             64
  M1            0              6
  MX            2             79
[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"
D28V7, binary
                cls
clus               0   1
  NEK2 MUTATED     1   2
  NEK2 WILD-TYPE  49 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK2 MUTATED      1    2
  NEK2 WILD-TYPE   49  113
        clus
vv       NEK2 MUTATED NEK2 WILD-TYPE
  FEMALE            1             49
  MALE              2            113
[1] 2 2
[1] FALSE
D28V8, continuous
[1] "Remove cluster labels:" "NEK2 MUTATED"          
clus
  NEK2 MUTATED NEK2 WILD-TYPE 
             1             37 
    TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8310     TCGA-A4-8311 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-A4-8312     TCGA-A4-8518     TCGA-A4-8630     TCGA-A4-A4ZT 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-AL-3466     TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-DW-7841     TCGA-DW-7842     TCGA-DW-7963     TCGA-EV-5901 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-G7-6790     TCGA-G7-6796 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A40X     TCGA-IA-A40Y     TCGA-J7-8537 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-Q2-A5QZ 
"NEK2 WILD-TYPE" 
D28V9, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEK2 MUTATED                                  0     0
  NEK2 WILD-TYPE                                2     2
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NEK2 MUTATED                           0     2
  NEK2 WILD-TYPE                        43   104
D28V10, multiclass
[1] "Remove cluster labels:" "NEK2 MUTATED"          
clus
  NEK2 MUTATED NEK2 WILD-TYPE 
             2            151 
    TCGA-A4-7286     TCGA-A4-7287     TCGA-A4-7288     TCGA-A4-7583 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-A4-7584     TCGA-A4-7585     TCGA-A4-7732     TCGA-A4-7734 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-A4-7828     TCGA-A4-7915     TCGA-A4-7996     TCGA-A4-7997 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-A4-8098     TCGA-A4-8310     TCGA-A4-8311     TCGA-A4-8312 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-A4-8515     TCGA-A4-8517     TCGA-A4-8518     TCGA-A4-8630 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A4ZT     TCGA-A4-A57E     TCGA-A4-A5DU 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-A4-A5XZ     TCGA-A4-A5Y0     TCGA-A4-A5Y1     TCGA-A4-A6HP 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-AL-3466     TCGA-AL-3467     TCGA-AL-3468     TCGA-AL-3472 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-AL-3473     TCGA-AL-7173     TCGA-AL-A5DJ     TCGA-AT-A5NU 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-B1-5398     TCGA-B1-A47M     TCGA-B1-A47N     TCGA-B1-A654 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-B1-A655     TCGA-B1-A656     TCGA-B3-3925     TCGA-B3-3926 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-B3-4103     TCGA-B3-4104     TCGA-B3-8121     TCGA-B9-4113 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-B9-4114     TCGA-B9-4115     TCGA-B9-4116     TCGA-B9-4117 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-B9-4617     TCGA-B9-5155     TCGA-B9-5156     TCGA-B9-7268 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-B9-A44B     TCGA-B9-A5W7     TCGA-B9-A5W8     TCGA-B9-A5W9 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-B9-A69E     TCGA-BQ-5875     TCGA-BQ-5876     TCGA-BQ-5877 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5881 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-5883     TCGA-BQ-5884     TCGA-BQ-5885     TCGA-BQ-5886 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-5887     TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-5891     TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-7044 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-7045     TCGA-BQ-7046     TCGA-BQ-7048     TCGA-BQ-7049 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7053     TCGA-BQ-7055 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-7056     TCGA-BQ-7058     TCGA-BQ-7059     TCGA-BQ-7060 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-BQ-7061     TCGA-BQ-7062     TCGA-DW-5560     TCGA-DW-5561 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-DW-7834     TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-DW-7840     TCGA-DW-7841     TCGA-DW-7842     TCGA-DW-7963 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-DZ-6131     TCGA-DZ-6133     TCGA-DZ-6134     TCGA-EV-5901 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-F9-A4JJ     TCGA-G7-6789 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-G7-6790     TCGA-G7-6792     TCGA-G7-6796     TCGA-G7-6797 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM     TCGA-GL-6846 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-7966     TCGA-GL-8500     TCGA-GL-A4EM 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-GL-A59R     TCGA-GL-A59T     TCGA-IA-A40U     TCGA-IA-A40X 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-IA-A40Y     TCGA-IZ-8195     TCGA-IZ-8196     TCGA-IZ-A6M8 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-IZ-A6M9     TCGA-J7-6720     TCGA-J7-8537     TCGA-KV-A6GD 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-KV-A6GE     TCGA-MH-A55W     TCGA-MH-A55Z     TCGA-MH-A560 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-MH-A561     TCGA-MH-A562     TCGA-P4-A5E6     TCGA-P4-A5E7 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-P4-A5E8     TCGA-P4-A5EA     TCGA-P4-A5EB     TCGA-P4-A5ED 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
    TCGA-PJ-A5Z8     TCGA-PJ-A5Z9     TCGA-Q2-A5QZ 
"NEK2 WILD-TYPE" "NEK2 WILD-TYPE" "NEK2 WILD-TYPE" 
D28V11, binary
                cls
clus               0   1
  NEK2 MUTATED     0   2
  NEK2 WILD-TYPE   6 122
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK2 MUTATED      0    2
  NEK2 WILD-TYPE    6  122
                        clus
vv                       NEK2 MUTATED NEK2 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            2            122
[1] 2 2
[1] FALSE
